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Neupane A, Tamburic-Llincic L, Brûlé-Babel A, McCartney C. QTL analysis of native Fusarium head blight and deoxynivalenol resistance in 'D8006W'/'Superior', soft white winter wheat population. BMC PLANT BIOLOGY 2024; 24:852. [PMID: 39256692 PMCID: PMC11389122 DOI: 10.1186/s12870-024-05536-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024]
Abstract
BACKGROUND Fusarium head blight (FHB), caused by Fusarium graminearum, is a major disease of wheat in North America. FHB infection causes fusarium damaged kernels (FDKs), accumulation of deoxynivalenol (DON) in the grain, and a reduction in quality and grain yield. Inheritance of FHB resistance is complex and involves multiple genes. The objective of this research was to identify QTL associated with native FHB and DON resistance in a 'D8006W'/'Superior', soft white winter wheat population. RESULTS Phenotyping was conducted in replicated FHB field disease nurseries across multiple environments and included assessments of morphological and FHB related traits. Parental lines had moderate FHB resistance, however, the population showed transgressive segregation. A 1913.2 cM linkage map for the population was developed with SNP markers from the wheat 90 K Infinium iSelect SNP array. QTL analysis detected major FHB resistance QTL on chromosomes 2D, 4B, 5A, and 7A across multiple environments, with resistance from both parents. Trait specific unique QTL were detected on chromosomes 1A (visual traits), 5D (FDK), 6B (FDK and DON), and 7D (DON). The plant height and days to anthesis QTL on chromosome 2D coincided with Ppd-D1 and were linked with FHB traits. The plant height QTL on chromosome 4B was also linked with FHB traits; however, the Rht-B1 locus did not segregate in the population. CONCLUSIONS This study identified several QTL, including on chromosome 2D linked with Ppd-D1, for FHB resistance in a native winter wheat germplasm.
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Affiliation(s)
- Anjan Neupane
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
- Present address: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - Ljiljana Tamburic-Llincic
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
- Ridgetown Campus, University of Guelph, 120 Main Street East, Ridgetown, ON, N0P 2C0, Canada
| | - Anita Brûlé-Babel
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
| | - Curt McCartney
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
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2
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Rehman F, Gong H, Ma Y, Zeng S, Ke D, Yang C, Zhao Y, Wang Y. An ultra-dense linkage map identified quantitative trait loci corresponding to fruit quality- and size-related traits in red goji berry. FRONTIERS IN PLANT SCIENCE 2024; 15:1390936. [PMID: 39297015 PMCID: PMC11408189 DOI: 10.3389/fpls.2024.1390936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 08/01/2024] [Indexed: 09/21/2024]
Abstract
Goji berries are a small-fruited shrub with industrial importance whose fruit considered beneficial in both fresh and dried forms. Current germplasms of goji berries include small fruits with a short shelf life, less sweet and bitter taste, and a lack of appropriate genetic information. This study aimed to employ whole genome resequencing to generate an ultra-dense bin linkage map and to elucidate the genetic basis of goji fruit quality and size using quantitative trait loci (QTL) mapping analysis in a cross-pollinated hybrid population. To achieve this goal, human sensory tests were carried out to determine the bitter taste (BT) and sweet taste (ST), and to quantify the soluble solid content (SSC), fruit firmness (FF), and fruit size-related traits of fresh goji fruits over three or four years. The results revealed that the goji bin linkage map based on resequencing spanned a total length of 966.42 cM and an average bin interval of 0.03 cM. Subsequent variant calling and ordering resulted in 3,058 bins containing 35,331 polymorphic markers across 12 chromosomes. A total of 99 QTLs, with individual loci in different environments explaining a phenotypic variance of 1.21-16.95% were identified for the studied traits. Ten major effects, including colocalized QTLs corresponding to different traits, were identified on chromosomes 1, 3, 5, 6, 7, and 8, with a maximum Logarithm of Odds (LOD) of 29.25 and 16.95% of explained phenotypic variance (PVE). In addition, four stable loci, one for FF, one for fruit weight (FW), and two for fruit shape index (FSI), were mainly mapped on chromosomes 5, 6, and 7, elucidating 2.10-16.95% PVE. These findings offer valuable insights into the genetic architecture of goji fruit traits along with identified specific loci and markers to further improve and develop sweeter, less bitter and larger fruited goji berry cultivars with extended shelf life.
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Affiliation(s)
- Fazal Rehman
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
| | - Haiguang Gong
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
| | - Yun Ma
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
| | - Shaohua Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, Jiangxi, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Danmin Ke
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yuling Zhao
- Jinghe County Goji Industrial Development Center, Jinghe County, Xinjiang Uygur Autonomous Region, China
| | - Ying Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, South China National Botanical Garden, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, Jiangxi, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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3
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Hu W, Wu D, Li D, Cheng X, Wang Z, Zhao D, Jia J. Two dwarfing genes Rht-B1b and Rht-D1b show pleiotropic effects on grain protein content in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:204. [PMID: 39141110 DOI: 10.1007/s00122-024-04713-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024]
Abstract
KEY MESSAGE Five QTL for wheat grain protein content were identified, and the effects of two dwarfing genes Rht-B1b and Rht-D1b on grain protein content were validated in multiple populations. Grain protein content (GPC) plays an important role in wheat quality. Here, a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) for GPC. Two hundred and five RILs and their parents were grown in three years in randomized complete blocks each with two replications, and genotyped using the wheat 55 K SNP array. Five QTL were identified for GPC on chromosomes 1A, 1B, 2D, 4B, and 4D. Notably, QGpc.yaas-4B (co-located with Rht-B1) and QGpc.yaas-4D (co-located with Rht-D1) were consistently detected across all experiments and best linear unbiased estimating, accounting for 6.61-8.39% and 6.05-10.21% of the phenotypic variances, respectively. The effects of these two dwarfing alleles Rht-B1b and Rht-D1b on reducing GPC and plant height were validated in two additional RIL populations and one natural population. This study lays a foundation for further investigating the effects of dwarfing genes Rht-B1b and Rht-D1b on wheat GPC.
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Affiliation(s)
- Wenjing Hu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Di Wu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007, China
| | - Dongshen Li
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007, China
| | - Xiaoming Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007, China
| | - Zunjie Wang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007, China
| | - Die Zhao
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
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4
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Wei X, Chen M, Zhang Q, Gong J, Liu J, Yong K, Wang Q, Fan J, Chen S, Hua H, Luo Z, Zhao X, Wang X, Li W, Cong J, Yu X, Wang Z, Huang R, Chen J, Zhou X, Qiu J, Xu P, Murray J, Wang H, Xu Y, Xu C, Xu G, Yang J, Han B, Huang X. Genomic investigation of 18,421 lines reveals the genetic architecture of rice. Science 2024; 385:eadm8762. [PMID: 38963845 DOI: 10.1126/science.adm8762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/29/2024] [Indexed: 07/06/2024]
Abstract
Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.
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Affiliation(s)
- Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kaicheng Yong
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiongjiong Fan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Suhui Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hua Hua
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhaowei Luo
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoyan Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wei Li
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jia Cong
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiting Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhihan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ruipeng Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jeremy Murray
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Bin Han
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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5
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Shrestha A, Shim J, Mangat PK, Dhaliwal LK, Sweeney M, Angeles-Shim RB. Genetic Analysis of an F 2 Population Derived from the Cotton Landrace Hopi Identified Novel Loci for Boll Glanding. Int J Mol Sci 2024; 25:7080. [PMID: 39000183 PMCID: PMC11241279 DOI: 10.3390/ijms25137080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Landraces are an important reservoir of genetic variation that can expand the narrow genetic base of cultivated cotton. In this study, quantitative trait loci (QTL) analysis was conducted using an F2 population developed from crosses between the landrace Hopi and inbred TM-1. A high-density genetic map spanning 2253.11 and 1932.21 cM for the A and D sub-genomes, respectively, with an average marker interval of 1.14 cM, was generated using the CottonSNP63K array. The linkage map showed a strong co-linearity with the physical map of cotton. A total of 21 QTLs were identified, controlling plant height (1), bract type (1), boll number (1), stem color (2), boll pitting (2), fuzz fiber development (2), boll shape (3), boll point (4), and boll glanding (5). In silico analysis of the novel QTLs for boll glanding identified a total of 13 candidate genes. Analysis of tissue-specific expression of the candidate genes suggests roles for the transcription factors bHLH1, MYB2, and ZF1 in gland formation. Comparative sequencing of open reading frames identified early stop codons in all three transcription factors in Hopi. Functional validation of these genes offers avenues to reduce glanding and, consequently, lower gossypol levels in cottonseeds without compromising the defense mechanisms of the plant against biotic stresses.
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Affiliation(s)
- Avinash Shrestha
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Junghyun Shim
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Puneet Kaur Mangat
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Lakhvir Kaur Dhaliwal
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
| | - Megan Sweeney
- BASF Corporation, 407 Davis Drive, Morrisville, NC 27560, USA;
| | - Rosalyn B. Angeles-Shim
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA; (A.S.); (J.S.); (P.K.M.); (L.K.D.)
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6
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Gangurde SS, Thompson E, Yaduru S, Wang H, Fountain JC, Chu Y, Ozias-Akins P, Isleib TG, Holbrook C, Dutta B, Culbreath AK, Pandey MK, Guo B. Linkage Mapping and Genome-Wide Association Study Identified Two Peanut Late Leaf Spot Resistance Loci, PLLSR-1 and PLLSR-2, Using Nested Association Mapping. PHYTOPATHOLOGY 2024; 114:1346-1355. [PMID: 38669464 DOI: 10.1094/phyto-04-23-0143-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Identification of candidate genes and molecular markers for late leaf spot (LLS) disease resistance in peanut (Arachis hypogaea) has been a focus of molecular breeding for the U.S. industry-funded peanut genome project. Efforts have been hindered by limited mapping resolution due to low levels of genetic recombination and marker density available in traditional biparental mapping populations. To address this, a multi-parental nested association mapping population has been genotyped with the peanut 58K single-nucleotide polymorphism (SNP) array and phenotyped for LLS severity in the field for 3 years. Joint linkage-based quantitative trait locus (QTL) mapping identified nine QTLs for LLS resistance with significant phenotypic variance explained up to 47.7%. A genome-wide association study identified 13 SNPs consistently associated with LLS resistance. Two genomic regions harboring the consistent QTLs and SNPs were identified from 1,336 to 1,520 kb (184 kb) on chromosome B02 and from 1,026.9 to 1,793.2 kb (767 kb) on chromosome B03, designated as peanut LLS resistance loci, PLLSR-1 and PLLSR-2, respectively. PLLSR-1 contains 10 nucleotide-binding site leucine-rich repeat disease resistance genes. A nucleotide-binding site leucine-rich repeat disease resistance gene, Arahy.VKVT6A, was also identified on homoeologous chromosome A02. PLLSR-2 contains five significant SNPs associated with five different genes encoding callose synthase, pollen defective in guidance protein, pentatricopeptide repeat, acyl-activating enzyme, and C2 GRAM domains-containing protein. This study highlights the power of multi-parent populations such as nested association mapping for genetic mapping and marker-trait association studies in peanuts. Validation of these two LLS resistance loci will be needed for marker-assisted breeding.
