Meloidogyne javanica causing root-knot nematode in soybean is an important problem in soybean areas, leading to several yield losses. Some accessions have been identified carrying resistance loci to this nematode specie. In this study, a set of 317 soybean accessions were characterized for resistance to M. javanica. Genome-wide association study (GWAS) was performed using SNPs from genotyping-by-sequencing (GBS), and a region of 29.2 Kbp on chromosome 13 was identified. The haplotype analysis showed that SNPs were able to discriminate susceptible and resistant accessions, leading to 25 accessions sharing the resistance locus. Furthermore, 5 accessions may be new M. javanica resistance sources. The screening of the SNPs in the USDA soybean germplasm showed that several accessions previous reported as resistance to other nematodes also showed the resistance haplotype on chromosome 13. High levels of concordance among the phenotypes of Brazilian cultivars and the SNPs in chromosome 13 were observed. A in silico analysis of the mapped region on soybean genome revealed a presence of 5 genes with structural similarity with major resistance genes. The expression levels of the candidate genes in the interval demonstrated a potential pseudogene, and other two model genes up-regulated in the resistance source after pathogen infection. The SNPs associated to the region conferring resistance is a important tool for introgression of the resistance by marker-assisted selection in soybean breeding programs.
Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is the main disease affecting soybean production in Brazil. The plant introduction PI 594756 is a resistance source that has been employed in breeding for resistance to ASR in this country. This study aimed at investigating the resistance of the PI 594756 to a panel of P. pachyrhizi isolates and mapping its resistance in populations derived from the cross with the susceptible PI 594891. The PI 594756 and resistant varieties were inoculated with seven ASR monosporic isolates. F2 and F2:3 populations were tested against ASR in a greenhouse and used to map a resistance gene to a likely genomic location by means of bulked segregant analysis. Bulks were genotyped with Infinium BeadChips and the genomic region identified was saturated with target GBS (tGBS). PI 594756 presented a unique resistance profile compared to the differential varieties, being resistant to six isolates and immune to one. The resistance was visually monogenic dominant; however, it was classified as incompletely dominant when quantitatively studied. Genetic and QTL mapping placed the PI 594756 gene between chromosome (chr) 18 55,863,741 and 56,123,516. This position is slightly upstream mapping positionsof Rpp1 (PI 200492) and Rpp1-b (PI 594538A). Finally, we performed a haplotype analysis of a panel composed of Brazilian historical germplasm, sources of Rpp genes and resistant varieties and found SNPs that can successfully differentiated the new allele from PI 594756 from Rpp1 and Rpp1-b sources. The haplotype identified can be used as a tool for marker assisted selection.
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