1
|
Ren Y, Sun X, Nie J, Guo P, Wu X, Zhang Y, Gao M, Niaz M, Yang X, Sun C, Zhang N, Chen F. Mapping QTL conferring flag leaf senescence in durum wheat cultivars. Mol Breed 2023; 43:66. [PMID: 37564974 PMCID: PMC10409934 DOI: 10.1007/s11032-023-01410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023]
Abstract
Flag leaf senescence is a critical factor affecting the yield and quality of wheat. The aim of this study was to identify QTLs associated with flag leaf senescence in an F10 recombinant inbred line population derived from durum wheats UC1113 and Kofa. Bulked segregant analysis using the wheat 660K SNP array identified 3225 SNPs between extreme-phenotype bulks, and the differential SNPs were mainly clustered on chromosomes 1A, 1B, 3B, 5A, 5B, and 7A. BSR-Seq indicated that the significant SNPs were mainly located in two intervals of 354.0-389.0 Mb and 8.0-15.0 Mb on 1B and 3B, respectively. Based on the distribution of significant SNPs on chromosomes 1B and 3B, a total of 109 insertion/deletion (InDel) markers were developed, and 8 of them were finally used to map QTL in UC1113/Kofa population for flag leaf senescence. Inclusive composite interval mapping identified two major QTL in marker intervals Mar2005-Mar2116 and Mar207-Mar289, explaining 14.2-15.4% and 31.4-68.6% of the phenotypic variances across environments, respectively. Using BSR-Seq, gene expression and sequence analysis, the TraesCS1B02G211600 and TraesCS3B02G023000 were identified as candidate senescence-associated genes. This study has potential to be used in cloning key genes for flag leaf senescence and provides available molecular markers for genotyping and marker-assisted selection breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01410-3.
Collapse
Affiliation(s)
- Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaonan Sun
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Jingyun Nie
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Peng Guo
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaohui Wu
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Yixiao Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Mengjuan Gao
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Mohsin Niaz
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xia Yang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Congwei Sun
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College/CIMMYT-China Wheat and Maize Joint Research Center, Henan Agricultural University, Zhengzhou, 450046 China
| |
Collapse
|
2
|
Banerjee N, Khan MS, Swapna M, Yadav S, Tiwari GJ, Jena SN, Patel JD, Manimekalai R, Kumar S, Dattamajuder SK, Kapur R, Koebernick JC, Singh RK. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotech 2023; 13:82. [PMID: 36778768 PMCID: PMC9911584 DOI: 10.1007/s13205-023-03481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03481-7.
Collapse
Affiliation(s)
- Nandita Banerjee
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - M. Swapna
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Sonia Yadav
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Gopal Ji Tiwari
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Satya N. Jena
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Jinesh D. Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - R. Manimekalai
- Biotechnology Lab, Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - S. K. Dattamajuder
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Jenny C. Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - Ram K. Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
- Present Address: Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001 India
| |
Collapse
|
3
|
Ahmad A, Li W, Zhang H, Wang H, Wang P, Jiao Y, Zhao C, Yang G, Hong D. Linkage and association mapping of ovule number per ovary (ON) in oilseed rape ( Brassica napus L.). Mol Breed 2023; 43:11. [PMID: 37313129 PMCID: PMC10248604 DOI: 10.1007/s11032-023-01355-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/11/2023] [Indexed: 06/15/2023]
Abstract
Ovule number (ON) produced during flower development determines the maximum number of seeds per silique and thereby affects crop productivity; however, the genetic basis of ON remains poorly understood in oilseed rape (Brassica napus). In this study, we genetically dissected the ON variations in a double haploid (DH) population and in natural population (NP) by linkage mapping and genome-wide association analysis. Phenotypic analysis showed that ON displayed normal distribution in both populations with the broad-sense heritability of 0.861 (DH population) and 0.930 (natural population). Linkage mapping identified 5 QTLs related to ON, including qON-A03, qON-A07, qON-A07-2, qON-A10, and qON-C06. Genome-wide association studies (GWAS) revealed 214, 48, and 40 significant single-nucleotide polymorphisms (SNPs) by individually using the single-locus model GLM and the multiple-locus model MrMLM and FASTMrMLM. The phenotypic variation explained (PVE) by these QTLs and SNPs ranged from 2.00-17.40% to 5.03-7.33%, respectively. Integration of the results from both strategies identified four consensus genomic regions associated with ON from the chromosomes A03, A07, and A10. Our results preliminarily resolved the genetic basis of ON and provides useful molecular markers for plant yield improvement in B. napus. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01355-7.
Collapse
Affiliation(s)
- Ali Ahmad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wenhui Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Chenqi Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| |
Collapse
|
4
|
Zhao R, Liu B, Wan W, Jiang Z, Chen T, Wang L, Bie T. Mapping and characterization of a novel adult-plant leaf rust resistance gene LrYang16G216 via bulked segregant analysis and conventional linkage method. Theor Appl Genet 2023; 136:1. [PMID: 36645449 DOI: 10.1007/s00122-023-04270-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
A novel adult-plant leaf rust resistance gene LrYang16G216 on wheat chromosome 6BL was identified and mapped to a 0.59 cM genetic interval by BSA and conventional linkage method. Leaf rust (Puccinia triticina) is one of the most devastating fungal diseases of wheat (Triticum aestivum L.). Discovery and identification of new resistance genes is essential to develop disease-resistant cultivars. An advanced breeding line Yang16G216 was previously identified to confer adult-plant resistance (APR) to leaf rust. In this research, a recombinant inbred line (RIL) population was constructed from the cross between Yang16G216 and a highly susceptible line Yang16M6393, and genotyped with exome capture sequencing and 55 K SNP array. Through bulked segregant analysis (BSA) and genetic linkage mapping, a stable APR gene, designated as LrYang16G216, was detected and mapped to the distal region of chromosome arm 6BL with a genetic interval of 2.8 cM. For further verification, another RIL population derived from the cross between Yang16G216 and a susceptible wheat variety Yangmai 29 was analyzed using the enriched markers in the target interval, and LrYang16G216 was further narrowed to a 0.59 cM genetic interval flanked by the KASP markers Ax109403980 and Ax95083494, corresponding to the physical position 712.34-713.94 Mb in the Chinese Spring reference genome, in which twenty-six disease resistance-related genes were annotated. Based on leaf rust resistance spectrum, mapping data and physical location, LrYang16G216 was identified to be a novel and effective APR gene. The LrYang16G216 with linked markers will be useful for marker-assisted selection in wheat resistance breeding.
Collapse
Affiliation(s)
- Renhui Zhao
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Bingliang Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225007, China
| | - Wentao Wan
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Zhengning Jiang
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Tiantian Chen
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Ling Wang
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China
| | - Tongde Bie
- Key Laboratory of Wheat Biology and Genetic Improvement On Low & Middle Yangtze River Valley Wheat Region (Ministry of Agriculture), Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007, China.
| |
Collapse
|
5
|
Ma L, An R, Jiang L, Zhang C, Li Z, Zou C, Yang C, Pan G, Lübberstedt T, Shen Y. Effects of ZmHIPP on lead tolerance in maize seedlings: Novel ideas for soil bioremediation. J Hazard Mater 2022; 430:128457. [PMID: 35180524 DOI: 10.1016/j.jhazmat.2022.128457] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 05/19/2023]
Abstract
Extensive lead (Pb) absorption by plants affects their growth and development and causes damage to the human body by entering the food chain. In this study, we cloned ZmHIPP, a gene associated with Pb tolerance and accumulation in maize, using combined linkage mapping and weighted gene co-expression network analysis. We show that ZmHIPP, which encodes a heavy metal-associated isoprenylated plant protein, positively modulated Pb tolerance and accumulation in maize seedlings, Arabidopsis, and yeast. The genetic variation locus (A/G) in the promoter of ZmHIPP contributed to the phenotypic disparity in Pb tolerance among different maize inbred lines by altering the expression abundance of ZmHIPP. Knockdown of ZmHIPP significantly inhibited growth and decreased Pb accumulation in maize seedlings under Pb stress. ZmHIPP facilitated Pb deposition in the cell wall and prevented it from entering the intracellular organelles, thereby alleviating Pb toxicity in maize seedlings. Compared to that in the mutant zmhipp, the accumulated Pb in the wild-type line mainly consisted of the low-toxicity forms of Pb. Our study increases the understanding of the mechanism underlying Pb tolerance in maize and provides new insights into the bioremediation of Pb-polluted soil.
