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Wang D, Cheng B, Zhang J. High-density genetic map and quantitative trait loci map of skin color in hawthorn ( Crataegus pinnatifida bge. Var. major N.E.Br.). Front Genet 2024; 15:1405604. [PMID: 38873113 PMCID: PMC11169616 DOI: 10.3389/fgene.2024.1405604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/09/2024] [Indexed: 06/15/2024] Open
Abstract
Fruit skin color is an important trait of the hawthorn tree, which has an important influence on fruit quality. Crataegus pinnatifida Bge. var. Major N.E.Br. Is one of the most widely cultivated varieties in China and has a long history of medicinal use. In recent years, it has attracted the attention of the world due to its nutritional and medicinal values. Skin color is the focus of breeders and food processors. At present, skin color-related genes have still not been mapped. In this study, "Shandong Da Mianqiu" (♀, red skin color), "Da Huang Mianzha" (♂, yellow skin color) and 131 F1 hybrids were used to construct genetic map of hawthorn by RAD-seq, and QTL mapping was performed by combining these features with the hue angle and the observed color. In this study, 13,260 SNP was assigned to 17 linkage groups, with an integrated map covering 2,297.75 cM was constructed. A total of 5 QTLs related to hawthorn skin color were detected on LG1, LG3 and LG15. Whether hue angle or pericarp color acts as phenotype for QTL mapping, the candidate genes include bHLH086, WD repeat regions and Myb-like. bHLH, WD and Myb play an important role in the color regulation of Hawthorn skin color. These results lay a solid foundation for QTL mapping and molecular marker-assisted breeding of hawthorn.
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Affiliation(s)
- Dongsheng Wang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Beibei Cheng
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Qinhuangdao, China
| | - Jijun Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Qinhuangdao, China
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2
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Pan J, Li X, Fu C, Bian J, Wang Z, Yu C, Liu X, Wang G, Tian R, Song X, Li C, Xia H, Zhao S, Hou L, Gao M, Zi H, Bertioli D, Leal-Bertioli S, Pandey MK, Wang X, Zhao C. High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:69. [PMID: 38441650 DOI: 10.1007/s00122-024-04580-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43 cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35-20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.
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Affiliation(s)
- Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaojie Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Chun Fu
- Weifang Academy of Agricultural Sciences, Weifang, 261071, People's Republic of China
| | - Jianxin Bian
- Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People's Republic of China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People's Republic of China
| | - Conghui Yu
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaoqin Liu
- Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People's Republic of China
| | - Guanghao Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaofeng Song
- Weifang Academy of Agricultural Sciences, Weifang, 261071, People's Republic of China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People's Republic of China
| | - Hailing Zi
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Soraya Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Jaiswal V, Bandyopadhyay T, Singh RK, Gahlaut V, Muthamilarasan M, Prasad M. Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica). PLANT CELL REPORTS 2023; 43:6. [PMID: 38127149 DOI: 10.1007/s00299-023-03127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
KEY MESSAGE A total of 104 foxtail millet accessions were evaluated for 11 nutrients in three environments and 67 high-confidence marker-trait associations (MTAs) were identified. Six SNPs showed pleiotropic effect and associated with two or more nutrients, whereas 24 candidate genes were identified for 28 MTAs involving seven traits. Millets are known for their better nutritional profiles compared to major cereals. Foxtail millet (Setaria italica) is rich in nutrients essential to circumvent malnutrition and hidden hunger. However, the genetic determinants underlying this trait remain elusive. In this context, we evaluated 104 diverse foxtail millet accessions in three different environments (E1, E2, and E3) for 11 nutrients and genotyped with 30K SNPs. The genome-wide association study showed 67 high-confidence (Bonferroni-corrected) marker-trait associations (MTAs) for the nutrients except for phosphorus. Six pleiotropic SNPs were also identified, which were associated with two or more nutrients. Around 24 candidate genes (CGs) were identified for 28 MTAs involving seven nutrients. A total of 17 associated SNPs were present within the gene region, and five (5) were mapped in the exon of the CGs. Significant SNPs, desirable alleles and CGs identified in the present study will be useful in breeding programmes for trait improvement.
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Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.
| | | | | | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Department of Biotechnology, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India.
