David R. Walker, Samuel C. McDonald, Donna K. Harris, H. Roger Boerma, James W. Buck, Edward J. Sikora, David B. Weaver, David L. Wright, James J. Marois & Zenglu Li

Theoretical and Applied Genetics September 2022; vol. 135: 3073–3086

Key message

Eight soybean genomic regions, including six never before reported, were found to be associated with resistance to soybean rust (Phakopsora pachyrhizi) in the southeastern USA.

Abstract

Soybean rust caused by Phakopsora pachyrhizi is one of the most important foliar diseases of soybean [Glycine max (L.) Merr.]. Although seven Rpp resistance gene loci have been reported, extensive pathotype variation in and among fungal populations increases the importance of identifying additional genes and loci associated with rust resistance. One hundred and ninety-one soybean plant introductions from Japan, Indonesia and Vietnam, and 65 plant introductions from other countries were screened for resistance to P. pachyrhizi under field conditions in the southeastern USA between 2008 and 2015. The results indicated that 84, 69, and 49% of the accessions from southern Japan, Vietnam or central Indonesia, respectively, had negative BLUP values, indicating less disease than the panel mean. A genome-wide association analysis using SoySNP50K Infinium BeadChip data identified eight genomic regions on seven chromosomes associated with SBR resistance, including previously unreported regions of Chromosomes 1, 4, 6, 9, 13, and 15, in addition to the locations of the Rpp3 and Rpp6 loci. The six unreported genomic regions might contain novel Rpp loci. The identification of additional sources of rust resistance and associated genomic regions will further efforts to develop soybean cultivars with broad and durable resistance to soybean rust in the southern USA.

See https://link.springer.com/article/10.1007/s00122-022-04168-y

Fig. 3 Manhattan plot generated from a genome-wide association analysis of a panel of soybean accessions evaluated for their reactions to soybean rust in the southeastern USA. The X-axis shows the location of SNPs along each chromosome in the genome, and the Y-axis shows the − log10 of the p-values. The signifcance threshold was − log10(P)=4.84