Collapse
Affiliation(s)
- Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Rong An
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chen Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhaoling Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | | | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| |
Collapse
|
6
|
Zhao M, Liu S, Pei Y, Jiang X, Jaqueth JS, Li B, Han J, Jeffers D, Wang J, Song X. Identification of genetic loci associated with rough dwarf disease resistance in maize by integrating GWAS and linkage mapping. Plant Sci 2022; 315:111100. [PMID: 35067294 DOI: 10.1016/j.plantsci.2021.111100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
Maize rough dwarf disease (MRDD) is a viral disease that causes substantial yield loss, especially in China's summer planted maize area. Discovery of resistance genes would help in developing high-yielding resistant maize hybrids. Genome-wide association studies (GWASs) have advanced quickly and are now a powerful tool for dissecting complex genetic architectures. In this study, the disease severity index (DSI) of 292 maize inbred lines and an F6 linkage population were investigated across multiple environments for two years. Using the genotypes obtained from the Maize SNP 50K chip, a GWAS was performed with four analytical models. The results showed that 22 SNPs distributed on chromosomes 1, 3, 4, 6, 7 and 8 were significantly associated with resistance to MRDD (P<0.0001). The SNPs on chromosomes 3, 6 and 8 were consistent with the quantitative trait locus (QTL) regions from linkage mapping in an RIL population. Candidate genes identified by GWAS included an LRR receptor-like serine/threonine-protein kinase (GRMZM2G141288), and a DRE-binding protein (GRMZM2G006745). In addition, we performed an allele variation analysis of the SNP loci selected by GWAS and linkage mapping and found that the main alleles of the two SNP loci PZE_101170408 and PZE_106082685 on chromosome 1 differed in terms of disease-resistant materials and disease-susceptible materials. The identified SNPs and genes provide useful information for MRDD-related gene cloning and insights on the underlying disease resistance mechanisms, and they can be used in marker-assisted breeding to develop MRDD-resistant maize.
Collapse
Affiliation(s)
- Meiai Zhao
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shuangshuang Liu
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuhe Pei
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xuwen Jiang
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | | | - Bailin Li
- Corteva Agriscience, 7300 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Jing Han
- Shandong Denghai Pioneer, Jinan, Shandong, 254000, China
| | - Daniel Jeffers
- Former CIMMYT Breeder, Yunnan Office, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, Sichuan, 160041, China.
| | - Xiyun Song
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
7
|
Singh P, Huang SY, Hernandez AG, Adhikari P, Jamann TM, Mideros SX. Genomic regions associated with virulence in Setosphaeria turcica identified by linkage mapping in a biparental population. Fungal Genet Biol 2021;:103655. [PMID: 34954385 DOI: 10.1016/j.fgb.2021.103655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/17/2021] [Accepted: 12/19/2021] [Indexed: 01/06/2023]
Abstract
Northern corn leaf blight (NCLB) and sorghum leaf blight (SLB) are significant diseases of maize and sorghum, respectively, caused by the filamentous fungus Setosphaeria turcica. Strains of S. turcica are typically host-specific and infect either maize or sorghum. Host specificity in this pathogen is attributed to a single locus for maize and a second distinct locus for sorghum. To identify the genetic basis of host specificity in S. turcica, we generated a biparental population of S. turcica by crossing strains specific to maize and sorghum, phenotyped the population for leaf blight on sorghum and maize, genotyped the population to create a linkage map of S. turcica, and located candidate virulence regions. A total of 190 ascospores from 35 pseudothecia were isolated from the cross of maize and sorghum-specific strains. Greenhouse phenotyping of the biparental population (n = 144) showed independent inheritance of virulence, as indicated by a 1:1:1:1 segregation for virulence to maize, sorghum, both maize and sorghum, and avirulence to both crops. The population and host-specific parent strains were genotyped using genome skim sequencing on an Illumina NovaSeq 6000 platform resulting in over 780 million reads. A total of 32,635 variants including single nucleotide polymorphisms and indels were scored. There was evidence for a large deletion in the sorghum-specific strain of S. turcica. A genetic map consisting of 17 linkage groups spanning 3,069 centimorgans was constructed. Virulence to sorghum and maize mapped on distinct linkage groups with a significant QTL detected for virulence to maize. Furthermore, a single locus each for the in vitro traits hyphal growth rate and conidiation were identified and mapped onto two other linkage groups. In vitro traits did not correlate with in planta virulence complexity, suggesting that virulence on both hosts does not incur a fitness cost. Hyphal growth rate and conidiation were negatively correlated, indicating differences in hyphal growth versus dispersal ability for this pathogen. Identification of genetic regions underlying virulence specificity and saprotrophic growth traits in S. turcica provides a better understanding of the S. turcica- Andropogoneae pathosystem.
Collapse
|
8
|
Kong W, Zhang C, Zhang S, Qiang Y, Zhang Y, Zhong H, Li Y. Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq. Rice (N Y) 2021; 14:93. [PMID: 34778931 PMCID: PMC8590990 DOI: 10.1186/s12284-021-00535-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/06/2021] [Indexed: 05/07/2023]
Abstract
Salinity is a major abiotic stress that limits plant growth and crop productivity. Indica rice and japonica rice show significant differences in tolerance to abiotic stress, and it is considered a feasible method to breed progeny with stronger tolerance to abiotic stress by crossing indica and japonica rice. We herein developed a high-generation recombinant inbred lines (RILs) from Luohui 9 (indica) X RPY geng (japonica). Based on the high-density bin map of this RILs population, salt tolerance QTLs controlling final survival rates were analyzed by linkage mapping and RTM-GWAS methods. A total of seven QTLs were identified on chromosome 3, 4, 5, 6, and 8. qST-3.1, qST-5.1, qST-6.1, and qST-6.2 were novel salt tolerance QTLs in this study and their function were functionally verified by comparative analysis of parental genotype RILs. The gene aggregation result of these four new QTLs emphasized that the combination of the four QTL synergistic genotypes can significantly improve the salt stress tolerance of rice. By comparing the transcriptomes of the root tissues of the parents' seedlings, at 3 days and 7 days after salt treatment, we then achieved fine mapping of QTLs based on differentially expressed genes (DEGs) identification and DEGs annotations, namely, LOC_Os06g01250 in qST-6.1, LOC_Os06g37300 in qST-6.2, LOC_Os05g14880 in qST-5.1. The homologous genes of these candidate genes were involved in abiotic stress tolerance in different plants. These results indicated that LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 were the candidate genes of qST-5.1, qST-6.1, and qST-6.2. Our finding provided novel salt tolerance-related QTLs, candidate genes, and several RILs with better tolerance, which will facilitate breeding for improved salt tolerance of rice varieties and promote the exploration tolerance mechanisms of rice salt stress.
