Abstract
Key messageWe constructed a high-density genetic linkage map comprising 4,593 SLAF markers using specific-locus amplified fragment sequencing and identified six quantitative trait loci for pod dehiscence resistance in soybean.Pod dehiscence is necessary for propagation in wild soybean (Glycine soja). It is a major component causing yield losses in cultivated soybean, however, and thus, cultivated soybean varieties have been artificially selected for resistance to pod dehiscence. Detecting quantitative trait loci (QTLs) related to pod dehiscence is required for molecular marker-assisted selection for breeding new varieties with pod dehiscence resistance. In this study, we constructed a high-density genetic linkage map using 260 recombinant inbred lines derived from the cultivars of Heihe 43 (pod-indehiscent) (ZDD24325) and Heihe 18 (pod-dehiscent) (ZDD23620). The map contained 4953 SLAF markers spanning 1478.86 cM on 20 linkage groups with an average distance between adjacent markers of 0.53 cM. In total, six novel QTLs related to pod dehiscence were mapped using inclusive composite interval mapping, explaining 7.22–24.44% of the phenotypic variance across 3 years, including three stable QTLs (qPD01, qPD05-1 and qPD08-1), that had been validated by developing CAPS/dCAPS markers. Based on the SNP/Indel and significant differential expression analyses of two parents, seven genes were selected as candidate genes for future study. The high-density map, three stable QTLs and their molecular markers will be helpful for map-based cloning of pod dehiscence resistance genes and marker-assisted selection of pod dehiscence resistance in soybean breeding.
Highlights
Pod dehiscence is necessary for spreading seeds of wild plant species that bear seeds in pods and allows wild plants to introduce their progeny into a broad range of environments (Fuller 2007)
There were 398,386 controlled sequencing reads that were used to evaluate the accuracy of library construction; these reads were compared with the reference soybean genome
Compared with the soybean reference genome, we identified a total of 6834 single-nucleotide polymorphisms (SNPs), of which 4576 were transition type (Tri) and 2258 were the transversion type (Trv) (Table 2)
Summary
Pod dehiscence is necessary for spreading seeds of wild plant species that bear seeds in pods and allows wild plants to introduce their progeny into a broad range of environments (Fuller 2007). Multiple studies have identified major QTLs for pod dehiscence in soybean using recombinant inbred lines (RILs) with RFLP (Bailey et al 1997) and SSR markers (Funatsuki et al 2006). These studies have shown that pod dehiscence is dominated by several major and minor QTLs. Due to the various genetic backgrounds in different soybean populations, pod dehiscence was found to be controlled by a single recessive major gene or multiple genes (Tsuchiya 1986, 1987; Kang et al 2005; Funatsuki et al 2008; Yamada et al 2009). Using SSR markers, three novel minor QTLs for pod dehiscence were confirmed on chromosomes 5, 10 and 14 from two sets of RILs (Kang et al 2009)
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