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Affiliation(s)
- Sunil S Gangurde
- U.S. Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, U.S.A
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Ethan Thompson
- U.S. Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, U.S.A
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
| | - Shasidhar Yaduru
- U.S. Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, U.S.A
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Hui Wang
- U.S. Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, U.S.A
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
| | - Jake C Fountain
- Department of Plant Pathology, University of Georgia, Griffin, GA, U.S.A
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA, U.S.A
| | - Peggy Ozias-Akins
- Department of Horticulture, University of Georgia, Tifton, GA, U.S.A
| | - Thomas G Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, U.S.A
| | - Corley Holbrook
- U.S. Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, U.S.A
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
| | | | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Baozhu Guo
- U.S. Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, U.S.A
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7
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Guo J, Guo J, Li L, Bai X, Huo X, Shi W, Gao L, Dai K, Jing R, Hao C. Combined linkage analysis and association mapping identifies genomic regions associated with yield-related and drought-tolerance traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:250. [PMID: 37982873 DOI: 10.1007/s00122-023-04494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023]
Abstract
KEY MESSAGE Combined linkage analysis and association mapping identified genomic regions associated with yield and drought tolerance, providing information to assist breeding for high yield and drought tolerance in wheat. Wheat (Triticum aestivum L.) is one of the most widely grown food crops and provides adequate amounts of protein to support human health. Drought stress is the most important abiotic stress constraining yield during the flowering and grain development periods. Precise targeting of genomic regions underlying yield- and drought tolerance-responsive traits would assist in breeding programs. In this study, two water treatments (well-watered, WW, and rain-fed water stress, WS) were applied, and five yield-related agronomic traits (plant height, PH; spike length, SL; spikelet number per spike, SNPS; kernel number per spike, KNPS; thousand kernel weight, TKW) and drought response values (DRVs) were used to characterize the drought sensitivity of each accession. Association mapping was performed on an association panel of 304 accessions, and linkage analysis was applied to a doubled haploid (DH) population of 152 lines. Eleven co-localized genomic regions associated with yield traits and DRV were identified in both populations. Many previously cloned key genes were located in these regions. In particular, a TKW-associated region on chromosome 2D was identified using both association mapping and linkage analysis and a key candidate gene, TraesCS2D02G142500, was detected based on gene annotation and differences in expression levels. Exonic SNPs were analyzed by sequencing the full length of TraesCS2D02G142500 in the association panel, and a rare haplotype, Hap-2, which reduced TKW to a lesser extent than Hap-1 under drought stress, and the Hap-2 varieties presented drought-insensitive. Altogether, this study provides fundamental insights into molecular targets for high yield and drought tolerance in wheat.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Jiahui Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
- College of Agronomy, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Long Li
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xionghui Bai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Xiaoyu Huo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China.
| | - Ruilian Jing
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chenyang Hao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China.
- State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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8
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Zhao D, Hu W, Fang Z, Cheng X, Liao S, Fu L. Two QTL regions for spike length showing pleiotropic effects on Fusarium head blight resistance and thousand-grain weight in bread wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:82. [PMID: 37974900 PMCID: PMC10645863 DOI: 10.1007/s11032-023-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Spike length (SL) plays an important role in the yield improvement of wheat and is significantly associated with other traits. Here, we used a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) to construct a genetic linkage map and identify quantitative trait loci (QTL) for SL. A total of 5 QTL were identified for SL, among which QSl.yaas-3A and QSl.yaas-5B are two novel QTL for SL. The YZ1 alleles at QSl.yaas-2D and QSl.yaas-5A, and the YM12 alleles at QSl.yaas-2A, QSl.yaas-3A, and QSl.yaas-5B conferred increasing SL effects. Two major QTL QSl.yaas-5A and QSl.yaas-5B explained 9.11-15.85% and 9.01-12.85% of the phenotypic variations, respectively. Moreover, the positive alleles of QSl.yaas-5A and QSl.yaas-5B could significantly increase Fusarium head blight (FHB) resistance (soil surface inoculation and spray inoculation were used) and thousand-grain weight (TGW) in the RIL population. Kompetitive allele-specific PCR (KASP) markers for QSl.yaas-5A and QSl.yaas-5B were developed and validated in an additional panel of 180 wheat cultivars/lines. The cultivars/lines harboring both the positive alleles of QSl.yaas-5A and QSl.yaas-5B accounted for only 28.33% of the validation populations and had the longest SL, best FHB resistance (using spray inoculation), and highest TGW. A total of 358 and 200 high-confidence annotated genes in QSl.yaas-5A and QSl.yaas-5B were identified, respectively. Some of the genes in these two regions were involved in cell development, disease resistance, and so on. The results of this study will provide a basis for directional breeding of longer SL, higher TGW, and better FHB resistance varieties and a solid foundation for fine-mapping QSl.yaas-5A and QSl.yaas-5B in future. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01427-8.
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Affiliation(s)
- Die Zhao
- College of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Wenjing Hu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Zhengwu Fang
- College of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Xiaoming Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
| | - Sen Liao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
| | - Luping Fu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, 225009 Jiangsu China
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9
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Hou M, Cao Y, Zhang X, Zhang S, Jia T, Yang J, Han S, Wang L, Li J, Wang H, Zhang L, Wu X, Duan C, Li H. Genome-wide association study of maize resistance to Pythium aristosporum stalk rot. FRONTIERS IN PLANT SCIENCE 2023; 14:1239635. [PMID: 37662167 PMCID: PMC10470045 DOI: 10.3389/fpls.2023.1239635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize's antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot.
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Affiliation(s)
- Mengwei Hou
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanyong Cao
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingrui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shulin Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Tengjiao Jia
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiwei Yang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shengbo Han
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lifeng Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jingjing Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hao Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lili Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaolin Wu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiyong Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
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10
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Maniruzzaman S, Rahman MA, Hasan M, Rasul MG, Molla AH, Khatun H, Iftekharuddaula KM, Kabir MS, Akter S. Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice. Int J Mol Sci 2023; 24:11141. [PMID: 37446320 DOI: 10.3390/ijms241311141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT, and salT locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.
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Affiliation(s)
- Sheikh Maniruzzaman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Akhlasur Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Mehfuz Hasan
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mohammad Golam Rasul
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Abul Hossain Molla
- Department of Environmental Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Hasina Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - K M Iftekharuddaula
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Md Shahjahan Kabir
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Salma Akter
- Plant Physiology Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
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11
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Yang Y, Zhao T, Wang F, Liu L, Liu B, Zhang K, Qin J, Yang C, Qiao Y. Identification of candidate genes for soybean seed coat-related traits using QTL mapping and GWAS. FRONTIERS IN PLANT SCIENCE 2023; 14:1190503. [PMID: 37384360 PMCID: PMC10293793 DOI: 10.3389/fpls.2023.1190503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/17/2023] [Indexed: 06/30/2023]
Abstract
Seed coat color is a typical morphological trait that can be used to reveal the evolution of soybean. The study of seed coat color-related traits in soybeans is of great significance for both evolutionary theory and breeding practices. In this study, 180 F10 recombinant inbred lines (RILs) derived from the cross between the yellow-seed coat cultivar Jidou12 (ZDD23040, JD12) and the wild black-seed coat accession Y9 (ZYD02739) were used as materials. Three methods, single-marker analysis (SMA), interval mapping (IM), and inclusive composite interval mapping (ICIM), were used to identify quantitative trait loci (QTLs) controlling seed coat color and seed hilum color. Simultaneously, two genome-wide association study (GWAS) models, the generalized linear model (GLM) and mixed linear model (MLM), were used to jointly identify seed coat color and seed hilum color QTLs in 250 natural populations. By integrating the results from QTL mapping and GWAS analysis, we identified two stable QTLs (qSCC02 and qSCC08) associated with seed coat color and one stable QTL (qSHC08) related to seed hilum color. By combining the results of linkage analysis and association analysis, two stable QTLs (qSCC02, qSCC08) for seed coat color and one stable QTL (qSHC08) for seed hilum color were identified. Upon further investigation using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we validated the previous findings that two candidate genes (CHS3C and CHS4A) reside within the qSCC08 region and identified a new QTL, qSCC02. There were a total of 28 candidate genes in the interval, among which Glyma.02G024600, Glyma.02G024700, and Glyma.02G024800 were mapped to the glutathione metabolic pathway, which is related to the transport or accumulation of anthocyanin. We considered the three genes as potential candidate genes for soybean seed coat-related traits. The QTLs and candidate genes detected in this study provide a foundation for further understanding the genetic mechanisms underlying soybean seed coat color and seed hilum color and are of significant value in marker-assisted breeding.
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Affiliation(s)
- Yue Yang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Tiantian Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Fengmin Wang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Luping Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Bingqiang Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jun Qin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Yake Qiao
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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12
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Adhikari TB, Siddique MI, Louws FJ, Sim SC, Panthee DR. Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes. FRONTIERS IN PLANT SCIENCE 2023; 14:1135884. [PMID: 37324699 PMCID: PMC10267708 DOI: 10.3389/fpls.2023.1135884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F2 and F2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F2 population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes.
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Affiliation(s)
- Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Muhammad Irfan Siddique
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC, United States
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul, Republic of Korea
| | - Dilip R. Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC, United States
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13
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Berraies S, Cuthbert R, Knox R, Singh A, DePauw R, Ruan Y, Bokore F, Henriquez MA, Kumar S, Burt A, Pozniak C, N’Diaye A, Meyer B. High-density genetic mapping of Fusarium head blight resistance and agronomic traits in spring wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1134132. [PMID: 37284725 PMCID: PMC10241073 DOI: 10.3389/fpls.2023.1134132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/03/2023] [Indexed: 06/08/2023]
Abstract
Fusarium head blight (FHB) has rapidly become a major challenge to successful wheat production and competitive end-use quality in western Canada. Continuous effort is required to develop germplasm with improved FHB resistance and understand how to incorporate the material into crossing schemes for marker-assisted selection and genomic selection. The aim of this study was to map quantitative trait loci (QTL) responsible for the expression of FHB resistance in two adapted cultivars and to evaluate their co-localization with plant height, days to maturity, days to heading, and awnedness. A large doubled haploid population of 775 lines developed from cultivars Carberry and AC Cadillac was assessed for FHB incidence and severity in nurseries near Portage la Prairie, Brandon, and Morden in different years, and for plant height, awnedness, days to heading, and days to maturity near Swift Current. An initial linkage map using a subset of 261 lines was constructed using 634 polymorphic DArT and SSR markers. QTL analysis revealed five resistance QTL on chromosomes 2A, 3B (two loci), 4B, and 5A. A second genetic map with increased marker density was constructed using the Infinium iSelect 90k SNP wheat array in addition to the previous DArT and SSR markers, which revealed two additional QTL on 6A and 6D. The complete population was genotyped, and a total of 6,806 Infinium iSelect 90k SNP polymorphic markers were used to identify 17 putative resistance QTL on 14 different chromosomes. As with the smaller population size and fewer markers, large-effect QTL were detected on 3B, 4B, and 5A that were consistently expressed across environments. FHB resistance QTL were co-localized with plant height QTL on chromosomes 4B, 6D, and 7D; days to heading on 2B, 3A, 4A, 4B, and 5A; and maturity on 3A, 4B, and 7D. A major QTL for awnedness was identified as being associated with FHB resistance on chromosome 5A. Nine small-effect QTL were not associated with any of the agronomic traits, whereas 13 QTL that were associated with agronomic traits did not co-localize with any of the FHB traits. There is an opportunity to select for improved FHB resistance within adapted cultivars by using markers associated with complementary QTL.