Collapse
Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Yalin Qiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Yue Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| |
Collapse
|
9
|
Wang J, Wang T, Wang Q, Tang X, Ren Y, Zheng H, Liu K, Yang L, Jiang H, Li Y, Liu Q, Zou D, Zheng H. QTL mapping and candidate gene mining of flag leaf size traits in Japonica rice based on linkage mapping and genome-wide association study. Mol Biol Rep 2021. [PMID: 34677716 DOI: 10.1007/s11033-021-06842-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/13/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND As one of the most important factors of the japonica rice plant, leaf shape affects the photosynthesis and carbohydrate accumulation directly. Mining and using new leaf shape related genes/QTLs can further enrich the theory of molecular breeding and accelerate the breeding process of japonica rice. METHODS In the present study, 2 RILs and a natural population with 295 japonica rice varieties were used to map QTLs for flag leaf length (FL), flag leaf width (FW) and flag leaf area (FLA) by linkage analysis and genome-wide association study (GWAS) throughout 2 years. RESULTS A total of 64 QTLs were detected by 2 ways, and pleiotropic QTLs qFL2 (Chr2_33,332,579) and qFL10 (Chr10_10,107,835; Chr10_10,230,100) consisted of overlapping QTLs mapped by linkage analysis and GWAS throughout the 2 years were identified. CONCLUSIONS The candidate genes LOC_Os02g54254, LOC_Os02g54550, LOC_Os10g20160, LOC_Os10g20240, LOC_Os10g20260 were obtained, filtered by linkage disequilibrium (LD), and haplotype analysis. LOC_Os10g20160 (SD-RLK-45) showed outstanding characteristics in quantitative real-time PCR (qRT-PCR) analysis in leaf development period, belongs to S-domain receptor-like protein kinases gene and probably to be a main gene regulating flag leaf width of japonica rice. The results of this study provide valuable resources for mining the main genes/QTLs of japonica rice leaf development and molecular breeding of japonica rice ideal leaf shape.
Collapse
|
10
|
Popowski E, Thomson SJ, Knäbel M, Tahir J, Crowhurst RN, Davy M, Foster TM, Schaffer RJ, Tustin DS, Allan AC, McCallum J, Chagné D. Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing. G3 (Bethesda) 2021; 11:6261761. [PMID: 34009255 PMCID: PMC8495948 DOI: 10.1093/g3journal/jkab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
Collapse
Affiliation(s)
- Elizabeth Popowski
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | | | | | | | - Marcus Davy
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | - Robert J Schaffer
- Plant & Food Research, Motueka, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Andrew C Allan
- Plant & Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - David Chagné
- Plant & Food Research, Palmerston North, New Zealand
| |
Collapse
|
11
|
Wang L, Jiang X, Zhao L, Wang F, Liu Y, Zhou H, He H, Han Y. A candidate PpRPH gene of the D locus controlling fruit acidity in peach. Plant Mol Biol 2021; 105:321-332. [PMID: 33128723 DOI: 10.1007/s11103-020-01089-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
A candidate gene, designate PpRPH, in the D locus was identified to control fruit acidity in peach. Fruit acidity has a strong impact on organoleptic quality of fruit. Peach fruit acidity is controlled by a large-effect D locus on chromosome 5. In this study, the D locus was mapped to a 509-kb interval, with two markers, 5dC720 and 5C1019, co-segregating with the non-acid/acid trait of peach fruit. Within this interval, a candidate gene encoding a putative small protein, designated PpRPH, showed a consistency between gene expression and fruit acidity, with up- and down-regulation in non-acidic and acidic fruits, respectively. Transient ectopic expression of PpRPH in tobacco leaves caused an increase of pH by approximately 40% compared to the control transformed with empty vector. Whereas, the concentrations of citrate and malate decreased significantly by 22% and 37%, respectively, with respect to the empty vector control. All these results suggest that PpRPH is a strong candidate gene of the D locus. These findings contribute to our overall understanding of the complex mechanism underlying fruit acidity in peach as well as that in other fruit crops.
Collapse
Affiliation(s)
- Lu Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiaohan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Li Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Furong Wang
- Institute of Fruit Tree and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430209, China
| | - Yudi Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Hui Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Huaping He
- Institute of Fruit Tree and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430209, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| |
Collapse
|
12
|
Li X, Zheng H, Wu W, Liu H, Wang J, Jia Y, Li J, Yang L, Lei L, Zou D, Zhao H. QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study. Rice (N Y) 2020; 13:48. [PMID: 32676742 PMCID: PMC7364718 DOI: 10.1186/s12284-020-00412-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/08/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage. RESULTS A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of LOC_Os11g37390. CONCLUSION Based on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
Collapse
Affiliation(s)
- Xianwei Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Wenshen Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jiaming Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
13
|
Yang W, Wang Y, Jiang D, Tian C, Zhu C, Li G, Chen H. ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus). BMC Genomics 2020; 21:278. [PMID: 32245399 PMCID: PMC7126399 DOI: 10.1186/s12864-020-6658-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/09/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits. RESULTS Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration. CONCLUSIONS The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growth-related traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.
Collapse
Affiliation(s)
- Wei Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Food and Environmental Engineering Department, Yangjiang Polytechnic, Yangjiang, 529566, China
| | - Yaorong Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Dongneng Jiang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Changxu Tian
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chunhua Zhu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Guangli Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Huapu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
| |
Collapse
|
14
|
Besnier F, Solberg MF, Harvey AC, Carvalho GR, Bekkevold D, Taylor MI, Creer S, Nielsen EE, Skaala Ø, Ayllon F, Dahle G, Glover KA. Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface. BMC Genet 2020; 21:13. [PMID: 32033538 PMCID: PMC7006396 DOI: 10.1186/s12863-020-0816-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022] Open
Abstract
Background Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations. Results After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets. Discussion The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
Collapse
Affiliation(s)
- Francois Besnier
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - Monica F Solberg
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Alison C Harvey
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Einar E Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Øystein Skaala
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Fernando Ayllon
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Geir Dahle
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| | - Kevin A Glover
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| |
Collapse
|
15
|
Daware A, Parida SK, Tyagi AK. Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping. Methods Mol Biol 2020; 2072:15-25. [PMID: 31541435 DOI: 10.1007/978-1-4939-9865-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Identification of genetic basis for important agronomic traits is essential for marker-assisted crop improvement. Linkage mapping is one of the most popular approaches utilized for identification of major quantitative trait loci (QTLs) governing important agronomic traits in cereals. However, the identified QTLs usually span large genomic intervals and very few of these are subsequently fine mapped to single major effect gene. This hinders application of these QTLs in marker-aided breeding and crop genetic enhancement. On the contrary, association mapping, another popular approach for identification of QTLs, provides very high resolution but suffers from high level of false positives. Joint linkage-association analysis provides a way to combine advantages and avoid the pitfalls associated with both these methods. In this context, we recently developed MetaQTL specific regional association analysis and demonstrated its utility to rapidly narrow down previously identified QTL intervals to few candidate genes. Here, we describe the detailed step-by-step guide for performing MetaQTL specific regional association analysis to identify important genomic regions and underlying potential major effect genes governing traits of agronomic importance in cereals.
Collapse
|
16
|
Wang T, Wei L, Wang J, Xie L, Li YY, Ran S, Ren L, Lu K, Li J, Timko MP, Liu L. Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed ( Brassica napus L.). Biotechnol Biofuels 2020; 13:134. [PMID: 32774455 PMCID: PMC7397576 DOI: 10.1186/s13068-020-01774-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/24/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. RESULTS To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. CONCLUSIONS The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments.
