Abstract
Soybean cyst nematode (Heterodera glycines Ichinohe) (SCN) is the most destructive pest affecting soybeans [Glycine max (L.) Merr.] in the U.S. To date, only two major SCN resistance alleles, rhg1 and Rhg4, identified in PI 88788 (rhg1) and Peking (rhg1/Rhg4), residing on chromosomes (Chr) 18 and 8, respectively, have been widely used to develop SCN resistant cultivars in the U.S. Thus, some SCN populations have evolved to overcome the PI 88788 and Peking derived resistance, making it a priority for breeders to identify new alleles and sources of SCN resistance. Toward that end, 461 soybean accessions from various origins were screened using a greenhouse SCN bioassay and genotyped with Illumina SoySNP50K iSelect BeadChips and three KASP SNP markers developed at the Rhg1 and Rhg4 loci to perform a genome-wide association study (GWAS) and a haplotype analysis at the Rhg1 and Rhg4 loci. In total, 35,820 SNPs were used for GWAS, which identified 12 SNPs at four genomic regions on Chrs 7, 8, 10, and 18 that were significantly associated with SCN resistance (P < 0.001). Of those, three SNPs were located at Rhg1 and Rhg4, and 24 predicted genes were found near the significant SNPs on Chrs 7 and 10. KASP SNP genotyping results of the 462 accessions at the Rhg1 and Rhg4 loci identified 30 that carried PI 88788-type resistance, 50 that carried Peking-type resistance, and 58 that carried neither the Peking-type nor the PI 88788-type resistance alleles, indicating they may possess novel SCN resistance alleles. By using two subsets of SNPs near the Rhg1 and Rhg4 loci obtained from SoySNP iSelect BeadChips, a haplotype analysis of 461 accessions grouped those 58 accessions differently from the accessions carrying Peking or PI 88788 derived resistance, thereby validating the genotyping results at Rhg1 and Rhg4. The significant SNPs, candidate genes, and newly characterized SCN resistant accessions will be beneficial for the development of DNA markers to be used for marker-assisted breeding and developing soybean cultivars carrying novel sources of SCN resistance.
Highlights
Soybean [Glycine max (L.) Merrill] is the most important economic crop in the legume family for both oil and food products
The objectives of this study were to: (1) identify new germplasm sources of resistance to HG Type 0 (SCN race 3) by genotyping a diverse soybean germplasm panel consisting of 462 accessions with three KASP single nucleotide polymorphism (SNP) markers developed at the Rhg1 and Rhg4 loci and screening those accessions with a greenhouse SCN bio-assay; (2) to use genome-wide association study (GWAS) to pinpoint the genomic regions associated with HG Type 0 resistance among the 461 accessions by utilizing genotypic data from Illumina SoySNP50K iSelect BeadChips and phenotypic data from the greenhouse SCN bio-assay, and (3) to conduct a haplotype analysis of the 461 accessions near the Rhg1 and Rhg4 loci by using two subsets of SNPs on Chr 18 (103 SNPs) and Chr 8 (64 SNPs) obtained from the SoySNP50K iSelect BeadChips
56 accessions were rated as moderately resistant (MR) with a calculated Female Index (FI) between 10 and 30% and 170 accessions were rated as moderately susceptible (MS) with a calculated FI between 30 and 60%
Summary
Soybean [Glycine max (L.) Merrill] is the most important economic crop in the legume family for both oil and food products. Soybean is the second most grown crop in the U.S behind only maize, totaling 33.8 million hectares planted annually, and grossing $40 billion in 2016 in the U.S (ASA, 2018). Soybean production in the U.S is strongly undermined by SCN, a pest that caused yield losses of ∼3.4 million tons in 20141. Virulence of SCN is variable with 16 possible races determined by four selected differential lines, including PI 548402 (hereafter referred to as Peking), Pickett, PI 88788 and PI 90763 (Riggs and Schmitt, 1988). The new population classification system, termed HG Type, is determined by comparing SCN fecundity on each indicator line to the standard susceptible cultivar Lee 74 (Niblack et al, 2002)
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