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Affiliation(s)
- Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Firdissa Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
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14
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Sgaramella N, Nigro D, Pasqualone A, Signorile MA, Laddomada B, Sonnante G, Blanco E, Simeone R, Blanco A. Genetic Mapping of Flavonoid Grain Pigments in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:1674. [PMID: 37111897 PMCID: PMC10142998 DOI: 10.3390/plants12081674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Pigmented cereal grains with high levels of flavonoid compounds have attracted the attention of nutritional science backing the development of functional foods with claimed health benefits. In this study, we report results on the genetic factors controlling grain pigmentation in durum wheat using a segregant population of recombinant inbred lines (RILs) derived from a cross between an Ethiopian purple grain accession and an Italian amber grain cultivar. The RIL population was genotyped by the wheat 25K SNP array and phenotyped for total anthocyanin content (TAC), grain color, and the L*, a*, and b* color index of wholemeal flour, based on four field trials. The mapping population showed a wide variation for the five traits in the different environments, a significant genotype x environment interaction, and high heritability. A total of 5942 SNP markers were used for constructing the genetic linkage map, with an SNP density ranging from 1.4 to 2.9 markers/cM. Two quantitative trait loci (QTL) were identified for TAC mapping on chromosome arms 2AL and 7BS in the same genomic regions of two detected QTL for purple grain. The interaction between the two QTL was indicative of an inheritance pattern of two loci having complementary effects. Moreover, two QTL for red grain color were detected on chromosome arms 3AL and 3BL. The projection of the four QTL genomic regions on the durum wheat Svevo reference genome disclosed the occurrence of the candidate genes Pp-A3, Pp-B1, R-A1, and R-B1 involved in flavonoid biosynthetic pathways and encoding of transcription factors bHLH (Myc-1) and MYB (Mpc1, Myb10), previously reported in common wheat. The present study provides a set of molecular markers associated with grain pigments useful for the selection of essential alleles for flavonoid synthesis in durum wheat breeding programs and enhancement of the health-promoting quality of derived foods.
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Affiliation(s)
- Natalia Sgaramella
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Antonella Pasqualone
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Massimo Antonio Signorile
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Barbara Laddomada
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Prov.le Monteroni, 73100 Lecce, Italy;
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy; (G.S.); (E.B.)
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy; (G.S.); (E.B.)
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
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15
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Wu X, Liu Y, Lu X, Tu L, Gao Y, Wang D, Guo S, Xiao Y, Xiao P, Guo X, Wang A, Liu P, Zhu Y, Chen L, Chen Z. Integration of GWAS, linkage analysis and transcriptome analysis to reveal the genetic basis of flowering time-related traits in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1145327. [PMID: 37035050 PMCID: PMC10073556 DOI: 10.3389/fpls.2023.1145327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Maize (Zea mays) inbred lines vary greatly in flowering time, but the genetic basis of this variation is unknown. In this study, three maize flowering-related traits (DTT, days to tasselling; DTP, days to pollen shed; DTS, days to silking) were evaluated with an association panel consisting of 226 maize inbred lines and an F2:3 population with 120 offspring from a cross between the T32 and Qi319 lines in different environments. A total of 82 significant single nucleotide polymorphisms (SNPs) and 117 candidate genes were identified by genome-wide association analysis. Twenty-one quantitative trait loci (QTLs) and 65 candidate genes were found for maize flowering time by linkage analysis with the constructed high-density genetic map. Transcriptome analysis was performed for Qi319, which is an early-maturing inbred line, and T32, which is a late-maturing inbred line, in two different environments. Compared with T32, Qi319 showed upregulation of 3815 genes and downregulation of 3906 genes. By integrating a genome-wide association study (GWAS), linkage analysis and transcriptome analysis, 25 important candidate genes for maize flowering time were identified. Together, our results provide an important resource and a foundation for an enhanced understanding of flowering time in maize.
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Affiliation(s)
- Xun Wu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Ying Liu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Xuefeng Lu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Liang Tu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuan Gao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Dong Wang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Shuang Guo
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Yifei Xiao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Pingfang Xiao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Xiangyang Guo
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Angui Wang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Pengfei Liu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yunfang Zhu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zehui Chen
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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Hu W, Gao D, Zhang Y, Zheng X, Lu C, Wu H, Xu W, Cheng S, Jia J. Mapping Quantitative Trait Loci for Type II Fusarium Head Blight Resistance in Two Wheat Recombinant Inbred Line Populations Derived from Yangmai 4 and Yangmai 5. PLANT DISEASE 2023; 107:422-430. [PMID: 35881872 DOI: 10.1094/pdis-06-22-1338-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fusarium head blight (FHB) is a destructive wheat disease worldwide and significantly affects grain yield and quality in wheat. To understand the genetic basis underlying type II FHB resistance in two elite wheat cultivars-Yangmai 4 (YM4) and Yangmai 5 (YM5)-quantitative trait loci (QTL) mapping was conducted in two recombinant inbred line (RIL) populations derived from the crosses of YM4 and YM5 with susceptible cultivar Yanzhan 1 (YZ1), respectively. A survey with markers linked to Fhb1, Fhb2, Fhb4, and Fhb5 in landrace Wangshuibai indicated the nonexistence of these known FHB resistance genes or QTL in YM4, YM5, and YZ1. One overlapped resistance QTL was identified in both RIL populations (namely, QFhb.Y4.2D/QFhb.Y5.2D) with a large effect on FHB resistance. One novel resistance QTL (QFhb.Y4.5A) mapped on chromosome 5A was detected only in the YM4/YZ1 population. The resistance alleles of both QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A did not increase the plant height and did not significantly affect the heading date and flowering date. Kompetitive allele-specific PCR markers for QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A had been developed to verify in an additional set of 244 geographically diverse cultivars or lines. Pyramiding of the two resistance alleles decreased the percentage of symptomatic spikelets by 51.77% relative to the cultivars or lines without these two resistance alleles. QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A were shown to be useful alternatives in FHB resistance breeding programs. The results will facilitate marker-assisted selection for introgression of the favorable alleles for improving FHB resistance in breeding programs.
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Affiliation(s)
- Wenjing Hu
- College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, Henan 450046, China
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, Jiangsu 225007, China
| | - Derong Gao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, Jiangsu 225007, China
| | - Yong Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, Jiangsu 225007, China
| | - Xu Zheng
- College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Chengbin Lu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, Jiangsu 225007, China
| | - Hongya Wu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, Jiangsu 225007, China
| | - Weigang Xu
- Institute of Crop Molecular Breeding/National Engineering Laboratory of Wheat/Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area/Ministry of Agriculture/Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Shunhe Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, Jiangsu 225007, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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Zhang L, Wang X, Wang K, Wang J. GAHP: An integrated software package on genetic analysis with bi-parental immortalized heterozygous populations. Front Genet 2022; 13:1021178. [PMID: 36276955 PMCID: PMC9579317 DOI: 10.3389/fgene.2022.1021178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
GAHP is a freely available software package for genetic analysis with bi-parental immortalized heterozygous and pure-line populations. The package is project-based and integrated with multiple functions. All operations and running results are properly saved in a project, which can be recovered when the project is re-open by the package. Four functionalities have been implemented in the current version of GAHP, i.e., 1) MHP: visualization of genetic linkage maps; 2) VHP: analysis of variance (ANOVA) and estimation of heritability on phenotypic data; 3) QHP: quantitative trait locus (QTL) mapping on both genotypic and phenotypic data; 4) SHP: simulation of bi-parental immortalized heterozygous and pure-line populations, and power analysis of QTL mapping. VHP and QHP can be conducted in individual populations, as well as in multiple populations by the combined analysis. Input files are arranged either in the plain text format with an extension name same as the functionality or in the MS Excel formats. Output files have the same prefix name as the input file, but with different extensions to indicate their contents. Three characters before the extension names stand for the types of populations used in analysis. In the interface of the software package, input files are grouped by functionality, and output files are grouped by individual or combined mapping populations. In addition to the text-format outputs, the constructed linkage map can be visualized per chromosome or for a number of selected chromosomes; line plots and bi-plots can be drawn from QTL mapping results and phenotypic data. Functionalities and analysis methods available in GAHP help the investigation of genetic architectures of complex traits and the mechanism of heterosis in plants.
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Affiliation(s)
- Luyan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xinhui Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Kaiyi Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Kaiyi Wang, ; Jiankang Wang,
| | - Jiankang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences (CAAS), Hainan, China
- *Correspondence: Kaiyi Wang, ; Jiankang Wang,
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Xue Y, Gao H, Liu X, Tang X, Cao D, Luan X, Zhao L, Qiu L. QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.). Int J Mol Sci 2022; 23:ijms231911273. [PMID: 36232577 PMCID: PMC9569734 DOI: 10.3390/ijms231911273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/27/2022] Open
Abstract
Soybeans are essential crops that supply protein and oil. The composition and contents of soybean fatty acids are relevant to human health and have a significant relationship with soybean oil processing and applications. Identifying quantitative trait locus (QTL) genes related to palmitic acid could facilitate the development of a range of nutritive soybean cultivars using molecular marker-assisted selection. In this study, we used a cultivar with higher palmitic acid content, ‘Dongnong42’, and a lower palmitic acid content cultivar, ‘Hobbit’, to establish F2:6 recombinant inbred lines. A high-density genetic map containing 9980 SLAF markers was constructed and distributed across 20 soybean chromosomes. The genetic map contained a total genetic distance of 2602.58 cM and an average genetic distance of 0.39 cM between adjacent markers. Two QTLs related to palmitic acid content were mapped using inclusive composite interval mapping, explaining 4.2–10.1% of the phenotypic variance in three different years and environments, including the QTL included in seed palmitic 7-3, which was validated by developing SSR markers. Based on the SNP/Indel and significant differential expression analyses of Dongnong42 and Hobbit, two genes, Glyma.15g119700 and Glyma.15g119800, were selected as candidate genes. The high-density genetic map, QTLs, and molecular markers will be helpful for the map-based cloning of palmitic acid content genes. These could be used to accelerate breeding for high nutritive value cultivars via molecular marker-assisted breeding.
