AUTHOR=Liu Jinyang , Lin Yun , Chen Jingbin , Yan Qiang , Xue Chenchen , Wu Ranran , Chen Xin , Yuan Xingxing 

TITLE=Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.997988

DOI=10.3389/fpls.2022.997988

ISSN=1664-462X

ABSTRACT=<p>Although mungbean (<italic>Vigna radiata</italic> (L.) R. Wilczek) is an important legume crop, its seed yield is relatively low. To address this issue, here 196 accessions with 3,607,508 SNP markers were used to identify quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and their candidate genes for seed length (SL), seed width, and 100-seed weight (HSW) in two environments. As a result, 98 QTNs and 20 QEIs were identified using 3VmrMLM, while 95, &gt;10,000, and 15 QTNs were identified using EMMAX, GEMMA, and CMLM, respectively. Among 809 genes around these QTNs, 12 were homologous to known seed-development genes in rice and <italic>Arabidopsis thaliana</italic>, in which 10, 2, 1, and 0 genes were found, respectively, by the above four methods to be associated with the three traits, such as <italic>VrEmp24/25</italic> for SL and <italic>VrKIX8</italic> for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and <italic>VrKIX8</italic>, <italic>VrPAT14</italic>, <italic>VrEmp24/25</italic>, <italic>VrIAR1</italic>, <italic>VrBEE3</italic>, <italic>VrSUC4</italic>, and <italic>Vrflo2</italic> were further verified by RT-qPCR. Among 65 genes around these QEIs, <italic>VrFATB</italic>, <italic>VrGSO1</italic>, <italic>VrLACS2</italic>, and <italic>VrPAT14</italic> were homologous to known seed-development genes in <italic>A. thaliana</italic>, although new experiments are necessary to explore these novel GEI-trait associations. In addition, 54 genes were identified in comparative genomics analysis to be associated with seed development pathway, in which <italic>VrKIX8</italic>, <italic>VrABA2</italic>, <italic>VrABI5</italic>, <italic>VrSHB1</italic>, and <italic>VrIKU2</italic> were also identified in genome-wide association studies. This result provided a reliable approach for identifying seed-size-related genes in mungbean and a solid foundation for further molecular biology research on seed-size-related genes.</p>