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
- Department of Genetics, University of Delhi South Campus, New Delhi, India.
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Gunguniya DF, Kumar S, Patel MP, Sakure AA, Patel R, Kumar D, Khandelwal V. Morpho-biochemical characterization and molecular marker based genetic diversity of pearl millet ( Pennisetum glaucum (L.) R. Br.). PeerJ 2023; 11:e15403. [PMID: 37304873 PMCID: PMC10249620 DOI: 10.7717/peerj.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/20/2023] [Indexed: 06/13/2023] Open
Abstract
Pearl millet is a key food for millions living in semi-arid and arid regions and is a main diet for poorer populations. The genetic diversity existing in the pearl millet germplasm can be used to improve the micronutrient content and grain yield. Effective and organized exploitation of diversity at morphological and DNA levels is the strategy for any crop improvement program. In this study, the genetic diversity of 48 pearl millet genotypes was evaluated for eight morphological traits and eleven biochemical characters. All genotypes were also characterized using twelve SSR and six SRAP markers to evaluate genetic diversity. The significant mean difference between morphological and biochemical traits were detected. The productive tillers per plant varied from 2.65 to 7.60 with a mean of 4.80. The grain yield of genotypes varied more than 3× from 15.85 g (ICMR 07222) to 56.75 g (Nandi 75) with an average of 29.54 g per plant. Higher levels of protein, iron, and zinc contents were found to be present in ICMR 12555 (20.6%), ICMR 08666 (77.38 ppm), and IC 139900 (55.48 ppm), respectively, during the experiment. Substantial variability was observed for grain calcium as it ranged from 100.00 ppm (ICMR 10222) to 256.00 ppm (ICMR 12888). The top eight nutrient-dense genotypes flowered in 34-74 days and had 5.71-9.39 g 1,000 grain weight. Genotype ICMR 08666 was superior for Fe, Zn, K and P. The inter-genotype similarity coefficient at the genetic level, generated using DNA markers, ranged from 0.616 to 0.877 with a mean of 0.743. A combination of morpho-biochemical traits and DNA markers based diversity may help to differentiate the genotypes and diverse genotypes can be used in breeding programs to improve the mineral content in pearl millet.
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Affiliation(s)
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Mukesh P. Patel
- Agriculture and Horticulture Research Station, Anand Agricultural University, Khambholaj, Gujarat, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Dileep Kumar
- Micronutrient Research Centre, Anand Agricultural University, Anand, Gujarat, India
| | - Vikas Khandelwal
- Plant Breeding, ICAR-All India Coordinated Research Project on Pearl Millet, Mandor, Rajasthan, India
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5
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Li R, Chen Z, Zheng R, Chen Q, Deng J, Li H, Huang J, Liang C, Shi T. QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat. BMC PLANT BIOLOGY 2023; 23:58. [PMID: 36703107 PMCID: PMC9878770 DOI: 10.1186/s12870-022-04004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs. RESULTS Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation. CONCLUSIONS Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.
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Affiliation(s)
- Ruiyuan Li
- Key Laboratory of Information and Computing Science of Guizhou Province, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Zhengfeng Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Ran Zheng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Jiao Deng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Hongyou Li
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Juan Huang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Chenggang Liang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China.
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Lydia Pramitha J, Ganesan J, Francis N, Rajasekharan R, Thinakaran J. Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches. Front Genet 2023; 13:1007552. [PMID: 36699471 PMCID: PMC9870178 DOI: 10.3389/fgene.2022.1007552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.