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Affiliation(s)
- Yongguo Xue
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Huawei Gao
- National Key Facility for Crop Gene Resources and Genetic Improvemen, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinlei Liu
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Xiaofei Tang
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Dan Cao
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Xiaoyan Luan
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (L.Z.); (L.Q.)
| | - Lijuan Qiu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
- National Key Facility for Crop Gene Resources and Genetic Improvemen, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (L.Z.); (L.Q.)
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19
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Chao H, Li H, Yan S, Zhao W, Chen K, Wang H, Raboanatahiry N, Huang J, Li M. Further insight into decreases in seed glucosinolate content based on QTL mapping and RNA-seq in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2969-2991. [PMID: 35841418 DOI: 10.1007/s00122-022-04161-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
The QTL hotspots determining seed glucosinolate content instead of only four HAG1 loci and elucidation of a potential regulatory model for rapeseed SGC variation. Glucosinolates (GSLs) are amino acid-derived, sulfur-rich secondary metabolites that function as biopesticides and flavor compounds, but the high seed glucosinolate content (SGC) reduces seed quality for rapeseed meal. To dissect the genetic mechanism and further reduce SGC in rapeseed, QTL mapping was performed using an updated high-density genetic map based on a doubled haploid (DH) population derived from two parents that showed significant differences in SGC. In 15 environments, a total of 162 significant QTLs were identified for SGC and then integrated into 59 consensus QTLs, of which 32 were novel QTLs. Four QTL hotspot regions (QTL-HRs) for SGC variation were discovered on chromosomes A09, C02, C07 and C09, including seven major QTLs that have previously been reported and four novel major QTLs in addition to HAG1 loci. SGC was largely determined by superimposition of advantage allele in the four QTL-HRs. Important candidate genes directly related to GSL pathways were identified underlying the four QTL-HRs, including BnaC09.MYB28, BnaA09.APK1, BnaC09.SUR1 and BnaC02.GTR2a. Related differentially expressed candidates identified in the minor but environment stable QTLs indicated that sulfur assimilation plays an important rather than dominant role in SGC variation. A potential regulatory model for rapeseed SGC variation constructed by combining candidate GSL gene identification and differentially expressed gene analysis based on RNA-seq contributed to a better understanding of the GSL accumulation mechanism. This study provides insights to further understand the genetic regulatory mechanism of GSLs, as well as the potential loci and a new route to further diminish the SGC in rapeseed.
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Affiliation(s)
- Hongbo Chao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Chen Q, Liu B, Ai L, Yan L, Lin J, Shi X, Zhao H, Wei Y, Feng Y, Liu C, Yang C, Zhang M. QTL and candidate genes for heterophylly in soybean based on two populations of recombinant inbred lines. FRONTIERS IN PLANT SCIENCE 2022; 13:961619. [PMID: 36051289 PMCID: PMC9427049 DOI: 10.3389/fpls.2022.961619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Heterophylly, the existence of different leaf shapes and sizes on the same plant, has been observed in many flowering plant species. Yet, the genetic characteristics and genetic basis of heterophylly in soybean remain unknown. Here, two populations of recombinant inbred lines (RILs) with distinctly different leaf shapes were used to identify loci controlling heterophylly in two environments. The ratio of apical leaf shape (LSUP) to basal leaf shape (LSDOWN) at the reproductive growth stage (RLS) was used as a parameter for classifying heterophylly. A total of eight QTL were detected for RLS between the two populations and four of them were stably identified in both environments. Among them, qRLS20 had the largest effect in the JS population, with a maximum LOD value of 46.9 explaining up to 47.2% of phenotypic variance. This locus was located in the same genomic region as the basal leaf shape QTL qLSDOWN20 on chromosome 20. The locus qRLS19 had the largest effect in the JJ population, with a maximum LOD value of 15.2 explaining up to 27.0% of phenotypic variance. This locus was located in the same genomic region as the apical leaf shape QTL qLSUP19 on chromosome 19. Four candidate genes for heterophylly were identified based on sequence differences among the three parents of the two mapping populations, RT-qPCR analysis, and gene functional annotation analysis. The QTL and candidate genes detected in this study lay a foundation for further understanding the genetic mechanism of heterophylly and are invaluable in marker-assisted breeding.
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Affiliation(s)
- Qiang Chen
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Bingqiang Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Lijuan Ai
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Jing Lin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Yu Wei
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Yan Feng
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
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21
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Hou X, Cheng S, Wang S, Yu T, Wang Y, Xu P, Xu X, Zhou Q, Hou X, Zhang G, Chen C. Characterization and Fine Mapping of qRPR1-3 and qRPR3-1, Two Major QTLs for Rind Penetrometer Resistance in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:944539. [PMID: 35928711 PMCID: PMC9344970 DOI: 10.3389/fpls.2022.944539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 05/31/2023]
Abstract
Stalk strength is one of the most important traits in maize, which affects stalk lodging resistance and, consequently, maize harvestable yield. Rind penetrometer resistance (RPR) as an effective and reliable measurement for evaluating maize stalk strength is positively correlated with stalk lodging resistance. In this study, one F2 and three F2:3 populations derived from the cross of inbred lines 3705I (the low RPR line) and LH277 (the high RPR line) were constructed for mapping quantitative trait loci (QTL), conferring RPR in maize. Fourteen RPR QTLs were identified in four environments and explained the phenotypic variation of RPR from 4.14 to 15.89%. By using a sequential fine-mapping strategy based on the progeny test, two major QTLs, qRPR1-3 and qRPR3-1, were narrowed down to 4-Mb and 550-kb genomic interval, respectively. The quantitative real-time PCR (qRT-PCR) assay was adopted to identify 12 candidate genes responsible for QTL qRPR3-1. These findings should facilitate the identification of the polymorphism loci underlying QTL qRPR3-1 and molecular breeding for RPR in maize.
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22
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He Y, Chen S, Liu K, Chen Y, Cheng Y, Zeng P, Zhu P, Xie T, Chen S, Zhang H, Cheng J. OsHIPL1, a hedgehog-interacting protein-like 1 protein, increases seed vigour in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1346-1362. [PMID: 35315188 PMCID: PMC9241377 DOI: 10.1111/pbi.13812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/19/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog-interacting protein-like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA-seq) revealed that the ABA-related genes were involved in the OsHIPL1 regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of OsHIPL1 mutants and NIL-qsv3 line compared to IR26 plants, with two up-regulated ABA biosynthesis genes (OsZEP and OsNCED4) and one down-regulated ABA catabolism gene OsABA8ox3. The expression of abscisic acid-insensitive 3 (OsABI3), OsABI4 and OsABI5 was significantly up-regulated in germinating seeds of OsHIPL1 mutants and NIL-qsv3 line compared to IR26 plants. These results indicate that the regulation of seed vigour of OsHIPL1 may be through modulating endogenous ABA levels and altering OsABIs expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single-nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of OsHIPL1 that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of OsHIPL1 on seed vigour.
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Affiliation(s)
- Ying He
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Shanshan Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Yongji Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Jinping Cheng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
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Zhao C, Xie M, Liang L, Yang L, Han H, Qin X, Zhao J, Hou Y, Dai W, Du C, Xiang Y, Liu S, Huang X. Genome-Wide Association Analysis Combined With Quantitative Trait Loci Mapping and Dynamic Transcriptome Unveil the Genetic Control of Seed Oil Content in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:929197. [PMID: 35845656 PMCID: PMC9283957 DOI: 10.3389/fpls.2022.929197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed, an allotetraploid oil crop, provides vegetable oil for human consumption. The growing demand for oilseeds has necessitated the development of rapeseed varieties with improved quality. Therefore, a clear understanding of the genetic basis underlying the seed oil content (SOC) is required. In this study, a natural population comprising 204 diverse accessions and recombinant inbred lines (RILs) derived from Brassica napus and Sinapis alba via distant hybridization were collected for genome-wide association analysis (GWAS) and quantitative trait loci (QTL) mapping of the SOC trait, respectively. The variable coefficient of the RIL and natural populations ranged from 7.43 to 10.43% and 8.40 to 10.91%. Then, a high-density linkage map was constructed based on whole genome re-sequencing (WGS); the map harbored 2,799 bin markers and covered a total distance of 1,835.21 cM, with an average marker interval of 0.66 cM. The QTLs for SOC on chromosome A07 were stably detected in both single and multiple environments. Finally, a novel locus qA07.SOC was identified as the major QTL for SOC based on the GWAS and RIL populations. In addition, the RNA-seq results showed that photosynthesis, lipid biosynthesis proteins, fatty acid metabolism, and unsaturated fatty acid biosynthesis were significantly different between the developed seeds of the two parents of the RIL population. By comparing the variation information and expression levels of the syntenic genes within qA07.SOC and its syntenic genomic regions, as well as through haplotype analysis via GWAS, BnaA07.STR18, BnaA07.NRT1, and BnaA07g12880D were predicted as candidate genes in the qA07.SOC interval. These stable QTLs containing candidate genes and haplotypes can potentially provide a reliable basis for marker-assisted selection in B. napus breeding for SOC.
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Affiliation(s)
- Chuanji Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Longbing Liang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Experimental Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Hongshi Han
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xinrong Qin
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Jixian Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yan Hou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wendong Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Caifu Du
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianqun Huang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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24
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Zheng H, Hou L, Xie J, Cao F, Wei R, Yang M, Qi Z, Zhu R, Zhang Z, Xin D, Li C, Liu C, Jiang H, Chen Q. Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:869455. [PMID: 35783974 PMCID: PMC9247457 DOI: 10.3389/fpls.2022.869455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.
