QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max)

Abstract

Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred line (RIL) populations derived from an elite cultivar having pod shattering tolerance, namely “Daewonkong”, and to predict novel candidate QTL/genes involved in pod shattering based on their allele patterns. We found several QTLs with more than 10% phenotypic variance explained (PVE) on seven different chromosomes and found a novel candidate QTL on chromosome 16 (qPS-DS16-1) from the allele patterns in the QTL region. Out of the 41 annotated genes in the QTL region, six were found to contain SNP (single-nucleotide polymorphism)/indel variations in the coding sequence of the parents compared to the soybean reference genome. Among the six potential candidate genes, Glyma.16g076600, one of the genes with known function, showed a highly differential expression levels between the tolerant and susceptible parents in the growth stages R3 to R6. Further, Glyma.16g076600 is a homolog of AT4G19230 in Arabidopsis, whose function is related to abscisic acid catabolism. The results provide useful information to understand the genetic mechanism of pod shattering and could be used for improving the efficiency of marker-assisted selection for developing varieties of soybeans tolerant to pod shattering.

Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean

“…For KASP markers, we selected the SNPs or InDel regions in the candidate genes of the major QTL [17] by comparing the DNA sequences of the tolerant parent Daewonkong (DW) and the susceptible parents Tawonkong (TW) and Saeolkong (SO). Of the five candidate genes from within the major QTL, three genes had five SNPs.…”

“…Previously, we reported a novel candidate gene Glyma.16g076600 related to abscisic acid (ABA) catabolism [17]. There were four SNPs, one insertion, and one deletion in the target region, causing amino acid changes (Table 2).…”

“…These regions were identified through linkage mapping using diverse molecular markers, including restriction fragment length polymorphism markers [10], simple-sequence repeat (SSR) markers [11][12][13], and high-density single nucleotide polymorphism (SNP) markers [14]. A few minor QTLs have been mapped on chromosomes 2, 5, 10, 14, and 19 by linkage mapping [10,11]; on chromosomes 1,4,6,8,9,11,17,18, and 20 through GWAS [15]; and on chromosomes 1, 5, 8, and 14 through linkage mapping using specific locus-amplified fragment sequencing [16]. We previously mapped major and minor QTLs on chromosome 16 and reported candidate genes for the pod-shattering tolerance in soybean [17].…”

“…A few minor QTLs have been mapped on chromosomes 2, 5, 10, 14, and 19 by linkage mapping [10,11]; on chromosomes 1,4,6,8,9,11,17,18, and 20 through GWAS [15]; and on chromosomes 1, 5, 8, and 14 through linkage mapping using specific locus-amplified fragment sequencing [16]. We previously mapped major and minor QTLs on chromosome 16 and reported candidate genes for the pod-shattering tolerance in soybean [17].…”

On-Farm Crop Diversity for Advancing Food Security and Nutrition

“…Many traits have been mapped to specific genes and as a result, more analyses are being conducted per unit of time that allow for more specific mapping of traits. Quantitative trait loci (QTL) mapping results provide useful information to understand the genetic mechanisms of important traits and improve the efficiency of marker-assisted selection and genomics-assisted breeding [112,113]. Taken together, existing genomics knowledge and tools may be used to overcome the constraints to the development of adapted varieties that combat malnutrition and climate change [114,115].…”