Collapse
Affiliation(s)
- Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Jia Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Ling Xie
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Yang Yang Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Shuyao Ran
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Lanyang Ren
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904 USA
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| |
Collapse
|
17
|
Zimmermann N, Gibbons WJ, Homan SM, Prows DR. Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci. BMC Genomics 2019; 20:727. [PMID: 31601172 PMCID: PMC6788080 DOI: 10.1186/s12864-019-6108-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Background Heart disease (HD) is the major cause of morbidity and mortality in patients with hypereosinophilic diseases. Due to a lack of adequate animal models, our understanding of the pathophysiology of eosinophil-mediated diseases with heart complications is limited. We have discovered a mouse mutant, now maintained on an A/J inbred background, that spontaneously develops hypereosinophilia in multiple organs. Cellular infiltration into the heart causes an eosinophilic myocarditis, with affected mice of the mutant line (i.e., A/JHD) demonstrating extensive myocardial damage and remodeling that leads to HD and premature death, usually by 15-weeks old. Results Maintaining the A/JHD line for many generations established that the HD trait was heritable and implied the mode of inheritance was not too complex. Backcross and intercross populations generated from mating A/JHD males with females from four different inbred strains produced recombinant populations with highly variable rates of affected offspring, ranging from none in C57BL/6 J intercrosses, to a few mice with HD using 129S1/SvImJ intercrosses and C57BL/6 J backcrosses, but nearly 8% of intercrosses and > 17% of backcrosses from SJL/J related populations developed HD. Linkage analyses of these SJL/J derived recombinants identified three highly significant loci: a recessive locus mapping to distal chromosome 5 (LOD = 4.88; named Emhd1 for eosinophilic myocarditis to heart disease-1); and two dominant variants mapping to chromosome 17, one (Emhd2; LOD = 7.51) proximal to the major histocompatibility complex, and a second (Emhd3; LOD = 6.89) that includes the major histocompatibility region. Haplotype analysis identified the specific crossovers that defined the Emhd1 (2.65 Mb), Emhd2 (8.46 Mb) and Emhd3 (14.59 Mb) intervals. Conclusions These results indicate the HD trait in this mutant mouse model of eosinophilic myocarditis is oligogenic with variable penetrance, due to multiple segregating variants and possibly additional genetic or nongenetic factors. The A/JHD mouse model represents a unique and valuable resource to understand the interplay of causal factors that underlie the pathology of this newly discovered eosinophil-associated disease with cardiac complications.
Collapse
Affiliation(s)
- Nives Zimmermann
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William J Gibbons
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Bldg. R. MLC 7016, Cincinnati, OH, 45229-3039, USA
| | - Shelli M Homan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Bldg. R. MLC 7016, Cincinnati, OH, 45229-3039, USA
| | - Daniel R Prows
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Bldg. R. MLC 7016, Cincinnati, OH, 45229-3039, USA.
| |
Collapse
|
18
|
Weitemier K, Straub SC, Fishbein M, Bailey CD, Cronn RC, Liston A. A draft genome and transcriptome of common milkweed ( Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PeerJ 2019; 7:e7649. [PMID: 31579586 PMCID: PMC6756140 DOI: 10.7717/peerj.7649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family.
Collapse
Affiliation(s)
- Kevin Weitemier
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | | | - Mark Fishbein
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, USA
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, USA
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
19
|
Rychel S, Książkiewicz M. Development of gene-based molecular markers tagging low alkaloid pauper locus in white lupin (Lupinus albus L.). J Appl Genet 2019; 60:269-281. [PMID: 31410824 PMCID: PMC6803572 DOI: 10.1007/s13353-019-00508-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
Abstract
White lupin (Lupinus albus L.) is a legume grain crop cultivated since ancient Greece and Egypt. Modern white lupin cultivars are appreciated as a source of protein with positive nutraceutical impact. However, white lupins produce anti-nutritional compounds, quinolizidine alkaloids, which provide bitter taste and have a negative influence on human health. During domestication of this species, several recessive alleles at unlinked loci controlling low alkaloid content were selected. One of these loci, pauper, was exploited worldwide providing numerous low-alkaloid cultivars. However, molecular tracking of pauper has been hampered due to the lack of diagnostic markers. In the present study, the synteny-based approach was harnessed to target pauper locus. Single-nucleotide polymorphisms flanking pauper locus on white lupin linkage map as well as candidate gene sequences elucidated from the narrow-leafed lupin (L. angustifolius L.) chromosome segment syntenic to the pauper linkage group region were transformed to PCR-based molecular markers. These markers were analyzed both in the mapping population and world germplasm collection. From fourteen markers screened, eleven were localized at a distance below 1.5 cM from this locus, including five co-segregating with pauper. The linkage of these markers was confirmed by high LOD values (up to 58.4). Validation performed in the set of 127 bitter and 23 sweet accessions evidenced high applicability of one marker, LAGI01_35805_F1_R1, for pauper locus selection, highlighted by the low ratio of false-positive scores (2.5%). LAGI01_35805 represents a homolog of L. angustifolius acyltransferase-like (LaAT) gene which might hypothetically participate in the alkaloid biosynthesis process in lupins.
Collapse
Affiliation(s)
- Sandra Rychel
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| |
Collapse
|
20
|
Piechota U, Czembor PC, Słowacki P, Czembor JH. Identifying a novel powdery mildew resistance gene in a barley landrace from Morocco. J Appl Genet 2019; 60:243-54. [PMID: 31313063 DOI: 10.1007/s13353-019-00505-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/23/2022]
Abstract
Powdery mildew is a barley foliar disease that causes great loss in yield. Because of the limited number of effective resistance genes, efforts to identify new sources of resistance are frequently focused on genetically diversified landraces. The goal of this study was to characterise the powdery mildew resistance gene in barley line 2553-3 selected from the Moroccan landrace. Phytopathological testing against a set of differential pathogen isolates revealed different pattern responses of this gene from those of other known resistance genes. F2 and F2:3 (2553-3 × Manchuria) mapping populations were employed to investigate resistance inheritance. Two approaches were applied for the linkage analysis: in the first approach, 22 resistant and 21 susceptible homozygous F2 plants genotyped by the DArTseq platform (Diversity Arrays Technology, Pty. Ltd.) were used; in the second, 94 F2 plants were genotyped by converted DArTseq markers and SSRs. Both analyses delineated a new resistance gene on the short arm of chromosome 2H. The authors propose MlMor as a gene symbol for newly characterized powdery mildew resistance genes in barley line 255-3-3. The results presented herein provide a good foundation for the development of closer linkage markers and MAS breeding.
Collapse
|
21
|
Daiger SP, Sullivan LS, Bowne SJ, Cadena ED, Koboldt D, Bujakowska KM, Pierce EA. Detection of Large Structural Variants Causing Inherited Retinal Diseases. Adv Exp Med Biol 2019; 1185:197-202. [PMID: 31884611 DOI: 10.1007/978-3-030-27378-1_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Current application of next-generation sequencing (NGS) leads to detection of the underlying disease-causing gene and mutation or mutations in from 60% to 85% of patients with inherited retinal diseases (IRDs), depending on the methods used, disease type, and population tested. In a cohort of 320 families with autosomal dominant retinitis pigmentosa (adRP), we have detected the mutation in 82% of cases using a variety of methods, leaving more than 50 families with "elusive" disease genotypes. All of the remaining families have been screened for mutations in known IRD genes using retinal-targeted-capture NGS, and most have been tested by whole-exome NGS. Linkage mapping has been conducted in several large families. In one of these families, with DNA samples from ten affected family members and six unaffected, linking members, we observed substantial maximum two-point LOD scores for linkage to both chromosomes 2 and 4. Subsequent 10X Genomics Chromium™ sequencing, which facilitates linked-read, phase-known chromosomal analysis, revealed a balanced translocation of the q terminus arms of chromosomes 2 and 4 involving 35 Mb and 73 Mb of 2 and 4, respectively. The balanced translocation is present in all affected family members and absent from all unaffected individuals. Family histories suggest multiple miscarriages are associated with the translocation. The breakpoint on chromosome 4 is within or 5' to the LRAT gene, whereas the chromosome 2 break is in a gene-poor region. We conclude that the balanced translocation is the cause of adRP in this family, which may lead to dysregulation of the LRAT gene. Since multiple miscarriages are a hallmark of balanced translocations, this possibility should be considered in evaluating family histories. Further, large structural variants, which are not easily detected by conventional sequencing methods, may account for a significant fraction of the remaining unsolved families.