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Affiliation(s)
| | - Lilong Hou
- Northeast Agricultural University, Harbin, China
| | - Jianguo Xie
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
| | - Fubin Cao
- Northeast Agricultural University, Harbin, China
| | - Ruru Wei
- Northeast Agricultural University, Harbin, China
| | | | - Zhaoming Qi
- Northeast Agricultural University, Harbin, China
| | | | | | - Dawei Xin
- Northeast Agricultural University, Harbin, China
| | - Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Chunyan Liu
- Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
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25
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Xie X, Li S, Liu H, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Chen G, Qi P, Li W, Pu Z, Ahsan Habib, Wei Y, Zheng Y, Lan X, Ma J. Identification and validation of a major QTL for kernel length in bread wheat based on two F 3 biparental populations. BMC Genomics 2022; 23:386. [PMID: 35590264 PMCID: PMC9121568 DOI: 10.1186/s12864-022-08608-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High yield and quality are essential goals of wheat (Triticum aestivum L.) breeding. Kernel length (KL), as a main component of kernel size, can indirectly change kernel weight and then affects yield. Identification and utilization of excellent loci in wheat genetic resources is of great significance for cultivating high yield and quality wheat. Genetic identification of loci for KL has been performed mainly through genome-wide association study in natural populations or QTL mapping based on genetic linkage map in high generation populations. RESULTS In this study, an F3 biparental population derived from the cross between an EMS mutant BLS1 selected from an EMS-induced wheat genotype LJ2135 (derived from the hybrid progeny of a spelt wheat (T. spelta L.) and a common wheat) mutant bank and a local breeding line 99E18 was used to rapidly identify loci controlling KL based on Bulked Segregant Analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array. The highest ratio of polymorphic SNPs was located on chromosome 4A. Linkage map analysis showed that 33 Kompetitive Allele Specific PCR markers were linked to the QTL for KL (Qkl.sicau-BLE18-4A) identified in three environments as well as the best linear unbiased prediction (BLUP) dataset. This QTL explained 10.87-19.30% of the phenotypic variation. Its effect was successfully confirmed in another F3 population with the two flanking markers KASP-AX-111536305 and KASP-AX-110174441. Compared with previous studies and given that the of BLS1 has the genetic background of spelt wheat, the major QTL was likely a new one. A few of predicted genes related to regulation of kernel development were identified in the interval of the detected QTL. CONCLUSION A major, novel and stable QTL (Qkl.sicau-BLE18-4A) for KL was identified and verified in two F3 biparental populations across three environments. Significant relationships among KL, kernel width (KW) and thousand kernel weight (TKW) were identified. Four predicted genes related to kernel growth regulation were detected in the interval of Qkl.sicau-BLE18-4A. Furthermore, this study laid foundation on subsequent fine mapping work and provided a possibility for breeding of elite wheat varieties.
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Affiliation(s)
- Xinlin Xie
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqin Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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26
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Cyplik A, Bocianowski J. Analytical and numerical comparisons of two methods of estimation of additive × additive × additive interaction of QTL effects. J Appl Genet 2022; 63:213-221. [PMID: 34940940 PMCID: PMC8979904 DOI: 10.1007/s13353-021-00676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/07/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
This paper presents the analytical and numerical comparison of two methods of estimation of additive × additive × additive (aaa) interaction of QTL effects. The first method takes into account only the plant phenotype, while in the second we also included genotypic information from molecular marker observation. Analysis was made on 150 doubled haploid (DH) lines of barley derived from cross Steptoe × Morex and 145 DH lines from Harrington × TR306 cross. In total, 153 sets of observation was analyzed. In most cases, aaa interactions were found with an exert effect on QTL. Results also show that with molecular marker observations, obtained estimators had smaller absolute values than phenotypic estimators.
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Affiliation(s)
- Adrian Cyplik
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland.
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27
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Xiang Neik T, Ghanbarnia K, Ollivier B, Scheben A, Severn‐Ellis A, Larkan NJ, Haddadi P, Fernando DWG, Rouxel T, Batley J, Borhan HM, Balesdent M. Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS-Lep2. MOLECULAR PLANT PATHOLOGY 2022; 23:733-748. [PMID: 35239989 PMCID: PMC8995059 DOI: 10.1111/mpp.13194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 05/10/2023]
Abstract
Brassica napus (oilseed rape, canola) seedling resistance to Leptosphaeria maculans, the causal agent of blackleg (stem canker) disease, follows a gene-for-gene relationship. The avirulence genes AvrLmS and AvrLep2 were described to be perceived by the resistance genes RlmS and LepR2, respectively, present in B. napus 'Surpass 400'. Here we report cloning of AvrLmS and AvrLep2 using two independent methods. AvrLmS was cloned using combined in vitro crossing between avirulent and virulent isolates with sequencing of DNA bulks from avirulent or virulent progeny (bulked segregant sequencing). AvrLep2 was cloned using a biparental cross of avirulent and virulent L. maculans isolates and a classical map-based cloning approach. Taking these two approaches independently, we found that AvrLmS and AvrLep2 are the same gene. Complementation of virulent isolates with this gene confirmed its role in inducing resistance on Surpass 400, Topas-LepR2, and an RlmS-line. The gene, renamed AvrLmS-Lep2, encodes a small cysteine-rich protein of unknown function with an N-terminal secretory signal peptide, which is a common feature of the majority of effectors from extracellular fungal plant pathogens. The AvrLmS-Lep2/LepR2 interaction phenotype was found to vary from a typical hypersensitive response through intermediate resistance sometimes towards susceptibility, depending on the inoculation conditions. AvrLmS-Lep2 was nevertheless sufficient to significantly slow the systemic growth of the pathogen and reduce the stem lesion size on plant genotypes with LepR2, indicating the potential efficiency of this resistance to control the disease in the field.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Kaveh Ghanbarnia
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
- Department of Plant SciencesUniversity of ManitobaWinnipegManitobaCanada
| | | | - Armin Scheben
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Anita Severn‐Ellis
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Nicholas J. Larkan
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
- Armatus Genetics Inc.SaskatoonSaskatchewanCanada
| | - Parham Haddadi
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
| | | | - Thierry Rouxel
- Université Paris‐SaclayINRAEUR BIOGERThiverval‐GrignonFrance
| | - Jacqueline Batley
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Hossein M. Borhan
- Agriculture and Agri‐Food CanadaSaskatoon Research CenterSaskatoonSaskatchewanCanada
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28
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Ding G, Hu B, Zhou Y, Yang W, Zhao M, Xie J, Zhang F. Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974. Genes (Basel) 2022; 13:genes13050735. [PMID: 35627119 PMCID: PMC9140843 DOI: 10.3390/genes13050735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems.
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Affiliation(s)
- Gumu Ding
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Biaolin Hu
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330022, China;
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Wanling Yang
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
| | - Minmin Zhao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Jiankun Xie
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
- Correspondence: (J.X.); (F.Z.)
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29
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Zhou Z, Geng S, Guan H, Liu C, Qin M, Li W, Shi X, Dai Z, Yao W, Lei Z, Wu Z, Hou J. Dissection of the Genetic Architecture for Quantities of Gliadins Fractions in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:826909. [PMID: 35401644 PMCID: PMC8988047 DOI: 10.3389/fpls.2022.826909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Gliadin is a group of grain storage proteins that confers extensibility/viscosity to the dough and are vital to end-use quality in wheat. Moreover, gliadins are one of the important components for nutritional quality because they contain the nutritional unprofitable epitopes that cause chronic immune-mediated intestinal disorder in genetically susceptible individuals designated celiac disease (CD). The main genetic loci encoding the gliadins were revealed by previous studies; however, the genes related to the content of gliadins and their fractions were less elucidated. To illustrate the genetic basis of the content of gliadins and their fractions comprehensively, a recombinant inbred line (RIL) population that consisted of 196 lines was constructed from the two parents, Luozhen No.1 and Zhengyumai 9987. Quantitative trait loci (QTL) controlling the content of total gliadins and their fractions (ω-, α-, and γ-gliadin) were screened genome-widely under four environments across 2 years. Totally, thirty QTL which explained 1.97-12.83% of the phenotypic variation were detected to be distributed on 17 chromosomes and they were gathered into 12 clusters. One hundred and one pairs of epistatic QTL (E-QTL) were revealed, among which five were involved with the total gliadins and its fractions content QTL located on chromosome 1AS, 1DS, 4DS, 1DL, and 6AS. Three Kompetitive Allele-Specific PCR (KASP) markers were developed from three major QTL clusters located on chromosomes 6A, 6D, and 7D, respectively. The present research not only dissects the genetic loci for improving the content of gliadins and their three fractions, but may also contribute to marker-assisted selection of varieties with appropriate gliadin fractions content for end-use quality and health benefit at the early developmental stages and early breeding generations.
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Affiliation(s)
- Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shenghui Geng
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiyue Guan
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Congcong Liu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Shi
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ziju Dai
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
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30
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Genome-Wide Association Study of Root-Lesion Nematodes Pratylenchus Species and Crown Rot Fusarium culmorum in Bread Wheat. Life (Basel) 2022; 12:life12030372. [PMID: 35330123 PMCID: PMC8949321 DOI: 10.3390/life12030372] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Triticum aestivum L., also known as common wheat, is affected by many biotic stresses. Root diseases are the most difficult to tackle due to the complexity of phenotypic evaluation and the lack of resistant sources compared to other biotic stress factors. Soil-borne pathogens such as the root-lesion nematodes caused by the Pratylenchus species and crown rot caused by various Fusarium species are major wheat root diseases, causing substantial yield losses globally. A set of 189 advanced spring bread wheat lines obtained from the International Maize and Wheat Improvement Center (CIMMYT) were genotyped with 4056 single nucleotide polymorphisms (SNP) markers and screened for root-lesion nematodes and crown rot resistance. Population structure revealed that the genotypes could be divided into five subpopulations. Genome-Wide Association Studies were carried out for both resistances to Pratylenchus and Fusarium species. Based on our results, 11 different SNPs on chromosomes 1A, 1B, 2A, 3A, 4A, 5B, and 5D were significantly associated with root-lesion nematode resistance. Seven markers demonstrated association with P. neglectus, while the remaining four were linked to P. thornei resistance. In the case of crown rot, eight different markers on chromosomes 1A, 2B, 3A, 4B, 5B, and 7D were associated with Fusarium crown rot resistance. Identification and screening of root diseases is a challenging task; therefore, the newly identified resistant sources/genotypes could be exploited by breeders to be incorporated in breeding programs. The use of the identified markers in marker-assisted selection could enhance the selection process and cultivar development with root-lesion nematode and crown rot resistance.
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31
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Che Y, He Y, Song N, Yang Y, Wei L, Yang X, Zhang Y, Zhang J, Han H, Li X, Zhou S, Liu W, Li L. Four-Year and Five-Developing-Stage Dynamic QTL Mapping for Tiller Number in the Hybrid Population of Agropyron Gaertn. FRONTIERS IN PLANT SCIENCE 2022; 13:835437. [PMID: 35283893 PMCID: PMC8907830 DOI: 10.3389/fpls.2022.835437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Tiller number (TN) is an important agronomic trait affecting gramineous crop yield. To understand the static and dynamic information of quantitative trait locus (QTLs) controlling TN of Agropyron Gaertn., both the unconditional and conditional quantitative trait loci (QTL) mapping of TN were conducted using a cross-pollinated (CP) hybrid population with a total of 113 plant lines from the cross between Agropyron cristatum (L.) Gaertn. Z1842 and Allium mongolicum Keng Z2098, based on the phenotypic data of TN at five developmental stages [i.e., recovering stage (RS), jointing stage (JS), heading stage (HS), flowering stage (FS), and maturity stage (MS)] in 4 years (i.e., 2017, 2018, 2020, and 2021) and the genetic map constructed of 1,023 single-nucleotide polymorphism (SNP) markers. Thirty-seven QTLs controlling TN were detected using two analysis methods in 4 years, which were distributed in six linkage groups. Each QTL explained 2.96-31.11% of the phenotypic variation, with a logarithum of odds (LOD) value of 2.51-13.95. Nine of these loci detected both unconditional and conditional QTLs. Twelve unconditional major QTLs and sixteen conditional major QTLs were detected. Three relatively major stable conditional QTLs, namely, cQTN1-3, cQTN1-5, and cQTN4-1, were expressed in 2020 and 2021. Meantime, two pairs of major QTLs cQTN1-5 and qTN1-4 and also cQTN2-4 and qTN2-3 were located at the same interval but in different years. Except for qTN2-2 and qTN3-5/cQTN3-5, other thirty-four QTLs were first detected in this study. This study provides a better interpretation of genetic factors that selectively control tiller at different developmental stages and a reference for molecular marker-assisted selection in the related plant improvement.
