AUTHOR=Li Yuan , Yang Kai , Yang Wei , Chu Liwei , Chen Chunhai , Zhao Bo , Li Yisong , Jian Jianbo , Yin Zhichao , Wang Tianqi , Wan Ping 

TITLE=Identification of QTL and Qualitative Trait Loci for Agronomic Traits Using SNP Markers in the Adzuki Bean

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.00840

DOI=10.3389/fpls.2017.00840

ISSN=1664-462X

ABSTRACT=<p>The adzuki bean (<italic>Vigna angularis</italic>) 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 F<sub>2</sub> 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 <italic>VaFld4.1</italic> (PEVs 71.3%), co-segregating with SNP marker s690-144110, and <italic>VaFld4.2</italic> (PEVs 67.6%) at a 0.974 cM genetic distance from the SNP marker s165-116310. Three QTLs for seed number per pod (<italic>Snp3.1, Snp3.2</italic>, and <italic>Snp4.1</italic>) were mapped on chromosomes 3 and 4. One QTL <italic>VaSdt4.1</italic> 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, <italic>VaAGL, VaPhyE</italic>, and <italic>VaAP2</italic>, were identified for flowering time and pod maturity. <italic>VaAGL</italic> encodes an agamous-like MADS-box protein of 379 amino acids. <italic>VaPhyE</italic> encodes a phytochrome E protein of 1,121 amino acids. Four phytochrome genes (<italic>VaPhyA1, VaPhyA2, VaPhyB</italic>, and <italic>VaPhyE</italic>) were identified in the adzuki bean genome. We found candidate genes <italic>VaAP2/ERF.81</italic> and <italic>VaAP2/ERF.82</italic> of SD100WT, <italic>VaAP2-s4</italic> of SDT, and <italic>VaAP2/ERF.86</italic> of LFMW. A candidate gene <italic>VaUGT</italic> 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.</p>