Abstract
Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes Glyma.16g141200, Glyma.16g141500, and Glyma.16g076600, identified in our previous study by quantitative trait locus (QTL) mapping and whole-genome resequencing, were selected for marker development. The whole-genome resequencing of three parental lines (one shattering-tolerant and two shattering-susceptible) identified single nucleotide polymorphism (SNP) and/or insertion/deletion (InDel) regions within or near the selected genes. Two SNPs and one InDel were converted to Kompetitive Allele-Specific PCR (KASP) and InDel markers, respectively. The accuracy of the markers was examined in the two recombinant inbred line populations used for the QTL mapping, as well as the 120 varieties and elite lines, through allelic discrimination and phenotyping by the oven-drying method. Both types of markers successfully discriminated the pod shattering-tolerant and shattering-susceptible genotypes. The prediction accuracy, which was as high as 90.9% for the RILs and was 100% for the varieties and elite lines, also supported the accuracy and usefulness of these markers. Thus, the markers can be used effectively for genetic and genomic studies and the marker-assisted selection for pod-shattering tolerance in soybean.
Highlights
Introduction published maps and institutional affilSoybean is an economically important crop worldwide
Glyma.16g076600, which are all candidate genes for pod-shattering that we identified within the quantitative trait locus (QTL) detected previously [17]
Two RIL populations, as well as 120 soybean varieties and elite lines used in this study, were developed in our institute according to the cultivation methods of the Agricultural Science Technology Standards for Investigation (Rural Development Administration, Jeonju, Korea) and they comply with the guidelines and legislation of Korea
Summary
Introduction published maps and institutional affilSoybean is an economically important crop worldwide. Pod-shattering is the opening of the mature pod along the dorsal or ventral suture with the dispersal of the seeds [3]. While it is essential for seed dispersal in wild species, in domesticated crops it can cause significant yield loss [4]. These losses vary from negligible to significant, depending on the harvest delay, the environmental conditions, and/or the tolerance of the variety [5,6,7]
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