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Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yutong He
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Nan Song
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinpeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiming Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Chankaew S, Sriwichai S, Rakvong T, Monkham T, Sanitchon J, Tangphatsornruang S, Kongkachana W, Sonthirod C, Pootakham W, Amkul K, Kaewwongwal A, Laosatit K, Somta P. The First Genetic Linkage Map of Winged Bean [ Psophocarpus tetragonolobus (L.) DC.] and QTL Mapping for Flower-, Pod-, and Seed-Related Traits. PLANTS (BASEL, SWITZERLAND) 2022; 11:500. [PMID: 35214834 PMCID: PMC8878720 DOI: 10.3390/plants11040500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Winged bean [Psophocarpus tetragonolobus (L.) DC.] (2n = 2× = 18) is a tropical legume crop with multipurpose usages. Recently, the winged bean has regained attention from scientists as a food protein source. Currently, there is no breeding program for winged bean cultivars. All winged bean cultivars are landraces or selections from landraces. Molecular markers and genetic linkage maps are pre-requisites for molecular plant breeding. The aim of this study was to develop a high-density linkage map and identify quantitative trait loci (QTLs) for pod and seed-related traits of the winged bean. An F2 population of 86 plants was developed from a cross between winged bean accessions W054 and TPT9 showing contrasting pod length, and pod, flower and seed colors. A genetic linkage map of 1384 single nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing was constructed. The map resolved nine haploid chromosomes of the winged bean and spanned the cumulative length of 4552.8 cM with the number of SNPs per linkage ranging from 36 to 218 with an average of 153.78. QTL analysis in the F2 population revealed 31 QTLs controlling pod length, pod color, pod anthocyanin content, flower color, and seed color. The number of QTLs per trait varied between 1 (seed length) to 7 (banner color). Interestingly, the major QTLs for pod color, anthocyanin content, and calyx color, and for seed color and flower wing color were located at the same position. The high-density linkage map QTLs reported in this study will be useful for molecular breeding of winged beans.
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Affiliation(s)
- Sompong Chankaew
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Sasiprapa Sriwichai
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Teppratan Rakvong
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Tidarat Monkham
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Jirawat Sanitchon
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Wasitthee Kongkachana
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
| | - Anochar Kaewwongwal
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
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Identification of Fruit Traits Related QTLs and a Candidate Gene, CaBRX, Controlling Locule Number in Pepper (Capsicum annuum L.). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fruit traits are important in pepper (Capsicum annuum L.) and affect its quality and yield. These traits are controlled by quantitative trait loci (QTLs). In this study, we identified many major QTLs that control fruit length (Ftl), fruit diameter (Ftd), fruit shape (Fts), fruit weight (Ftw) and locule number (Lcn) in the F2 and F2:3 populations developed from the QTL mapping of GS6 (P1) and Qiemen (P2). A total of 111 simple sequence repeats and insertion/deletion markers were utilized to construct a linkage map with 12 linkage groups over a length of 1320.72 cM. An inclusive composite interval mapping analysis indicated that many QTLs were detected and included ftl2.1, ftd2.1, fts1.1, ftw2.1 and lcn1.1. As a novel QTL, lcn1.1 was located between HM1112 and EPMS709, and the genetic distance was 3.18 cM covering 60 predicted genes. Within the region, we identified Capana01g004285 as a candidate gene by functional annotation and expression analysis and found that it encodes the BREVIS RADIX (BRX) protein. Knockdown of CaBRX through the virus-induced gene silencing approach in GS6 reduced the number of locules and influenced the expressions of genes related to flower and locule development, suggesting that CaBRX plays an important function in the development of locules.
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Wang J, Hu B, Jing Y, Hu X, Guo Y, Chen J, Liu Y, Hao J, Li WX, Ning H. Detecting QTL and Candidate Genes for Plant Height in Soybean via Linkage Analysis and GWAS. FRONTIERS IN PLANT SCIENCE 2022; 12:803820. [PMID: 35126428 PMCID: PMC8813865 DOI: 10.3389/fpls.2021.803820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
Soybean is an important global crop for edible protein and oil, and plant height is a main breeding goal which is closely related to its plant shape and yield. In this research, a high-density genetic linkage map was constructed by 1996 SNP-bin markers on the basis of a recombinant inbred line population derived from Dongnong L13 × Henong 60. A total of 33 QTL related to plant height were identified, of which five were repeatedly detected in multiple environments. In addition, a 455-germplasm population with 63,306 SNP markers was used for multi-locus association analysis. A total of 62 plant height QTN were detected, of which 26 were detected repeatedly under multiple methods. Two candidate genes, Glyma.02G133000 and Glyma.05G240600, involving in plant height were predicted by pathway analysis in the regions identified by multiple environments and backgrounds, and validated by qRT-PCR. These results enriched the soybean plant height regulatory network and contributed to molecular selection-assisted breeding.
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Affiliation(s)
- Jiajing Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Bo Hu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yuliang Jing
- Suihua Branch of Heilongjiang Academy of Agricultural Science, Suihua, China
| | - Xiping Hu
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, China
| | - Yue Guo
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jiankun Chen
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yuxi Liu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jianhui Hao
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
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35
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Ma C, Rehman A, Li HG, Zhao ZB, Sun G, Du XM. Mapping of dwarfing QTL of Ari1327, a semi-dwarf mutant of upland cotton. BMC PLANT BIOLOGY 2022; 22:5. [PMID: 34979924 PMCID: PMC8722190 DOI: 10.1186/s12870-021-03359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Upland Cotton (Gossypium hirsutum L.) has few cotton varieties suitable for mechanical harvesting. The plant height of the cultivar is one of the key features that need to modify. Hence, this study was planned to locate the QTL for plant height in a 60Co γ treated upland cotton semi-dwarf mutant Ari1327. RESULTS Interestingly, bulk segregant analysis (BSA) and genotyping by sequencing (GBS) methods exhibited that candidate QTL was co-located in the region of 5.80-9.66 Mb at D01 chromosome in two F2 populations. Using three InDel markers to genotype a population of 1241 individuals confirmed that the offspring's phenotype is consistent with the genotype. Comparative analysis of RNA-seq between the mutant and wild variety exhibited that Gh_D01G0592 was identified as the source of dwarfness from 200 genes. In addition, it was also revealed that the appropriate use of partial separation markers in QTL mapping can escalate linkage information. CONCLUSIONS Overwhelmingly, the results will provide the basis to reveal the function of candidate genes and the utilization of excellent dwarf genetic resources in the future.
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Affiliation(s)
- Chenhui Ma
- State Key Laboratory of cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 66000, Pakistan
| | - Hong Ge Li
- State Key Laboratory of cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zi Bo Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Gaofei Sun
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Anyang, China
| | - Xiong Ming Du
- State Key Laboratory of cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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36
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Zhang X, Wang M, Zhang C, Dai C, Guan H, Zhang R. Genetic dissection of QTLs for starch content in four maize DH populations. FRONTIERS IN PLANT SCIENCE 2022; 13:950664. [PMID: 36275573 PMCID: PMC9583244 DOI: 10.3389/fpls.2022.950664] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/30/2022] [Indexed: 05/17/2023]
Abstract
Starch is the principal carbohydrate source in maize kernels. Understanding the genetic basis of starch content (SC) benefits greatly in improving maize yield and optimizing end-use quality. Here, four double haploid (DH) populations were generated and were used to identify quantitative trait loci (QTLs) associated with SC. The phenotype of SC exhibited continuous and approximate normal distribution in each population. A total of 13 QTLs for SC in maize kernels was detected in a range of 3.65-16.18% of phenotypic variation explained (PVE). Among those, only some partly overlapped with QTLs previously known to be related to SC. Meanwhile, 12 genes involved in starch synthesis and metabolism located within QTLs were identified in this study. These QTLs will lay the foundation to explore candidate genes regulating SC in maize kernel and facilitate the application of molecular marker-assisted selection for a breeding program to cultivate maize varieties with a deal of grain quality.
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Affiliation(s)
- Xiaolei Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Min Wang
- Institute of Advanced Agricultural Technology, Qilu Normal University, Jinan, China
| | | | - Changjun Dai
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Haitao Guan
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ruiying Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Ruiying Zhang
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37
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Ge C, Wentzel E, D'Souza N, Chen K, Oliver RP, Ellwood SR. Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad-spectrum resistance. THE PLANT GENOME 2021; 14:e20129. [PMID: 34392613 DOI: 10.1002/tpg2.20129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew isa major disease of barley (Hordeum vulgare L.) for which breeders have traditionally relied on dominant, pathogen race-specific resistance genes for genetic control. Directional selection pressures in extensive monocultures invariably result in such genes being overcome as the pathogen mutates to evade recognition. This has led to a widespread reliance on fungicides and a single broad-spectrum recessive resistance provided by the mlo gene. The range of resistance genes and alleles found in wild crop relatives and landraces has been reduced in agricultural cultivars through an erosion of genetic diversity during domestication and selective breeding. Three novel major-effect adult plant resistance (APR) genes from landraces, designated Resistance to Blumeria graminis f. sp. hordei (Rbgh1 to Rbgh3), were identified in the terminal regions of barley chromosomes 5HL, 7HS, and 1HS, respectively. The phenotype of the new APR genes showed neither pronounced penetration resistance, nor the spontaneous necrosis and mesophyll cell death typical of mlo resistance, nor a whole epidermal cell hypersensitive response, typical of race-specific resistance. Instead, resistance was localized to the site of attempted penetration in an epidermal cell and was associated with cell wall appositions and cytosolic vesicle-like bodies, and lacked strong induction of reactive oxygen species. The APR genes exhibited differences in vesicle-like body sizes, their distribution, and the extent of localized 3,3-diaminobenzidine staining in individual doubled haploid lines. The results revealed a set of unique basal penetration resistance genes that offer opportunities for combining different resistance mechanisms in breeding programs for robust mildew resistance.