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Affiliation(s)
- J. Lydia Pramitha
- Karunya Institute of Technology and Sciences, Coimbatore, India,*Correspondence: J. Lydia Pramitha,
| | - Jeeva Ganesan
- Tamil Nadu Agricultural University, Coimbatore, India
| | - Neethu Francis
- Karunya Institute of Technology and Sciences, Coimbatore, India
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Gao Y, Yuan Y, Zhang X, Song H, Yang Q, Yang P, Gao X, Gao J, Feng B. Conuping BSA-Seq and RNA-Seq Reveal the Molecular Pathway and Genes Associated with the Plant Height of Foxtail Millet (Setaria italica). Int J Mol Sci 2022; 23:ijms231911824. [PMID: 36233125 PMCID: PMC9569614 DOI: 10.3390/ijms231911824] [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: 09/02/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Foxtail millet (Setaria italica) plays an important role in C4 crop research and agricultural development in arid areas due to its short growth period, drought tolerance, and barren tolerance. Exploration of the dwarfing mechanism and the dwarf genes of foxtail millet can provide a reference for dwarf breeding and dwarf research of other C4 crops. In this study, genetic analysis was performed using phenotypic data, candidate genes were screened by bulk segregant analysis sequencing (BSA-Seq); differentially expressed genes and metabolic pathways in different strains of high samples were analyzed by RNA sequencing (RNA-Seq). The association analysis of BSA-Seq and RNA-Seq further narrowed the candidate range. As a result, a total of three quantitative trait loci (QTLs) and nine candidate genes related to plant height were obtained on chromosomes I and IX. Based on the functional prediction of the candidate genes, we propose a hypothetical mechanism for the formation of millet dwarfing, in which, metabolism and MAPK signaling play important roles in the formation of foxtail millet plant height.
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Affiliation(s)
- Yongbin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
- Dexing Township Agro-Pastoral Comprehensive Service Center, Nyingchi 860700, China
| | - Yuhao Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Xiongying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Hui Song
- Anyang Academy of Agricultural Sciences, Anyang 455099, China
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Pu Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Jinfeng Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
- Correspondence:
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [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: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Liu T, He J, Dong K, Wang X, Zhang L, Ren R, Huang S, Sun X, Pan W, Wang W, Yang P, Yang T, Zhang Z. Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments. Mol Genet Genomics 2022; 297:873-888. [PMID: 35451683 PMCID: PMC9130181 DOI: 10.1007/s00438-022-01894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/31/2022] [Indexed: 11/21/2022]
Abstract
Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 74 SSR markers was constructed, spanning 1315.1 cM with an average distance of 0.56 cM between adjacent markers. A total of 221 QTL for 17 morpho-agronomic and yield-related traits explaining 5.5 ~ 36% of phenotypic variation were identified across multi-environments. Of these, 109 QTL were detected in two to nine environments, including the most stable qLMS6.1 harboring a promising candidate gene Seita.6G250500, of which 70 were repeatedly identified in different trials in the same geographic location, suggesting that foxtail millet has more identical genetic modules under the similar ecological environment. One hundred-thirty QTL with overlapping intervals formed 22 QTL clusters. Furthermore, six superior recombinant inbred lines, RIL35, RIL48, RIL77, RIL80, RIL115 and RIL125 with transgressive inheritance and enrichment of favorable alleles in plant height, tiller, panicle morphology and yield related-traits were screened by hierarchical cluster. These identified QTL, QTL clusters and superior lines lay ground for further gene-trait association studies and breeding practice in foxtail millet.
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Affiliation(s)
- Tianpeng Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Xuewen Wang
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, 30601, USA
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Sha Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xiaoting Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wanxiang Pan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Peng Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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10
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Khan H, Wani SH, Bhardwaj SC, Rani K, Bishnoi SK, Singh GP. Wheat spike blast: genetic interventions for effective management. Mol Biol Rep 2022; 49:5483-5494. [PMID: 35478296 DOI: 10.1007/s11033-022-07356-7] [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: 11/14/2021] [Revised: 02/05/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The fundamental concepts of the genetics, race classification and epidemiology of the Wheat spike blast causing fungus Magnaporthe oryzae pathotype Triticum (MoT) are still evolving despite of its discovery in 1985 in Brazil for the first time. The fungus seems to defy the research progress that is being made globally by continuously evolving into pathotypes which have already overcome the much celebrated 2NS resistance in wheat lines as well as few of the initially effective fungicides. The compartmentalized i.e. two speed genome of the MoT, conferring the fungus an evolutionary advantage, has emerged as a challenge for the wheat spike blast researchers complicating its already difficult management. The airborne fungus with a range of alternative hosts is finding new geographical niches situated on different continents and is a matter of great apprehension among the nations whose food security is primarily dependent on wheat. The wheat blast outbreak in Bangladesh during 2016 was attributed to an isolate from Latin America escaping through a seed import consignment while the latest Zambian outbreak is still to be studied in detail regarding its origin and entry. The challenges in dealing wheat spike blast are not only on the level of genetics and epidemiology alone but also on the levels of policy making regarding international seed movement and research collaborations. The present review deals with these issues mainly concerning the effective management and controlling the international spread of this deadly disease of wheat, with a particular reference to India. We describe the origin, taxonomy, epidemiology and symptomology of MoT and briefly highlight its impact and management practices from different countries. We also discuss the advances in genomics and genome editing technologies that can be used to develop elite wheat genotypes resistant against different stains of wheat spike blast.