Collapse
|
22
|
Pereira GS, Garcia AAF, Margarido GRA. A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids. BMC Bioinformatics 2018; 19:398. [PMID: 30382832 DOI: 10.1186/s12859-018-2433-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/15/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heterozygous classes based on allele dosage. RESULTS VCF2SM is a Python script that integrates sequencing depth information of polymorphisms in variant call format (VCF) files and SUPERMASSA software for quantitative genotype calling. VCFs can be obtained from any variant discovery software that outputs exact allele sequencing depth, such as a modified version of the TASSEL-GBS pipeline provided here. VCF2SM was successfully applied in analyzing GBS data from diverse panels (alfalfa and potato) and full-sib mapping populations (alfalfa and switchgrass) of polyploid species. CONCLUSIONS We demonstrate that our approach can help plant geneticists working with autopolyploid species to advance their studies by distinguishing allele dosage from GBS data.
Collapse
|
23
|
Aslam ML, Carraro R, Bestin A, Cariou S, Sonesson AK, Bruant JS, Haffray P, Bargelloni L, Meuwissen THE. Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. BMC Genet 2018; 19:43. [PMID: 29996763 PMCID: PMC6042378 DOI: 10.1186/s12863-018-0631-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs. Electronic supplementary material The online version of this article (10.1186/s12863-018-0631-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Anastasia Bestin
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | | | | | | | - Pierrick Haffray
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | | | | |
Collapse
|
24
|
Zhang X, Wang W, Guo N, Zhang Y, Bu Y, Zhao J, Xing H. Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height. BMC Genomics 2018; 19:226. [PMID: 29587637 PMCID: PMC5870336 DOI: 10.1186/s12864-018-4582-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant height (PH) is an important agronomic trait and is closely related to yield in soybean [Glycine max (L.) Merr.]. Previous studies have identified many QTLs for PH. Due to the complex genetic background of PH in soybean, there are few reports on its fine mapping. RESULTS In this study, we used a mapping population derived from a cross between a chromosome segment substitution line CSSL3228 (donor N24852 (G. Soja), a receptor NN1138-2 (G. max)) and NN1138-2 to fine map a wild soybean allele of greater PH by QTL-seq and linkage mapping. We identified a QTL for PH in a 1.73 Mb region on soybean chromosome 13 through QTL-seq, which was confirmed by SSR marker-based classical QTL mapping in the mapping population. The linkage analysis showed that the QTLs of PH were located between the SSR markers BARCSOYSSR_13_1417 and BARCSOYSSR_13_1421 on chromosome 13, and the physical distance was 69.3 kb. RT-PCR and sequence analysis of possible candidate genes showed that Glyma.13 g249400 revealed significantly higher expression in higher PH genotypes, and the gene existed 6 differences in the amino acids encoding between the two parents. CONCLUSIONS Data presented here provide support for Glyma.13 g249400 as a possible candidate genes for higher PH in wild soybean line N24852.
Collapse
Affiliation(s)
- Xiaoli Zhang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wubin Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| | - Na Guo
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| | - Youyi Zhang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuanpeng Bu
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinming Zhao
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| | - Han Xing
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural University, Nanjing 210095, China, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
25
|
Gao W, Qu J, Zhang J, Sonnenberg A, Chen Q, Zhang Y, Huang C. A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci. BMC Genomics 2018; 19:18. [PMID: 29304732 PMCID: PMC5755439 DOI: 10.1186/s12864-017-4421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/27/2017] [Indexed: 11/21/2022] Open
Abstract
Background Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Developing saturated genetic linkage and physical maps is a start for applying genetic and molecular approaches to accelerate the precise breeding programs. Results Here we present a genetic linkage map for P. tuoliensis constructed by using 115 haploid monokaryons derived from a hybrid strain H6. One thousand one hundred and eighty-two SNP markers developed by 2b–RAD (type IIB restriction-site associated DNA) approach were mapped to 12 linkage groups. The map covers 1073 cM with an average marker spacing of 1.0 cM. The genome of P. tuoliensis was de novo sequenced as 40.8 Mb and consisted of 500 scaffolds (>500 bp), which showed a high level of colinearity to the genome of P. eryngii var. eryngii. A total of 97.4% SNP markers (1151) were physically localized on 78 scaffolds, and the physical length of these anchored scaffolds were 33.9 Mb representing 83.1% of the whole genome. Mating type loci A and B were mapped on separate linkage groups and identified physically on the assembled genomes. Five putative pheromone receptors and two putative pheromone precursors were identified for the mating type B locus. Conclusions This study reported a first genetic linkage map integrated with physical mapping of the de novo sequenced genome and the mating type loci of an important cultivated mushroom in China, P. tuoliensis. The de novo sequenced and annotated genome, assembled using a 2b–RAD generated linkage map, provides a basis for marker-assisted breeding of this economic important mushroom species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4421-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wei Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Anton Sonnenberg
- Plant Breeding, Wageningen University & Research Centre, 6708, PB, Wageningen, The Netherlands
| | - Qiang Chen
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Yan Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China. .,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
| |
Collapse
|
26
|
Daiger SP, Bowne SJ, Sullivan LS, Branham K, Wheaton DK, Jones KD, Avery CE, Cadena ED, Heckenlively JR, Birch DG. Molecular Findings in Families with an Initial Diagnose of Autosomal Dominant Retinitis Pigmentosa (adRP). Adv Exp Med Biol 2018; 1074:237-245. [PMID: 29721949 DOI: 10.1007/978-3-319-75402-4_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Genetic testing of probands in families with an initial diagnosis of autosomal dominant retinitis pigmentosa (adRP) usually confirms the diagnosis, but there are exceptions. We report results of genetic testing in a large cohort of adRP families with an emphasis on exceptional cases including X-linked RP with affected females; homozygous affected individuals in families with heterozygous, dominant disease; and independently segregating mutations in the same family. Genetic testing was conducted in more than 700 families with a provisional or probable diagnosis of adRP. Exceptions to the proposed mode of inheritance were extracted from our comprehensive patient and family database. In a subset of 300 well-characterized families with a probable diagnosis of adRP, 195 (70%) have dominant mutations in known adRP genes but 25 (8%) have X-linked mutations, 3 (1%) have multiple segregating mutations, and 3 (1%) have dominant-acting mutations in genes previously associated with recessive disease. It is currently possible to determine the underlying disease-causing gene and mutation in approximately 80% of families with an initial diagnosis of adRP, but 10% of "adRP" families have a variant mode of inheritance. Informed genetic diagnosis requires close collaboration between clinicians, genetic counselors, and laboratory scientists.
Collapse
Affiliation(s)
- Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA. .,Ruiz Department of Ophthalmology and Visual Science, UTHealth, Houston, TX, USA.
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Kari Branham
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Cheryl E Avery
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Elizabeth D Cadena
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | | | - David G Birch
- The Retina Foundation of the Southwest, Dallas, TX, USA
| |
Collapse
|
27
|
Abstract
Hereditary hemochromatosis (HH) is one of the most common genetically transmitted conditions in individuals of Northern European ancestry. The disease is characterized by excessive intestinal absorption of dietary iron, resulting in pathologically high iron storage in tissues and organs. If left untreated, HH can damage joints and organs, and eventually lead to death. There are four main classes of HH, as well as five individual molecular subtypes, caused by mutations in five genes, and the approaches implemented in the discovery of each HH type have specific histories and unique aspects. In this chapter, we review the genetics of the different HH types, including the strategies used to detect the causal variants in each case and the manner in which genetic variants were found to affect iron metabolism.
