Abstract
BackgroundSudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, two independent association panels of elite soybean cultivars, consisting of 392 and 300 unique accessions, respectively, were evaluated for SDS resistance in multiple environments and years. The two association panels were genotyped with 52,041 and 5,361 single nucleotide polymorphisms (SNPs), respectively. Genome-wide association mapping was carried out using a mixed linear model that accounted for population structure and cryptic relatedness.ResultA total of 20 loci underlying SDS resistance were identified in the two independent studies, including 7 loci localized in previously mapped QTL intervals and 13 novel loci. One strong peak of association on chromosome 18, associated with all disease assessment criteria across the two panels, spanned a physical region of 1.2 Mb around a previously cloned SDS resistance gene (GmRLK18-1) in locus Rfs2. An additional variant independently associated with SDS resistance was also found in this genomic region. Other peaks were within, or close to, sequences annotated as homologous to genes previously shown to be involved in plant disease resistance. The identified loci explained an average of 54.5% of the phenotypic variance measured by different disease assessment criteria.ConclusionsThis study identified multiple novel loci and refined the map locations of known loci related to SDS resistance. These insights into the genetic basis of SDS resistance can now be used to further enhance durable resistance to SDS in soybean. Additionally, the associations identified here provide a basis for further efforts to pinpoint causal variants and to clarify how the implicated genes affect SDS resistance in soybean.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-809) contains supplementary material, which is available to authorized users.
Highlights
Sudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance
The associations identified here provide a basis for further efforts to pinpoint causal variants and to clarify how the implicated genes affect SDS resistance in soybean
Compared with a previous study [33], these estimates showed that the overall genetic variation of the elite cultivars we studied represents about 80% diversity of soybean landraces
Summary
Sudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, two independent association panels of elite soybean cultivars, consisting of 392 and 300 unique accessions, respectively, were evaluated for SDS resistance in multiple environments and years. Most of what we know about the genetic architecture of SDS resistance is based on traditional quantitative trait locus (QTL) linkage mapping using biparental populations. A more specific strategy, genome-wide association (GWA) mapping, is a powerful complementary strategy for classical bi-parental linkage mapping to dissect complex traits and has been used with success in Arabidopsis [13], rice [14] and maize [15,16]. To the best of our knowledge, GWA mapping has not yet been employed to study any traits related to soybean disease resistance. Association mapping with released elite cultivars is more likely to identify superior resistance alleles that have been captured and accumulated by SCN or SDS breeding practices
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