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, 132001, Karnal, Haryana, India.
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, 192101, Khudwani, J & K, India
| | - Subhash Chander Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, 171 002, Shimla, Himachal Pradesh, India
| | - Kirti Rani
- ICAR-Directorate of Groundnut Research (DGR), 362001, Junagadh, Gujarat, India
| | - Santosh Kumar Bishnoi
- ICAR- Indian Institute of Wheat and Barley Research, Seed & Research Farm, 125001, Hisar, Haryana, India
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11
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Zhu X, Weng Q, Bush D, Zhou C, Zhao H, Wang P, Li F. High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus. FRONTIERS IN PLANT SCIENCE 2022; 13:1099705. [PMID: 37082511 PMCID: PMC10112524 DOI: 10.3389/fpls.2022.1099705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 05/03/2023]
Abstract
Introduction Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms. Method A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis. Results Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation. Discussion While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.
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Affiliation(s)
- Xianliang Zhu
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qijie Weng
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - David Bush
- Commonwealth Scientific and Industrial Research Organisation (CRISO) Australian Tree Seed Centre, Canberra, ACT, Australia
| | - Changpin Zhou
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Haiwen Zhao
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Ping Wang
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Fagen Li
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- *Correspondence: Fagen Li,
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12
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Du X, Wang ·Z, Han ·K, Lian ·S, Li ·Y, Zhang ·L, Guo ·E, Wang J. Fine mapping of qPH9, a major quantitative trait locus, responsible for plant height in foxtail millet [ Setaria italica (L.) P. Beauv.]. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:77. [PMID: 37309515 PMCID: PMC10236064 DOI: 10.1007/s11032-021-01261-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
Plant height is vital for crop yield by influencing plant architecture and resistance to lodging. Although lots of quantitative trait loci (QTLs) controlling plant height had been mapped in foxtail millet, their contributions to phenotypic variation were generally small and mapping regions were relatively large, indicating the difficult application in molecular breeding using marker-assisted selection (MAS). In the present paper, a total of 23 QTLs involving in 15 traits were identified via a high-density Bin map containing 3024 Bin markers with an average distance of 0.48 cM through an F2 population. Among them, qPH9, with a large phenotypic variation explained (51.6%) related to plant height, was one of the major QTLs. Furthermore, qPH9 was repeatedly detected in multi-environments under field conditions using two new developed F2 populations from the same F1 plant, and was narrowed down to a smaller interval of 281 kb using 1024 recessive F2 individuals from the same F1 plant. Finally, we found that there was an extremely significant correlation between marker MRI1016 and plant height, and further speculated that Seita.9G088900 and Seita.9G089700 could be key candidates of qPH9. This study laid an important foundation for the cloning of qPH9 and molecular breeding of dwarf varieties via MAS. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01261-w.
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Affiliation(s)
- Xiaofen Du
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - ·Zhilan Wang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - ·Kangni Han
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - ·Shichao Lian
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - ·Yuxin Li
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - ·Linyi Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - ·Erhu Guo
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
| | - Jun Wang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011 China
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13
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Du Z, Huang Z, Li J, Bao J, Tu H, Zeng C, Wu Z, Fu H, Xu J, Zhou D, Zhu C, Fu J, He H. qTGW12a, a naturally varying QTL, regulates grain weight in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2767-2776. [PMID: 34021769 PMCID: PMC8354980 DOI: 10.1007/s00122-021-03857-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/10/2021] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE A stable QTL associated with rice grain type with a large effect value was found in multiple environments, and its candidate genes were verified by genetic transformation. Rice (Oryza sativa L.) grain size is critical to both yield and appearance quality. Therefore, the discovery and identification of rice grain size genes can provide pathways for the cultivation of high-yielding varieties. In the present work, 45,607 SNP markers were used to construct a high-density genetic map of rice recombinant inbred lines, and hence a total of 14 quantitative trait loci (QTLs) were detected based on the phenotypic data of grain weight, grain length and grain width under four different environments. qTGW12a and qGL12 are newly detected QTLs related to grain weight, and are located between 22.43 Mb and 22.45 Mb on chromosome 12. Gene annotation shows that the QTL region contains the LOC_Os12g36660 annotated gene, which encodes the multidrug and toxic compound extrusion (MATE) transporter. Mutations in exons and the splice site were responsible for the changes in grain type and weight. Gene knockout experiments were used to verify these results. Hence, these results provide a basis for the cloning of qTGW12a. This discovery provides new insights for studying the genetic mechanism of rice grain morphology, and reveals a promising gene to ultimately increase rice yield.
