Abstract
BackgroundSoybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only the Rhg1 allele. Although simple sequence repeat (SSR) markers have been reported for both loci, they are linked markers and limited to be applied in breeding programs due to accuracy, throughput and cost of detection methods. The objectives of this study were to develop robust functional marker assays for high-throughput selection of SCN resistance and to differentiate the sources of resistance.ResultsBased on the genomic DNA sequences of 27 soybean lines with known SCN phenotypes, we have developed Kompetitive Allele Specific PCR (KASP) assays for two Single nucleotide polymorphisms (SNPs) from Glyma08g11490 for the selection of the Rhg4 resistance allele. Moreover, the genomic DNA of Glyma18g02590 at the Rhg1 locus from 11 soybean lines and cDNA of Forrest, Essex, Williams 82 and PI 88788 were fully sequenced. Pairwise sequence alignment revealed seven SNPs/insertion/deletions (InDels), five in the 6th exon and two in the last exon. Using the same 27 soybean lines, we identified one SNP that can be used to select the Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. These SNP markers have been validated and a strong correlation was observed between the SNP genotypes and reactions to SCN race 3 using a panel of 153 soybean lines, as well as a bi-parental population, F5–derived recombinant inbred lines (RILs) from G00-3213 x LG04-6000.ConclusionsThree functional SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide genotype information for the selection of SCN resistance and differentiate Peking from PI 88788 source for most germplasm lines. The robust KASP SNP marker assays were developed. In most contexts, use of one or two of these markers is sufficient for high-throughput marker-assisted selection of plants that will exhibit SCN resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1531-3) contains supplementary material, which is available to authorized users.
Highlights
Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean
We fully sequenced the genomic DNA of Glyma18g02590 from 11 soybean lines and cDNA of Glyma18g02590 from Forrest, Essex, Williams 82 and PI 88788 at the Rhg1 locus
Three Single nucleotide polymorphism (SNP) were identified in Glyma18g02580 from the comparison between Williams 82 and PI 88788, one synonymous SNP in the first exon, one in the intron and one in the 3’ untranslated region (UTR) (Figure 1B)
Summary
Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Rhg and Rhg primarily contribute resistance to SCN race 3 in soybean. Race 3 is the most frequently found SCN populations in major soybean producing states in the USA [8,9]. Soybean lines PI 88788 and Peking are the two main sources of resistance to SCN race 3 [10,11]. Two polymorphisms have been identified in the coding sequence of SHMT, 389 G/C in the first exon and 1,165 A/T in the second exon, which resulted in the amino acid change of Arginine (R) to Proline (P) and Tyrosine(Y) to Asparagine (N), respectively These polymorphisms change the property of the enzyme and may correlate with Rhg4-dependent resistance and susceptibility [14]. Sequencing of cDNA from several soybean lines revealed that multiple alleles of Glyma18g02590 were present in the different multi-copy Rhg categories [16]
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