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Affiliation(s)
- Cynthia Ge
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Elzette Wentzel
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Nola D'Souza
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Kefei Chen
- Statistics for the Australian Grains Industry-West, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Richard P Oliver
- School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
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Zhou Z, Zhang Z, Mason AS, Chen L, Liu C, Qin M, Li W, Tian B, Wu Z, Lei Z, Hou J. Quantitative traits loci mapping and molecular marker development for total glutenin and glutenin fraction contents in wheat. BMC PLANT BIOLOGY 2021; 21:455. [PMID: 34615486 PMCID: PMC8493754 DOI: 10.1186/s12870-021-03221-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Glutenin contents and compositions are crucial factors influencing the end-use quality of wheat. Although the composition of glutenin fractions is well known, there has been relatively little research on the genetic basis of glutenin fractions in wheat. RESULTS To elucidate the genetic basis for the contents of glutenin and its fractions, a population comprising 196 recombinant inbred lines (RILs) was constructed from two parents, Luozhen No.1 and Zhengyumai 9987, which differ regarding their total glutenin and its fraction contents (except for the By fraction). Forty-one additive Quantitative Trait Loci (QTL) were detected in four environments over two years. These QTL explained 1.3% - 53.4% of the phenotypic variation in the examined traits. Forty-three pairs of epistatic QTL (E-QTL) were detected in the RIL population across four environments. The QTL controlling the content of total glutenin and its seven fractions were detected in clusters. Seven clusters enriched with QTL for more than three traits were identified, including a QTL cluster 6AS-3, which was revealed as a novel genetic locus for glutenin and related traits. Kompetitive Allele-Specific PCR (KASP) markers developed from the main QTL cluster 1DL-2 and the previously developed KASP marker for the QTL cluster 6AS-3 were validated as significantly associated with the target traits in the RIL population and in natural varieties. CONCLUSIONS This study identified novel genetic loci related to glutenin and its seven fractions. Additionally, the developed KASP markers may be useful for the marker-assisted selection of varieties with high glutenin fraction content and for identifying individuals in the early developmental stages without the need for phenotyping mature plants. On the basis of the results of this study and the KASP markers described herein, breeders will be able to efficiently select wheat lines with favorable glutenin properties and develop elite lines with high glutenin subunit contents.
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Affiliation(s)
- Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- Agronomy College, Zhengzhou University, 450001, Zhengzhou, China
| | - Ziwei Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Chair of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Lingzhi Chen
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Congcong Liu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Baoming Tian
- Agronomy College, Zhengzhou University, 450001, Zhengzhou, China
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- Agronomy College, Zhengzhou University, 450001, Zhengzhou, China.
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- Agronomy College, Zhengzhou University, 450001, Zhengzhou, China.
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- Agronomy College, Zhengzhou University, 450001, Zhengzhou, China.
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Ye W, Yang Y, Wang P, Zhang Y, Zhang L, Tian D, Zhang L, Zhang L, Zhou B. InDel marker development and QTL analysis of agronomic traits in mung bean [ Vigna radiate (L.) Wilczek]. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:66. [PMID: 37309317 PMCID: PMC10236061 DOI: 10.1007/s11032-021-01233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/11/2021] [Indexed: 06/14/2023]
Abstract
The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption and yield. However, few studies have focused on elucidating the genetic mechanisms that regulate these five particular traits: young stem color (YSC), days to first flowering (DFF), days to maturity (DM), PH, and nodes on the main stem (NMS). In this study, a genetic linkage map for the F2 population was constructed using 129 InDel markers that were developed based on the sequence variations between parents. A total of 14 QTLs related to YSC, DFF, DM, PH, and NMS were detected. These QTLs were distributed on six chromosomes (1, 3, 4, 6, 7, and 10), which individually accounted for 1.32 to 90.07% of the total phenotypic variation. Using a short and high-density linkage map for the F3 population, six of the seven QTLs which clustered at two intervals on chromosomes 3 and 10 were detected again. Further analysis found that four QTLs between InDel markers R3-15 and R3-19 controlled DFF, DM, PH, and NMS, and each QTL accounted for a large percent of the total phenotypic variation. Analysis of two separated F2:3 lines also found that the phenotype was highly corresponded to its genotype which was between R3-15 and R3-19. Phenotype and genotype analysis for 30 mung bean accessions showed that the major effect QTL qDFF3 was a key regulator for DFF. Using a map-based cloning method, the major effect QTL qYSC4 for YSC was mapped in a 347 Kb interval on chromosome 4. Candidate gene analysis showed that sequence variations and expression level differences existed in the predicted candidate gene between the parents. These results provide a theoretical basis for cloning these QTLs and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01233-0.
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Affiliation(s)
- Weijun Ye
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
- Anhui Province Key Laboratory of Crop Quality Improvement, Hefei, 230000 Anhui China
| | - Yong Yang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Peiran Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Yin Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Liya Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Dongfeng Tian
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Lei Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Lingling Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Bin Zhou
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
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Kim KS, Kim JM, Jung J, Shin I, Park S, Lee JS, Jeong SC, Lee JD, Jung JK, Ha BK, Kang S. Fine-mapping and candidate gene analysis for the foxglove aphid resistance gene Raso2 from wild soybean PI 366121. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2687-2698. [PMID: 33974087 DOI: 10.1007/s00122-021-03853-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE The foxglove aphid resistance gene Raso2 from PI 366121 was fine-mapped to 77 Kb region, and one candidate gene was identified. The foxglove aphid (FA: Aulacorthum solani Kaltenbach) is an important insect pest that causes serious yield losses in soybean. The FA resistance gene Raso2 from wild soybean PI 366121 was previously mapped to a 13 cM interval on soybean chromosome 7. However, fine-mapping of Raso2 was needed to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to fine-map Raso2 from PI 366121 using Axiom® 180 K SoyaSNP array, to confirm the resistance and inheritance of Raso2 in a different background, and to identify candidate gene(s). The 105 F4:8 recombinant inbred lines were used to fine-map the gene and to test antibiosis and antixenosis of Raso2 to FA. These efforts resulted in the mapping of Raso2 on 1 cM interval which corresponds to 77 Kb containing eight annotated genes based on the Williams 82 reference genome assembly (Wm82.a2.v1). Interestingly, all nonsynonymous substitutions were in Glyma.07g077700 which encodes the disease resistance protein containing LRR domain and expression of the gene in PI 366121 was significantly higher than that in Williams 82. In addition, distinct SNPs within Glyma.07g077700 that can distinguish PI 366121 and diverse FA-susceptible soybeans were identified. We also confirmed that Raso2 presented the resistance to FA and the Mendelian inheritance for single dominant gene in a different background. The results of this study would provide fundamental information on MAS for development of FA-resistant cultivars as well as functional study and cloning of the candidate gene in soybean.
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Affiliation(s)
- Ki-Seung Kim
- Deparment of Innovative Technology, FarmHannong, Ltd., Nonsan, 33010, Korea
| | - Ji-Min Kim
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Jiyeong Jung
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Ilseob Shin
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Sumin Park
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
- Business Incubation Center, Sae Han Agricultural Technology Research Station, Hwaseong, 18330, Korea
| | - Ju Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Jin Kyo Jung
- Rural Development Administration, National Institute of Crop Science, Suwon, 16613, Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju, 61186, Korea
| | - Sungtaeg Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea.
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Zhuo X, Zheng T, Li S, Zhang Z, Zhang M, Zhang Y, Ahmad S, Sun L, Wang J, Cheng T, Zhang Q. Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping. HORTICULTURE RESEARCH 2021; 8:131. [PMID: 34059642 PMCID: PMC8167129 DOI: 10.1038/s41438-021-00573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/20/2021] [Accepted: 04/07/2021] [Indexed: 05/20/2023]
Abstract
Weeping Prunus mume (mei) has long been cultivated in East Asia for its specific ornamental value. However, little is known about the regulatory mechanism of the weeping trait in mei, which limits molecular breeding for the improvement of weeping-type cultivars. Here, we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F1 hybrids. Two major associated loci were identified from the genome-wide association study (GWAS), which was conducted using 3,014,409 single nucleotide polymorphisms (SNPs) derived from resequencing, and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment (SLAF) markers. Notably, an overlapping PmWEEP major QTL was fine mapped within a 0.29 Mb region on chromosome 7 (Pa7), and a core SNP locus closely associated with the weeping trait was screened and validated. Furthermore, a total of 22 genes in the PmWEEP QTL region were expressed in weeping or upright mei based on RNA-seq analysis. Among them, only a novel gene (Pm024213) containing a thioredoxin (Trx) domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei. Co-expression analysis of Pm024213 showed that most of the related genes were involved in auxin and lignin biosynthesis. These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding in Prunus mume.
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Affiliation(s)
- Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China.
| | - Suzhen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Zhiyong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Man Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Sagheer Ahmad
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Lidan Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China.
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Nakhla WR, Sun W, Fan K, Yang K, Zhang C, Yu S. Identification of QTLs for Salt Tolerance at the Germination and Seedling Stages in Rice. PLANTS (BASEL, SWITZERLAND) 2021; 10:428. [PMID: 33668277 PMCID: PMC7996262 DOI: 10.3390/plants10030428] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 11/30/2022]
Abstract
Rice is highly sensitive to salinity stress during the seedling establishment phase. Salt stress is widely occurring in cultivated areas and severely affects seed germination ability and seedling establishment, which may result in a complete crop failure. The objective of the present study is to identify quantitative trait loci (QTLs) related to salt tolerance of the germination and seedling stages in a rice backcross inbred line (BIL) population that was derived from a backcross of an Africa rice ACC9 as donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent. Under salt stress, ACC9 exhibited a higher germination percentage, but more repressed seedling growth than ZS97. Using the BIL population, 23 loci for germination parameters were detected at the germination stage and 46 loci were identified for several morphological and physiological parameters at the seedling stage. Among them, nine and 33 loci with the ACC9 alleles increased salt tolerance at the germination and seedling stages, respectively. Moreover, several major QTLs were found to be co-localized in the same or overlapping regions of previously reported genes for salt stress. These major loci will facilitate improving salt-tolerance rice in genome-breeding programs.
