Association mapping and genomic prediction for resistance to sudden death syndrome in early maturing soybean germplasm

Abstract

Sudden death syndrome (SDS), caused by Fusarium virguliforme, has spread to northern soybean growing regions in the US causing significant yield losses. The objectives of this study were to identify loci underlying variation in plant responses to SDS through association mapping (AM) and to assess prediction accuracy of genomic selection (GS) in a panel of early maturing soybean germplasm. A set of 282 soybean breeding lines was selected from the University of Minnesota soybean breeding program and then genotyped using a genome-wide panel of 1536 single-nucleotide polymorphism markers. Four resistance traits, root lesion severity (RLS), foliar symptom severity (FSS), root retention (RR), and dry matter reduction (DMR), were evaluated using soil inoculation in the greenhouse. AM identified significant peaks in genomic regions of known SDS resistance quantitative trait loci cqSDS001, cqRfs4, and SDS11-2. Additionally, two novel loci, one on chromosome 3 and another on chromosome 18, were tentatively identified. A ninefold cross-validation scheme was used to assess the prediction accuracy of GS for SDS resistance. The prediction accuracy of single-trait GS (ST-GS) was 0.64 for RLS, but less than 0.30 for RR, DMR, and FSS. Compared to ST-GS, none of multi-trait GS (MT-GS) models significantly improved the prediction accuracy due to weak correlations between the four traits. This study suggests both AM and GS hold promise for implementation in genetic improvement of SDS resistance in existing soybean breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-015-0324-3) contains supplementary material, which is available to authorized users.

Two Decades of Molecular Marker‐Assisted Breeding for Resistance to Soybean Sudden Death Syndrome

“…Therefore, more regulatory genes in the loci are yet to be identified (Fig. A more recent GWAS study with rigorous greenhouse assay data found many fewer QTL of which 8 were previously report and ony 3 might be new (Bao et al, 2015). Moreover, on chromosome 7 near a SCN resistant loci (Rzd, resistance to zygote death), a cluster of associations within 0.7 Mbp interval was repeatedly detected with DS, DI, and DX (Wen et al, 2014).…”

Genomic Selection for Yield and Seed Protein Content in Soybean: A Study of Breeding Program Data and Assessment of Prediction Accuracy

“…For soybean, studies have reported genomic selection accuracy for production traits, development traits, or resistance to pathogens ( Jarquín et al, 2014;Bao et al, 2015;Zhang et al, 2016). Jarquín et al (2014) reported the prediction accuracies for yield and other agronomic traits obtained using genotyping-by-sequencing data.…”

GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

“…It is interesting that this region was also associated with resistance to P. sojae . The region on the chromosome 17 has the same location with a QTL identified in GWAS for resistance to Fusarium virguliforme (Bao et al, 2015;Zhang et al, 2015). SNP marker Gm17.8109237 identified in this study has located approximately 4 Mb from SNP marker ss715611120_C_T identified by J.…”

“…GWAS is based on use of whole genome genotyping and a detailed phytopathological and morphological description of collections with a high level of genetic diversity (Klein, 2007). A survey of recent reports has shown successful use of GWAS for studying soybean resistance to fungal diseases (Bao et al, 2015;Iquira et al, 2015;Schneider et al, 2016;Qin et al, 2017).…”