Genome-wide association analysis of stable stripe rust resistance loci in a Chinese wheat landrace panel using the 660K SNP array

Authors: YAO, FANGJIE - Washington State University; GUAN, FANGNIAN - Sichuan Agricultural University; DUAN, LUYAO - Sichuan Agricultural University; LONG, LI - Sichuan Agricultural University; TANG, HAO - Sichuan Agricultural University; JIANG, YUNFENG - Sichuan Agricultural University; LI, HAO - Sichuan Agricultural University; JIANG, QIANTAO - Sichuan Agricultural University; WANG, JIRUI - Sichuan Agricultural University; QI, PENGFEI - Sichuan Agricultural University; KANG, HOUYANG - Sichuan Agricultural University; LI, WEI - Sichuan Agricultural University; MA, JIA - Sichuan Agricultural University; PU, Z - Sichuan Agricultural University; DENG, M - Sichuan Agricultural University; WEI, Y - Sichuan Agricultural University; ZHENG, Y - Sichuan Agricultural University; Chen, Xianming; CHEN, GUOYUE - Sichuan Agricultural University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2021
Publication Date: 12/22/2021
Citation: Yao, F., Guan, F., Duan, L., Long, L., Tang, H., Jiang, Y., Li, H., Jiang, Q., Wang, J., Qi, P., Kang, H., Li, W., Ma, J., Pu, Z., Deng, M., Wei, Y., Zheng, Y., Chen, X., Chen, G. 2021. Genome-wide association analysis of stable stripe rust resistance loci in a Chinese wheat landrace panel using the 660K SNP array. Frontiers in Plant Science. 12. Article 783830. https://doi.org/10.3389/fpls.2021.783830.
DOI: https://doi.org/10.3389/fpls.2021.783830

Interpretive Summary: Stripe rust is one of the most severe diseases affecting wheat production. Chinese wheat landraces have excellent resistance to stripe rust. The objectives of this study were to identify stable resistant wheat landraces and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of the pathogen in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including 8 associated to all-stage resistance and 9 to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D and 7A. These QTL explained 6.06% to 16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL, QYrCL.sicau-3B.4, QYrCL.sicau-3B.5, QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL, were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust.

Technical Abstract: Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases affecting wheat production. Chinese wheat (Triticum aestivum) landraces have excellent resistance to stripe rust. The objectives of this study were to identify stable resistant wheat landraces and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study (GWAS) approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of P. striiformis f. sp. tritici in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including 8 associated to all-stage resistance and 9 to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D and 7A. These QTL explained 6.06% to 16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL, QYrCL.sicau-3B.4, QYrCL.sicau-3B.5, QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL, were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust.