Genomic regions associated with resistance to soybean rust (Phakopsora pachyrhizi) under field conditions in soybean accessions from Japan, Indonesia and Vietnam

Authors: Walker, David; MCDONALD, SAMUEL - University Of Georgia; HARRIS, DONNA - University Of Georgia; BOERMA, H - University Of Georgia; BUCK, JAMES - University Of Georgia; SIKORA, EDWARD - Auburn University; WEAVER, DAVID - Auburn University; WRIGHT, DAVID - University Of Florida; MAROIS, JAMES - University Of Florida; LI, ZENGLU - University Of Georgia

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2022
Publication Date: 7/28/2022
Citation: Walker, D.R., McDonald, S.C., Harris, D.K., Boerma, H.R., Buck, J.W., Sikora, E.J., Weaver, D.B., Wright, D.L., Marois, J.J., Li, Z. 2022. Genomic regions associated with resistance to soybean rust (Phakopsora pachyrhizi) under field conditions in soybean accessions from Japan, Indonesia and Vietnam. G3, Genes/Genomes/Genetics. 135:3073-3086. https://doi.org/10.1007/s00122-022-04168-y.
DOI: https://doi.org/10.1007/s00122-022-04168-y

Interpretive Summary: Soybean rust is one of the most important foliar diseases of soybean. Resistance genes have been found at seven different genetic loci, but only some of the genes are known to be effective against the strains of the fungal pathogen causing soybean rust in the United States. In this study, field tests conducted over eight years and four locations in the southern United States revealed that a large percentage of soybean germplasm accessions from Japan, Indonesia and Vietnam were resistant to rust. Disease ratings were used with DNA marker data in a genome-wide association study to identify chromosomal regions associated with resistance to soybean rust. Eight genomic regions were detected, of which six have not been reported before. These results, together with further investigations of the resistance genes in these regions, could be useful for developing cultivars with novel genes and gene combinations for resistance to soybean rust. Soybean cultivars with broad and durable resistance to rust would ultimately benefit growers by reducing their need to use pesticides to manage this disease.

Technical Abstract: Soybean rust (SBR) caused by Phakopsora pachyrhizi is one of the most important foliar diseases of soybean [Glycine max (L.) Merrill]. 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 SBR resistance. One hundred and ninety-one soybean plant introductions (PIs) from Japan, Indonesia and Vietnam, and 65 PIs from other countries were screened for resistance to P. pachyrhizi under field conditions in the southeastern United States between 2008 and 2015. The results indicated that 84%, 69%, and 49% of the PIs 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 United States.