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Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean

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. The two association panels were genotyped with 52,041 and 5,361 single nucleotide polymorphisms (SNPs), respectively.

Wen Z, Tan R, Yuan J, Bales C, Du W, Zhang S, Chilvers MI, Schmidt C, Song Q, Cregan PB, Wang D.

 

BMC Genomics. 2014 Sep 23;15(1):809. [Epub ahead of print]

http://www.ncbi.nlm.nih.gov/pubmed/25249039

Abstract

BACKGROUND:

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. 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.Result: A 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.

CONCLUSIONS:

This 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.

 

Figure 3 Genome-wide association study of SDS in the two association panels. (a) Manhattan plots of the simple model for DX in the association panel P1. The − log10 P-values from a genome-wide scan are plotted against the position on each of the 20 chromosomes. The horizontal red line indicates the genome-wide significance threshold (FDR < 0.05).

(b) Quantile-quantile (QQ) plot of simple model for DX in the association panel P1.

(c) Manhattan plots of MLM for DX in association panel P1, as in a.

(d) Quantile-quantile plot of MLM for DX in association panel P1.

(e) Manhattan plots of the simple model for DX in association panel P2, as in a.

(f) Quantile-quantile plot of simple model for DX in the association panel P2.

(g) Manhattan plots of MLM for DX in association panel P2, as in a.

(h) Quantile-quantile plot of MLM for DX in association panel P2

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