High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat

Authors: PANG, YUNLONG - Shandong Agricultural University; WU, YUYE - Shandong Agricultural University; LIU, CHUNXIA - Shandong Agricultural University; LI, WENHUI - Shandong Agricultural University; St Amand, Paul; Bernardo, Amy; WANG, DAFENG - Shandong Agricultural University; DONG, LEI - Shandong Agricultural University; YUNG, XIUFANG - Shandong Agricultural University; ZHANG, HUIRUI - Shandong Agricultural University; ZHAO, MENG - Shandong Agricultural University; WANG, LIMING - Henan University Of Technology; HE, FANG - Guizhou University; LIANG, YUNLONG - Shandong Agricultural University; YAN, QIANG - Shandong Agricultural University; LU, YUE - Shandong Agricultural University; YU, SU - Shandong Agricultural University; WU, JIAJIE - Shandong Agricultural University; LI, ANFEI - Shandong Agricultural University; KONG, LINGRANG - Shandong Agricultural University; Bai, Guihua; LIU, SHUBING - Shandong Agricultural University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/3/2021
Publication Date: 6/1/2021
Citation: Pang, Y., Wu, Y., Liu, C., Li, W., St Amand, P.C., Bernardo, A.E., Wang, D., Dong, L., Yung, X., Zhang, H., Zhao, M., Wang, L., He, F., Liang, Y., Yan, Q., Lu, Y., Yu, S., Wu, J., Li, A., Kong, L., Bai, G., Liu, S. 2021. High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat. Theoretical and Applied Genetics. 134:2857–2873. https://doi.org/10.1007/s00122-021-03863-6.
DOI: https://doi.org/10.1007/s00122-021-03863-6

Interpretive Summary: Diseases and cold stresses significantly affect wheat production in many wheat growing areas worldwide. Here we conducted a genome-wide association study (GWAS) on a panel of 768 Chinese wheat cultivars to identify wheat genes for resistance to leaf rust, yellow rust, powdery mildew, and cold tolerance. Data were collected in five to six environments for each trait. A total of 23 reproducible resistance genes were detected for disease resistances. A total of 11 reproducible tolerance genes were detected for cold tolerance. Genomic prediction using a pre-selected set of markers showed high prediction accuracies of 0.73 to 0.83 for the four traits. The results provide useful sources of resistance for breeding and genomic information for candidate gene validation and genomic selection in wheat.

Technical Abstract: Genome-wide association study (GWAS) and genomic selection (GS) for wheat stress tolerance related traits is critical to understand their genetic architecture to accelerate breeding process. Here, we conducted a high-resolution GWAS for wheat leaf rust (LR), yellow rust (YR), powdery mildew (PM) and cold tolerance (CT) by genotyping a panel of 768 wheat cultivars via genotyping-by-sequencing. Totally, 153 QTL were identified with 81 of them delimited to = 1.0 Mb intervals, and three QTL were validated using bi-parental populations. Furthermore, 837 stress resistance related genes were identified in the QTL region with 12 showed induced expression by YR and PM pathogens. Genomic prediction using 2,608, 4,064, 3,907, and 2,136 pre-selected SNPs based on GWAS and genotypic correlations between the SNPs showed high prediction accuracies of 0.76 for LR, 0.73 for YR, 0.78 for PM and 0.83 for CT, respectively. Our study laid a solid foundation for large-scale QTL fine mapping, candidate gene validation and GS in wheat.