Collapse
Affiliation(s)
- Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, 960 Medical Education and Research Building (MERB), Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
| | - Barbara V Paynton
- Department of Medical Genetics and Molecular Biology, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | |
Collapse
|
28
|
Vining KJ, Salinas N, Tennessen JA, Zurn JD, Sargent DJ, Hancock J, Bassil NV. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families. PeerJ 2017; 5:e3731. [PMID: 28875078 PMCID: PMC5581533 DOI: 10.7717/peerj.3731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.
Collapse
Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America
| | - Natalia Salinas
- Department of Horticulture, University of Florida, Wimauma, FL, United States of America
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States of America
| | - Jason D Zurn
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
| | - Daniel James Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,East Malling Enterprise Centre, Driscoll's Genetics Limited, East Malling, United Kingdom
| | - James Hancock
- Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
| | - Nahla V Bassil
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America.,National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
| |
Collapse
|
29
|
Yu Y, Zhang X, Yuan J, Wang Q, Li S, Huang H, Li F, Xiang J. Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis. Mar Biotechnol (NY) 2017; 19:277-286. [PMID: 28508952 DOI: 10.1007/s10126-017-9749-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
The Pacific white shrimp Litopenaeus vannamei is a predominant aquaculture shrimp species in the world. Like other animals, the L. vannamei exhibited sexual dimorphism in growth trait. Mapping of the sex-determining locus will be very helpful to clarify the sex determination system and further benefit the shrimp aquaculture industry towards the production of mono-sex stocks. Based on the data used for high-density linkage map construction, linkage-mapping analysis was conducted. The sex determination region was mapped in linkage group (LG) 18. A large region from 0 to 21.205 cM in LG18 showed significant association with sex. However, none of the markers in this region showed complete association with sex in the other populations. So an association analysis was designed using the female parent, pool of female progenies, male parent, and pool of male progenies. Markers were de novo developed and those showing significant differences between female and male pools were identified. Among them, three sex-associated markers including one fully associated marker were identified. Integration of linkage and association analysis showed that the sex determination region was fine-mapped in a small region along LG18. The identified sex-associated marker can be used for the sex detection of this species at genetic level. The fine-mapped sex-determining region will contribute to the mapping of sex-determining gene and help to clarify sex determination system for L. vannamei.
Collapse
Affiliation(s)
- Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Quanchao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Huang
- Hainan Guangtai Ocean Breeding Co., Ltd., Wenchang, 571300, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| |
Collapse
|
30
|
Butler JB, Vaillancourt RE, Potts BM, Lee DJ, King GJ, Baten A, Shepherd M, Freeman JS. Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement. BMC Genomics 2017; 18:397. [PMID: 28532390 PMCID: PMC5441008 DOI: 10.1186/s12864-017-3782-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/10/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. RESULTS We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. CONCLUSIONS These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.
Collapse
Affiliation(s)
- J B Butler
- School of Biological Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - R E Vaillancourt
- School of Biological Science and ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - B M Potts
- School of Biological Science and ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - D J Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD, 4558, Australia
| | - G J King
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - A Baten
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - M Shepherd
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - J S Freeman
- School of Biological Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
| |
Collapse
|
31
|
Yu J, Xiong H, Zhu X, Zhang H, Li H, Miao J, Wang W, Tang Z, Zhang Z, Yao G, Zhang Q, Pan Y, Wang X, Rashid MAR, Li J, Gao Y, Li Z, Yang W, Fu X, Li Z. OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap. BMC Biol 2017; 15:28. [PMID: 28385155 PMCID: PMC5383996 DOI: 10.1186/s12915-017-0365-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/10/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs. RESULTS Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding. CONCLUSIONS The results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.
Collapse
Affiliation(s)
- Jianping Yu
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Haiyan Xiong
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoyang Zhu
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinli Miao
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zuoshun Tang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhanying Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Guoxin Yao
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qiang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yinghua Pan
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xin Wang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - M A R Rashid
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yongming Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weicai Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
32
|
Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics 2017. [PMID: 28284188 DOI: 10.1186/s12864-017-3606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. RESULTS Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. CONCLUSIONS The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
Collapse
Affiliation(s)
- Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Luca Dondini
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Giulia Pagliarani
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Elisa Vendramin
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Roberta Paris
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
- Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centre of Research for Industrial Crops, 40128, Bologna, Italy
| | - Valeria Aramini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Laura Gazza
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
- Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Research Unit for Cereal Quality, Rome, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
- Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010, San Michele all'Adige, TN, Italy
| | - Shengqiang Shu
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Stefano Tartarini
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Maria Teresa Dettori
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| |
Collapse
|
33
|
Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics 2017; 18:225. [PMID: 28284188 PMCID: PMC5346207 DOI: 10.1186/s12864-017-3606-9] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. RESULTS Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. CONCLUSIONS The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
Collapse
Affiliation(s)
- Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Luca Dondini
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Giulia Pagliarani
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Elisa Vendramin
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Roberta Paris
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.,Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centre of Research for Industrial Crops, 40128, Bologna, Italy
| | - Valeria Aramini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Laura Gazza
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.,Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Research Unit for Cereal Quality, Rome, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy.,Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010, San Michele all'Adige, TN, Italy
| | - Shengqiang Shu
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Stefano Tartarini
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Maria Teresa Dettori
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.,U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| |
Collapse
|
34
|
Jin M, Zhang X, Zhao M, Deng M, Du Y, Zhou Y, Wang S, Tohge T, Fernie AR, Willmitzer L, Brotman Y, Yan J, Wen W. Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis. BMC Plant Biol 2017; 17:17. [PMID: 28100172 PMCID: PMC5242060 DOI: 10.1186/s12870-017-0972-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/05/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway. RESULTS We repeatedly detected 25 QTL corresponding to 23 distinct flavonoids across different environments or populations. In addition, a total of 39 genes were revealed both by an expression based network analysis and genetic mapping. Finally, the function of three candidate genes, including two UDP-glycosyltransferases (UGT) and an oxygenase which belongs to the flavone synthase super family, was revealed via preliminary molecular functional characterization. CONCLUSION We explored the genetic influences on the flavonoid biosynthesis based on integrating the genomic, transcriptomic and metabolomic information which provided a rich source of potential candidate genes. The integrated genomics based genetic mapping strategy is highly efficient for defining the complexity of functional genetic variants and their respective regulatory networks as well as in helping to select candidate genes and allelic variance before embarking on laborious transgenic validations.
Collapse
Affiliation(s)
- Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Takayuki Tohge
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
35
|
Grandke F, Ranganathan S, van Bers N, de Haan JR, Metzler D. PERGOLA: fast and deterministic linkage mapping of polyploids. BMC Bioinformatics 2017; 18:12. [PMID: 28049428 PMCID: PMC5210299 DOI: 10.1186/s12859-016-1416-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creation for polyploid species is not supported by standard tools. We want to overcome this limitation and validate our results with simulation studies. RESULTS We developed PERGOLA, a deterministic and heuristic method that addresses this problem. We show that it creates correct linkage groups, marker orders and distances for simulated and real datasets. We compare it to existing tools and demonstrate that it overcomes limitations in ploidy and outperforms them in computational time and mapping accuracy. We represent linkage maps as dendrograms and show that this has advantages in the comparison of different maps. CONCLUSIONS PERGOLA can be used successfully to calculate linkage maps for diploid and polyploid species and outperforms existing tools.
