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Genome-wide association analysis of stripe rust resistance in modern Chinese wheat.
BMC Plant Biol. 2020 Oct 27; 20(1):491.BP

Abstract

BACKGROUND

Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm.

RESULTS

Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation.

CONCLUSION

The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.

Links

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Authors+Show Affiliations

Jia M
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China. College of Life Sciences, Wuhan University, Wuhan, 430072, China.
Yang L
Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
Zhang W
Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58108-6050, USA.
Rosewarne G
Department of Jobs, Precincts and Regions, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria, 3400, Australia. International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico D.F., Mexico.
Li J
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
Yang E
Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
Chen L
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
Wang W
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
Liu Y
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
Tong H
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
He W
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
Zhang Y
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.
Zhu Z
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China. zhuzhanwang@163.com.
Gao C
Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China. gcbgybwj@163.com. Hubei Collaborative Innovation Center for Grain Industry, Yangtze university, Jingzhou, 434025, China. gcbgybwj@163.com.

MeSH

AllelesChinaDisease ResistanceGenetic MarkersGenetic VariationGenome-Wide Association StudyPlant DiseasesPolymorphism, Single NucleotidePucciniaQuantitative Trait LociTriticum

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33109074

Citation

Jia, Mengjie, et al. "Genome-wide Association Analysis of Stripe Rust Resistance in Modern Chinese Wheat." BMC Plant Biology, vol. 20, no. 1, 2020, p. 491.
Jia M, Yang L, Zhang W, et al. Genome-wide association analysis of stripe rust resistance in modern Chinese wheat. BMC Plant Biol. 2020;20(1):491.
Jia, M., Yang, L., Zhang, W., Rosewarne, G., Li, J., Yang, E., Chen, L., Wang, W., Liu, Y., Tong, H., He, W., Zhang, Y., Zhu, Z., & Gao, C. (2020). Genome-wide association analysis of stripe rust resistance in modern Chinese wheat. BMC Plant Biology, 20(1), 491. https://doi.org/10.1186/s12870-020-02693-w
Jia M, et al. Genome-wide Association Analysis of Stripe Rust Resistance in Modern Chinese Wheat. BMC Plant Biol. 2020 Oct 27;20(1):491. PubMed PMID: 33109074.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide association analysis of stripe rust resistance in modern Chinese wheat. AU - Jia,Mengjie, AU - Yang,Lijun, AU - Zhang,Wei, AU - Rosewarne,Garry, AU - Li,Junhui, AU - Yang,Enian, AU - Chen,Ling, AU - Wang,Wenxue, AU - Liu,Yike, AU - Tong,Hanwen, AU - He,Weijie, AU - Zhang,Yuqing, AU - Zhu,Zhanwang, AU - Gao,Chunbao, Y1 - 2020/10/27/ PY - 2020/04/08/received PY - 2020/10/12/accepted PY - 2020/10/28/entrez PY - 2020/10/29/pubmed PY - 2021/3/24/medline KW - Marker-trait association KW - Single nucleotide polymorphism (SNP) KW - Triticum aestivum KW - Yellow rust SP - 491 EP - 491 JF - BMC plant biology JO - BMC Plant Biol VL - 20 IS - 1 N2 - BACKGROUND: Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm. RESULTS: Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation. CONCLUSION: The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/33109074/Genome_wide_association_analysis_of_stripe_rust_resistance_in_modern_Chinese_wheat_ DB - PRIME DP - Unbound Medicine ER -