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Affiliation(s)
- Walid Raafat Nakhla
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Li L, Peng Z, Mao X, Wang J, Li C, Chang X, Jing R. Genetic insights into natural variation underlying salt tolerance in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1135-1150. [PMID: 33130904 DOI: 10.1093/jxb/eraa500] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/26/2020] [Indexed: 05/06/2023]
Abstract
Developing salt-tolerant crop varieties is one of the important approaches to cope with increasing soil salinization worldwide. In this study, a diversity panel of 323 wheat accessions and 150 doubled haploid lines were phenotyped for salt-responsive morphological and physiological traits across two growth stages. The comprehensive salt tolerance of each wheat accession was evaluated based on principal component analysis. A total of 269 associated loci for salt-responsive traits and/or salt tolerance indices were identified by genome-wide association studies using 395 675 single nucleotide polymorphisms, among which 22 overlapping loci were simultaneously identified by biparental quantitative trait loci mapping. Two novel candidate genes ROOT NUMBER 1 (TaRN1) and ROOT NUMBER 2 (TaRN2) involved in root responses to salt stress fell within overlapping loci, showing different expression patterns and a frameshift mutation (in TaRN2) in contrasting salt-tolerant wheat genotypes. Moreover, the decline in salt tolerance of Chinese wheat varieties was observed from genetic and phenotypic data. We demonstrate that a haplotype controlling root responses to salt stress has been diminished by strong selection for grain yield, which highlights that linkage drag constrains the salt tolerance of Chinese wheat. This study will facilitate salt-tolerant wheat breeding in terms of elite germplasm, favorable alleles and selection strategies.
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Affiliation(s)
- Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi Peng
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Thambugala D, Pozniak CJ, Kumar S, Burt AJ, Wise IL, Smith MAH, Fox SL, Costamagna AC, McCartney CA. Genetic analysis of oviposition deterrence to orange wheat blossom midge in spring wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:647-660. [PMID: 33200319 DOI: 10.1007/s00122-020-03720-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
A major QTL for oviposition deterrence to orange wheat blossom midge was detected on chromosome 1A in the Canadian breeding line BW278 that was inherited from the Chinese variety Sumai-3. Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin, Diptera: Cecidomyiidae) is an important insect pest of wheat (Triticum aestivum L.) that reduces both grain yield and quality. Oviposition deterrence results in a reduction of eggs deposited on spikes relative to that observed on a wheat line preferred by OWBM. Quantification of oviposition deterrence is labor-intensive, so wheat breeders require efficient DNA markers for the selection of this trait. The objective of this study was to identify quantitative trait loci (QTL) for oviposition deterrence in a doubled haploid (DH) population developed from the spring wheat cross Superb/BW278. The DH population and check varieties were evaluated for OWBM kernel damage from five field nurseries over three growing seasons. QTL analysis identified major effect loci on chromosomes 1A (QSm.mrc-1A) and 5A (QSm.mrc-5A). Reduced kernel damage was contributed by BW278 at QSm.mrc-1A and Superb at QSm.mrc-5A. QSm.mrc-1A mapped to the approximate location of the oviposition deterrence QTL previously found in the American variety Reeder. However, haplotype analysis revealed that BW278 inherited this oviposition deterrence allele from the Chinese spring wheat variety Sumai-3. QSm.mrc-5A mapped to the location of awn inhibitor gene B1, suggesting that awns hinder OWBM oviposition. Single-nucleotide polymorphisms (SNPs) were identified for predicting the presence or absence of QSm.mrc-1A based upon haplotype. Functional annotation of candidate genes in 1A QTL intervals revealed eleven potential candidate genes, including a gene involved in terpenoid biosynthesis. SNPs for QSm.mrc-1A and fully awned spikes provide a basis for the selection of oviposition deterrence to OWBM.
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Affiliation(s)
- Dinushika Thambugala
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew J Burt
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Ian L Wise
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Marjorie A H Smith
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Stephen L Fox
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- DL Seeds Inc., Winnipeg, MB, Canada
| | | | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada.
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Zeng P, Zhu P, Qian L, Qian X, Mi Y, Lin Z, Dong S, Aronsson H, Zhang H, Cheng J. Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress. BMC PLANT BIOLOGY 2021; 21:36. [PMID: 33422012 PMCID: PMC7797128 DOI: 10.1186/s12870-020-02820-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/25/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding. RESULTS In this study, an indica landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BC1F2 population derived from the crossing WJZ/Nip (japonica, Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under H2O and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under H2O conditions and nine QTLs under salt conditions. Six QTLs, qGR6.1, qGR8.1, qGR8.2, qGR10.1, qGR10.2 and qGI10.1 were simultaneously identified under two conditions. Under salt conditions, three QTLs, qGR6.2, qGR10.1 and qGR10.2 for GR were identified at different time points during seed germination, which shared the same chromosomal region with qGI6.2, qGI10.1 and qGI10.2 for GI respectively. The qGR6.2 accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore, qGR6.2 was verified via the BC2F2 population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which LOC_Os06g10650 and LOC_Os06g10710 were differentially expressed after seed imbibition. RT-qPCR results showed the expression of LOC_Os06g10650 was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that LOC_Os06g10650, encoding tyrosine phosphatase family protein, might be the causal candidate gene for qGR6.2. CONCLUSIONS In this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under H2O and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS).
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Affiliation(s)
- Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Luofeng Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Xumei Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Yuxin Mi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Zefeng Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Shinan Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Henrik Aronsson
- Department of Biological and Environment Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China.
| | - Jinping Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Nanjing Agricultural University, Nanjing, China.
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Rao J, Wang X, Cai Z, Fan Y, Yang J. Genetic Analysis of S5-Interacting Genes Regulating Hybrid Sterility in Rice. RICE (NEW YORK, N.Y.) 2021; 14:11. [PMID: 33423160 PMCID: PMC7797014 DOI: 10.1186/s12284-020-00452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Asian cultivated rice (Oryza sativa L.) comprises two subspecies, O. sativa subsp. indica and subsp. japonica, and the hybrids between them display strong heterosis. However, hybrid sterility (HS) limits practical use of the heterosis between these two subspecies. S5 is a major-effect locus controlling the HS of female gametes in rice, consisting of three closely-linked genes ORF3, ORF4 and ORF5 that act as a killer-protector system. The HS effects of S5 are inconsistent for different genetic backgrounds, indicating the existence of interacting genes within the genome. RESULTS In the present study, the S5-interacting genes (SIG) and their effects on HS were analyzed by studying the hybrid progeny between an indica rice, Dular (DL) and a japonica rice, BalillaORF5+ (BLORF5+), with a transgenic ORF5+ allele. Four interacting quantitative trait loci (QTL): qSIG3.1, qSIG3.2, qSIG6.1, and qSIG12.1, were genetically mapped. To analyze the effect of each interacting locus, four near-isogenic lines (NILs) were developed. The effect of each specific locus was investigated while the other three loci were kept DL homozygous (DL/DL). Of the four loci, qSIG3.1 was the SIG with the greatest effects in which the DL allele was completely dominant. Furthermore, the DL allele displayed incomplete dominance at qSIG3.2, qSIG6.1, and qSIG12.1. qSIG3.1 will be the first choice for further fine-mapping. CONCLUSIONS Four S5-interacting QTL were identified by genetic mapping and the effect of each locus was analyzed using advanced backcrossed NILs. The present study will facilitate elucidation of the molecular mechanism of rice HS caused by S5. Additionally, it would provide the basis to explore the origin and differentiation of cultivated rice, having practical significance for inter-subspecific hybrid rice breeding programs.
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Affiliation(s)
- Jianglei Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xing Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Zhongquan Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yourong Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
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Mo Z, Zhu J, Wei J, Zhou J, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Li W, Wei Y, Zheng Y, Lan X, Ma J. The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat ( Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:732837. [PMID: 34531890 PMCID: PMC8439258 DOI: 10.3389/fpls.2021.732837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace "Ailanmai" × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.
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Affiliation(s)
- Ziqiang Mo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xiujin Lan
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jian Ma
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Hammenhag C, Saripella GV, Ortiz R, Geleta M. QTL Mapping for Domestication-Related Characteristics in Field Cress ( Lepidium campestre)-A Novel Oil Crop for the Subarctic Region. Genes (Basel) 2020; 11:genes11101223. [PMID: 33086591 PMCID: PMC7603098 DOI: 10.3390/genes11101223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/02/2020] [Accepted: 10/16/2020] [Indexed: 11/24/2022] Open
Abstract
Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F2 mapping population and its F3 progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p < 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress.
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Zheng X, Liu C, Qiao L, Zhao J, Han R, Wang X, Ge C, Zhang W, Zhang S, Qiao L, Zheng J, Hao C. The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5808-5822. [PMID: 32725154 DOI: 10.1093/jxb/eraa355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.
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Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Chuan Ge
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Wenyun Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Linyi Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Thambugala D, Brûlé-Babel AL, Blackwell BA, Fedak G, Foster AJ, MacEachern D, Gilbert J, Henriquez MA, Martin RA, McCallum BD, Spaner D, Iqbal M, Pozniak CJ, N'Diaye A, McCartney CA. Genetic analyses of native Fusarium head blight resistance in two spring wheat populations identifies QTL near the B1, Ppd-D1, Rht-1, Vrn-1, Fhb1, Fhb2, and Fhb5 loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2775-2796. [PMID: 32556394 DOI: 10.1007/s00122-020-03631-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
QTL analyses of two bi-parental mapping populations with AC Barrie as a parent revealed numerous FHB-resistance QTL unique to each population and uncovered novel variation near Fhb1. Fusarium head blight (FHB) is a destructive disease of wheat worldwide, leading to severe yield and quality losses. The genetic basis of native FHB resistance was examined in two populations: a recombinant inbred line population from the cross Cutler/AC Barrie and a doubled haploid (DH) population from the cross AC Barrie/Reeder. Numerous QTL were detected among the two mapping populations with many being cross-specific. Photoperiod insensitivity at Ppd-D1 and dwarfing at Rht-B1 and Rht-D1 was associated with increased FHB susceptibility. Anthesis date QTL at or near the Vrn-A1 and Vrn-B1 loci co-located with major FHB-resistance QTL in the AC Barrie/Reeder population. The loci were epistatic for both traits, such that DH lines with both late alleles were considerably later to anthesis and had reduced FHB symptoms (i.e., responsible for the epistatic interaction). Interestingly, AC Barrie contributed FHB resistance near the Fhb1 locus in the Cutler population and susceptibility in the Reeder population. Analyses of the Fhb1 candidate genes PFT and TaHRC confirmed that AC Barrie, Cutler, and Reeder do not carry the Sumai-3 Fhb1 gene. Resistance QTL were also detected at the expected locations of Fhb2 and Fhb5. The native FHB-resistance QTL detected near Fhb1, Fhb2, and Fhb5 do not appear to be as effective as Fhb1, Fhb2, and Fhb5 from Sumai-3. The presence of awns segregated at the B1 awn inhibitor locus in both populations, but was only associated with FHB resistance in the Cutler/AC Barrie population suggesting linkage caused the association rather than pleiotropy.
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Affiliation(s)
- Dinushika Thambugala
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Anita L Brûlé-Babel
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Barbara A Blackwell
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Adam J Foster
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PEI, C1A 4N6, Canada
| | - Dan MacEachern
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PEI, C1A 4N6, Canada
| | - Jeannie Gilbert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Richard A Martin
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PEI, C1A 4N6, Canada
| | - Brent D McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Dean Spaner
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
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