Collapse
Affiliation(s)
- Fabian Grandke
- Genetwister Technologies B.V., Wageningen, The Netherlands. .,Fakultät für Biologie, University of Munich (LMU), Munich, Germany.
| | | | | | - Jorn R de Haan
- Genetwister Technologies B.V., Wageningen, The Netherlands
| | - Dirk Metzler
- Fakultät für Biologie, University of Munich (LMU), Munich, Germany
| |
Collapse
|
36
|
Abstract
Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| |
Collapse
|
37
|
Abstract
Possibility to make doubled haploids (DHs) from varying crossing populations is a useful tool for enhancing cultivar breeding, and a source of valuable material for genetic research. Oats is reported to be recalcitrant in anther culture with low response and genotype dependency. However, the best recoveries reported have reached up to 30 green regenerants per 100 isolated anthers, which clearly addresses the potential of this technique. In this chapter, one successful oat anther culture protocol is described in detail. Due to the total homozygosity reached in one generation, DH-lines are also an excellent material for genetic mapping. In this chapter, the use of DH-mapping population for marker analyses and linkage mapping is presented.
Collapse
Affiliation(s)
- Elina Kiviharju
- Natural Resources Institute Finland, Green Technology, Myllytie 1, Jokioinen, 31600, Finland.
| | - Sirpa Moisander
- Natural Resources Institute Finland, Green Technology, Myllytie 1, Jokioinen, 31600, Finland
| | - Pirjo Tanhuanpää
- Natural Resources Institute Finland, Green Technology, Myllytie 1, Jokioinen, 31600, Finland
| |
Collapse
|
38
|
Sun F, Liu J, Hua W, Sun X, Wang X, Wang H. Identification of stable QTLs for seed oil content by combined linkage and association mapping in Brassica napus. Plant Sci 2016; 252:388-399. [PMID: 27717475 DOI: 10.1016/j.plantsci.2016.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/01/2016] [Accepted: 09/06/2016] [Indexed: 05/21/2023]
Abstract
Seed oil content is an important agricultural trait in rapeseed breeding. Although numerous quantitative trait locus (QTL) have been identified, most of them cannot be applied in practical breeding mainly due to environmental instability or large confidence intervals. The purpose of this study was to identify and validate high quality and more stable QTLs by combining linkage mapping and genome-wide association study (GWAS). For linkage mapping, we constructed two F2 populations from crosses of high-oil content (∼50%) lines 6F313 and 61616 with a low-oil content (∼40%) line 51070. Two high density linkage maps spanned 1987cM (1659 bins) and 1856cM (1746 bins), respectively. For GWAS, we developed more than 34,000 high-quality SNP markers based on 227 accessions. Finally, 40 QTLs and 29 associations were established by linkage and association mapping in different environments. After merging the results, 32 consensus QTLs were obtained and 7 of them were identified by both mapping methods. Seven overlapping QTLs covered an average confidence interval of 183kb and explained the phenotypic variation of 10.23 to 24.45%. We further developed allele-specific PCR primers to identify each of the seven QTLs. These stable QTLs should be useful in gene cloning and practical breeding application.
Collapse
Affiliation(s)
- Fengming Sun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China.
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China.
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China.
| | - Xingchao Sun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China.
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China.
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China.
| |
Collapse
|
39
|
Kushanov FN, Pepper AE, Yu JZ, Buriev ZT, Shermatov SE, Saha S, Ulloa M, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers. BMC Genet 2016; 17:141. [PMID: 27776497 PMCID: PMC5078887 DOI: 10.1186/s12863-016-0448-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs. RESULTS Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of 'Texas Marker-1' ('TM-1'), 'Pima 3-79' and their F1 hybrids. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference 'TM-1' x 'Pima 3-79' RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies. CONCLUSION This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.
Collapse
Affiliation(s)
- Fakhriddin N. Kushanov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, TX 77843 USA
| | - John Z. Yu
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845 USA
| | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Shukhrat E. Shermatov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Sukumar Saha
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS 39762 USA
| | - Mauricio Ulloa
- USDA-ARS, Plant Stress and Germplasm Development Research, 3810 4th Street, Lubbock, TX 79415 USA
| | - Johnie N. Jenkins
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS 39762 USA
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| |
Collapse
|
40
|
Agerholm JS, McEvoy FJ, Menzi F, Jagannathan V, Drögemüller C. A CHRNB1 frameshift mutation is associated with familial arthrogryposis multiplex congenita in Red dairy cattle. BMC Genomics 2016; 17:479. [PMID: 27364156 PMCID: PMC4929742 DOI: 10.1186/s12864-016-2832-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bovine arthrogryposis multiplex congenita (AMC) is a syndromic term for a congenital condition characterized by multiple joint contractures. Rare inherited forms of bovine AMC have been reported in different breeds. For AMC in Angus cattle a causative genomic deletion encompassing the agrin (AGRN) gene, encoding an essential neural regulator that induces the aggregation of acetylcholine receptors (AChRs), is known. In 2015, three genetically related cases of generalized AMC affecting Red dairy calves were diagnosed in Denmark. RESULTS The family history of three affected calves suggested an autosomal recessive inheritance. Single nucleotide polymorphism (SNP) genotyping showed a single genomic region of extended homozygosity of 21.5 Mb on chromosome 19. Linkage analysis revealed a maximal parametric LOD score of 1.8 at this region. By whole genome re-sequencing of the three cases, two private homozygous non-synonymous variants were detected in the critical interval. Both variants, located in the myosin phosphatase Rho interacting protein (MPRIP) and the cholinergic receptor nicotinic beta 1 subunit gene (CHRNB1), were perfectly associated with the AMC phenotype. Previously described CHRNB1 variants in humans lead to a congenital myasthenic syndrome with impaired neuromuscular transmission. The cattle variant represents a single base deletion in the first exon of CHRNB1 (c.55delG) introducing a premature stop codon (p.Ala19Profs47*) in the second exon, truncating 96 % of the protein. CONCLUSIONS This study provides the first phenotypically and genetically characterized example of a bovine AMC phenotype that represents an inherited neuromuscular disorder corresponding to human congenital myasthenic syndrome. The identified CHRNB1 loss of function variant is predicted to have a deleterious effect on fetal AChR function, which could explain the lethal phenotype reported in this study. The identification of this candidate causative mutation thus widens the known phenotypic spectrum of CHRNB1 mutations and enables selection against this pathogenic variant in Red dairy cattle.
Collapse
Affiliation(s)
- Jørgen S Agerholm
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 68, Frederiksberg C, DK-1870, Denmark.
| | - Fintan J McEvoy
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, Frederiksberg C, DK-1870, Denmark
| | - Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| |
Collapse
|
41
|
Daiger SP, Sullivan LS, Bowne SJ, Koboldt DC, Blanton SH, Wheaton DK, Avery CE, Cadena ED, Koenekoop RK, Fulton RS, Wilson RK, Weinstock GM, Lewis RA, Birch DG. Identification of a Novel Gene on 10q22.1 Causing Autosomal Dominant Retinitis Pigmentosa (adRP). Adv Exp Med Biol 2016; 854:193-200. [PMID: 26427411 DOI: 10.1007/978-3-319-17121-0_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Whole-genome linkage mapping identified a region on chromosome 10q21.3-q22.1 with a maximum LOD score of 3.0 at 0 % recombination in a six-generation family with autosomal dominant retinitis pigmentosa (adRP). All known adRP genes and X-linked RP genes were excluded in the family by a combination of methods. Whole-exome next-generation sequencing revealed a missense mutation in hexokinase 1, HK1 c.2539G > A, p.Glu847Lys, tracking with disease in all affected family members. One severely-affected male is homozygous for this region by linkage analysis and has two copies of the mutation. No other potential mutations were detected in the linkage region nor were any candidates identified elsewhere in the genome. Subsequent testing detected the same mutation in four additional, unrelated adRP families, for a total of five mutations in 404 probands tested (1.2 %). Of the five families, three are from the Acadian population in Louisiana, one is French Canadian and one is Sicilian. Haplotype analysis of the affected chromosome in each family and the homozygous individual revealed a rare, shared haplotype of 450 kb, suggesting an ancient founder mutation. HK1 is a widely-expressed gene, with multiple, abundant retinal transcripts, coding for hexokinase 1. Hexokinase catalyzes phosphorylation of glucose to glusose-6-phospate, the first step in glycolysis. The Glu847Lys mutation is in a highly-conserved site, outside of the active site or known functional sites.