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Affiliation(s)
- Zhixuan Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Zhou Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Jianbin Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Jianzhong Bao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Hang Tu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Chuihai Zeng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Zheng Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Jie Xu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China.
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China.
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14
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Zhi H, He Q, Tang S, Yang J, Zhang W, Liu H, Jia Y, Jia G, Zhang A, Li Y, Guo E, Gao M, Li S, Li J, Qin N, Zhu C, Ma C, Zhang H, Chen G, Zhang W, Wang H, Qiao Z, Li S, Cheng R, Xing L, Wang S, Liu J, Liu J, Diao X. Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3023-3036. [PMID: 34081150 DOI: 10.1007/s00122-021-03875-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Multi-environment QTL mapping identified 23 stable loci and 34 co-located QTL clusters for panicle architecture and grain yield-related traits, which provide a genetic basis for foxtail millet yield improvement. Panicle architecture and grain weight, both of which are influenced by genetic and environmental factors, have significant effects on grain yield potential. Here, we used a recombinant inbred line (RIL) population of 333 lines of foxtail millet, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) controlling nine agronomic traits related to panicle architecture and grain yield. We found that panicle weight, grain weight per panicle, panicle length, panicle diameter, and panicle exsertion length varied across different geographical locations. QTL mapping revealed 159 QTL for nine traits. Of the 159 QTL, 34 were identified in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod and/or other environmental factors. Eighty-eight QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, which was detected 23 times in 13 environments. Several candidate genes, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700, were identified in the genomic intervals of multi-environmental QTL or co-located QTL clusters. Using available phenotypic and genotype data, we conducted haplotype analysis for Seita.2G002300 and Seita.9G064000,which showed high correlations with panicle weight and panicle exsertion length, respectively. These results not only provided a basis for further fine mapping, functional studies and marker-assisted selection of traits related to panicle architecture in foxtail millet, but also provide information for comparative genomics analyses of cereal crops.
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Affiliation(s)
- Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Junjun Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Huifang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Yanchao Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Aiying Zhang
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Yuhui Li
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Erhu Guo
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Ming Gao
- Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, Jilin, China
| | - Shujie Li
- Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, Jilin, China
| | - Junxia Li
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Na Qin
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Cancan Zhu
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Chunye Ma
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Haijin Zhang
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Guoqiu Chen
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Wenfei Zhang
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Shunguo Li
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Lu Xing
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Suying Wang
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinrong Liu
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China.
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15
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Xie H, Hou J, Fu N, Wei M, Li Y, Yu K, Song H, Li S, Liu J. Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. BMC Genomics 2021; 22:556. [PMID: 34281524 PMCID: PMC8290542 DOI: 10.1186/s12864-021-07882-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C4 grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet. Results Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F6 and F7 recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively. Conclusions This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07882-x.
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Affiliation(s)
- Huifang Xie
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Junliang Hou
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Nan Fu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Menghan Wei
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Yunfei Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China.
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China.
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Zhang H, Tang S, Schnable JC, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H, Diao X. Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1. FRONTIERS IN PLANT SCIENCE 2021; 12:743782. [PMID: 34858451 PMCID: PMC8632227 DOI: 10.3389/fpls.2021.743782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/13/2021] [Indexed: 05/03/2023]
Abstract
Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.
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Affiliation(s)
- Hui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Sha Tang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Qiang He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingzhao Luo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hui Zhi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianmin Diao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xianmin Diao,
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