Abstract
The adzuki bean (Vigna angularis) is an important grain legume. Fine mapping of quantitative trait loci (QTL) and qualitative trait genes plays an important role in gene cloning, molecular-marker-assisted selection (MAS), and trait improvement. However, the genetic control of agronomic traits in the adzuki bean remains poorly understood. Single-nucleotide polymorphisms (SNPs) are invaluable in the construction of high-density genetic maps. We mapped 26 agronomic QTLs and five qualitative trait genes related to pigmentation using 1,571 polymorphic SNP markers from the adzuki bean genome via restriction-site-associated DNA sequencing of 150 members of an F2 population derived from a cross between cultivated and wild adzuki beans. We mapped 11 QTLs for flowering time and pod maturity on chromosomes 4, 7, and 10. Six 100-seed weight (SD100WT) QTLs were detected. Two major flowering time QTLs were located on chromosome 4, firstly VaFld4.1 (PEVs 71.3%), co-segregating with SNP marker s690-144110, and VaFld4.2 (PEVs 67.6%) at a 0.974 cM genetic distance from the SNP marker s165-116310. Three QTLs for seed number per pod (Snp3.1, Snp3.2, and Snp4.1) were mapped on chromosomes 3 and 4. One QTL VaSdt4.1 of seed thickness (SDT) and three QTLs for branch number on the main stem were detected on chromosome 4. QTLs for maximum leaf width (LFMW) and stem internode length were mapped to chromosomes 2 and 9, respectively. Trait genes controlling the color of the seed coat, pod, stem and flower were mapped to chromosomes 3 and 1. Three candidate genes, VaAGL, VaPhyE, and VaAP2, were identified for flowering time and pod maturity. VaAGL encodes an agamous-like MADS-box protein of 379 amino acids. VaPhyE encodes a phytochrome E protein of 1,121 amino acids. Four phytochrome genes (VaPhyA1, VaPhyA2, VaPhyB, and VaPhyE) were identified in the adzuki bean genome. We found candidate genes VaAP2/ERF.81 and VaAP2/ERF.82 of SD100WT, VaAP2-s4 of SDT, and VaAP2/ERF.86 of LFMW. A candidate gene VaUGT related to black seed coat color was identified. These mapped QTL and qualitative trait genes provide information helpful for future adzuki bean candidate gene cloning and MAS breeding to improve cultivars with desirable growth periods, yields, and seed coat color types.
Highlights
The adzuki bean (Vigna angularis) is an important diploid pulse crop (2n = 2x = 22) that is rich in digestible protein with extremely low fat content (Lin, 2002)
Our results elucidate how genetic features control the agronomic traits of the adzuki bean, and the major quantitative trait loci (QTL) and genes that we have identified will expedite marker-assisted selection (MAS) breeding and the improvement of these traits in adzuki bean
Gene mapping and QTL detection are very useful for gene cloning, MAS breeding, and trait improvement; only a few studies have been performed using SSR markers in adzuki bean (Isemura et al, 2007; Kaga et al, 2008)
Summary
The adzuki bean (Vigna angularis) is an important diploid pulse crop (2n = 2x = 22) that is rich in digestible protein with extremely low fat content (Lin, 2002). It was domesticated about 12,000 years ago in China (Liu et al, 2013), and is cultivated today in over 30 countries of the world, principally those of eastern and northern Asia (Tomooka et al, 2002; Kramer et al, 2012). Germination efficacy, seed size, and lower stem length mapped to LGs 1 and 2. The QTLs of LGs 7 and 9 were associated with upper-stem length, maximum leaf size, and pod and seed sizes (Isemura et al, 2007)
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