Collapse
Affiliation(s)
- Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas HSC, 1200 Pressler St., Houston, TX, 77030, USA. .,Ruiz Department of Ophthalmology and Visual Science, Medical School, The University of Texas Health Science Center, Houston, TX, 77030, USA.
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas HSC, 1200 Pressler St., Houston, TX, 77030, USA.
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas HSC, 1200 Pressler St., Houston, TX, 77030, USA.
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| | | | - Cheryl E Avery
- Human Genetics Center, School of Public Health, The University of Texas HSC, 1200 Pressler St., Houston, TX, 77030, USA.
| | - Elizabeth D Cadena
- Human Genetics Center, School of Public Health, The University of Texas HSC, 1200 Pressler St., Houston, TX, 77030, USA.
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, Departments of Paediatric Surgery, Human Genetics and Ophthalmology, Montreal Children's Hospital, McGill University Health Center, Montreal, QC, H3H 1P3, Canada.
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - George M Weinstock
- Microbial Genomics, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
| | - Richard A Lewis
- Departments of Ophthalmology, Medicine, Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - David G Birch
- The Retina Foundation of the Southwest, Dallas, TX, 75231, USA.
| |
Collapse
|
42
|
Abstract
Both genetic and environmental factors play roles in the development of refractive errors. Identification of genes involved in refractive errors may help in elucidating the underlying molecular mechanism related to both genetic defects and environmental pressure. Recent development of techniques for genome wide analysis provides unique opportunity in dissecting the genetic basis related to refractive errors. This chapter tries to give a brief overview on the recent progress of genetic study of refractive errors, especially myopia.
Collapse
Affiliation(s)
- Qingjiong Zhang
- State Key Lab of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, PR China.
| |
Collapse
|
43
|
Kudo Y, Nikaido M, Kondo A, Suzuki H, Yoshida K, Kikuchi K, Okada N. A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids. Gene 2015; 560:156-64. [PMID: 25639358 DOI: 10.1016/j.gene.2015.01.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 01/06/2023]
Abstract
Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity.
Collapse
|
44
|
King AJ, Montes LR, Clarke JG, Itzep J, Perez CAA, Jongschaap REE, Visser RGF, van Loo EN, Graham IA. Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L. Biotechnol Biofuels 2015; 8:160. [PMID: 26413159 PMCID: PMC4583170 DOI: 10.1186/s13068-015-0326-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/25/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Economical cultivation of the oilseed crop Jatropha curcas is currently hampered in part due to the non-availability of purpose-bred cultivars. Although genetic maps and genome sequence data exist for this crop, marker-assisted breeding has not yet been implemented due to a lack of available marker-trait association studies. To identify the location of beneficial alleles for use in plant breeding, we performed quantitative trait loci (QTL) analysis for a number of agronomic traits in two biparental mapping populations. RESULTS The mapping populations segregated for a range of traits contributing to oil yield, including plant height, stem diameter, number of branches, total seeds per plant, 100-seed weight, seed oil content and fatty acid composition. QTL were detected for each of these traits and often over multiple years, with some variation in the phenotypic variance explained between different years. In one of the mapping populations where we recorded vegetative traits, we also observed co-localization of QTL for stem diameter and plant height, which were both overdominant, suggesting a possible locus conferring a pleotropic heterosis effect. By using a candidate gene approach and integrating physical mapping data from a recent high-quality release of the Jatropha genome, we were also able to position a large number of genes involved in the biosynthesis of storage lipids onto the genetic map. By comparing the position of these genes with QTL, we were able to detect a number of genes potentially underlying seed traits, including phosphatidate phosphatase genes. CONCLUSIONS The QTL we have identified will serve as a useful starting point in the creation of new varieties of J. curcas with improved agronomic performance for seed and oil productivity. Our ability to physically map a significant proportion of the Jatropha genome sequence onto our genetic map could also prove useful in identifying the genes underlying particular traits, allowing more controlled and precise introgression of desirable alleles and permitting the pyramiding or stacking of multiple QTL.
Collapse
Affiliation(s)
- Andrew J. King
- />Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Luis R. Montes
- />Biocombustibles de Guatemala, Guatemala Ciudad, Guatemala
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
- />Graduate School of Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Jasper G. Clarke
- />Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Jose Itzep
- />Biocombustibles de Guatemala, Guatemala Ciudad, Guatemala
| | - Cesar A. A. Perez
- />Facultad de Agronomia, Universidad de San Carlos de Guatemala, Edifico T-8 y T-9 Ciudad Universitaria zona 12, Guatemala Cuidad, Guatemala
| | - Raymond E. E. Jongschaap
- />Wageningen UR Agrosystems Research, Wageningen University and Research Centre, PO Box 16, 6708 AP Wageningen, The Netherlands
| | - Richard G. F. Visser
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Eibertus N. van Loo
- />Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Ian A. Graham
- />Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| |
Collapse
|
45
|
Grzebelus D, Iorizzo M, Senalik D, Ellison S, Cavagnaro P, Macko-Podgorni A, Heller-Uszynska K, Kilian A, Nothnagel T, Allender C, Simon PW, Baranski R. Diversity, genetic mapping, and signatures of domestication in the carrot ( Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breed 2013; 33:625-637. [PMID: 24532979 PMCID: PMC3918115 DOI: 10.1007/s11032-013-9979-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/18/2013] [Indexed: 05/25/2023]
Abstract
Carrot is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94 cultivated and 65 wild carrot accessions. The accessions were attributed to three separate groups: wild, Eastern cultivated and Western cultivated. Twenty-seven markers showing signatures for selection were identified. They showed a directional shift in frequency from the wild to the cultivated, likely reflecting diversifying selection imposed in the course of domestication. A genetic linkage map constructed using 188 F2 plants comprised 431 markers with an average distance of 1.1 cM, divided into nine linkage groups. Using previously anchored single nucleotide polymorphisms, the linkage groups were physically attributed to the nine carrot chromosomes. A cluster of markers mapping to chromosome 8 showed significant segregation distortion. Two of the 27 DArT markers with signatures for selection were segregating in the mapping population and were localized on chromosomes 2 and 6. Chromosome 2 was previously shown to carry the Vrn1 gene governing the biennial growth habit essential for cultivated carrot. The results reported here provide background for further research on the history of carrot domestication and identify genomic regions potentially important for modern carrot breeding.
Collapse
Affiliation(s)
- Dariusz Grzebelus
- Insitute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland
| | - Massimo Iorizzo
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Douglas Senalik
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- Vegetable Crops Research Unit, USDA-Agricultural Research Service, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706 USA
| | - Shelby Ellison
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Pablo Cavagnaro
- CONICET and INTA EEA La Consulta, CC8 La Consulta (5567), Mendoza, Argentina
| | - Alicja Macko-Podgorni
- Insitute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland
| | - Kasia Heller-Uszynska
- Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, ACT 2600 Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, ACT 2600 Australia
| | - Thomas Nothnagel
- Institute for Breeding Research on Horticultural and Fruit Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Charlotte Allender
- Warwick Crop Centre, University of Warwick, Wellesbourne, Warwick, CV35 9EF UK
| | - Philipp W. Simon
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- Vegetable Crops Research Unit, USDA-Agricultural Research Service, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706 USA
| | - Rafal Baranski
- Insitute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland
| |
Collapse
|