Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean
Although mungbean ( (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...
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Published in | Frontiers in plant science Vol. 13; p. 997988 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Switzerland
Frontiers Media S.A
13.10.2022
|
Subjects | |
Online Access | Get full text |
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Summary: | Although mungbean (
(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, >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
, 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
for SL and
for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and
,
,
,
,
,
, and
were further verified by RT-qPCR. Among 65 genes around these QEIs,
,
,
, and
were homologous to known seed-development genes in
, 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
,
,
,
, and
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. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Jia Wen, The University of North Carolina at Chapel Hill, United States; Youlu Yuan, Cotton Research Institute (CAAS), China This article was submitted to Technical Advances in Plant Science, a section of the journal Frontiers in Plant Science Edited by: Zhenyu Jia, University of California, Riverside, United States |
ISSN: | 1664-462X 1664-462X |
DOI: | 10.3389/fpls.2022.997988 |