期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 21, 期 3, 页码 -出版社
MDPI
DOI: 10.3390/ijms21031040
关键词
Soybean; seed shape; seed size; QTL mapping; high-density genetic map; QTL hotspot; epistatic interactions; candidate genes
资金
- National Key Research and Development Program [2018YFD0201006]
- National Natural Science Foundation of China [31871646, 31571691]
- MOE Program for Changjiang Scholars and Innovative Research Team in University [PCSIRT_17R55]
- Fundamental Research Funds for the Central Universities [KYT201801]
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP) Program
Seed size and shape are important traits determining yield and quality in soybean. However, the genetic mechanism and genes underlying these traits remain largely unexplored. In this regard, this study used two related recombinant inbred line (RIL) populations (ZY and K3N) evaluated in multiple environments to identify main and epistatic-effect quantitative trait loci (QTLs) for six seed size and shape traits in soybean. A total of 88 and 48 QTLs were detected through composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 15 QTLs were common among both methods; two of them were major (R-2 > 10%) and novel QTLs (viz., qSW-1-1(ZN) and qSLT-20-1(K3N)). Additionally, 51 and 27 QTLs were identified for the first time through CIM and MCIM methods, respectively. Colocalization of QTLs occurred in four major QTL hotspots/clusters, viz., QTL Hotspot A, QTL Hotspot B, QTL Hotspot C, and QTL Hotspot D located on Chr06, Chr10, Chr13, and Chr20, respectively. Based on gene annotation, gene ontology (GO) enrichment, and RNA-Seq analysis, 23 genes within four QTL Hotspots were predicted as possible candidates, regulating soybean seed size and shape. Network analyses demonstrated that 15 QTLs showed significant additive x environment (AE) effects, and 16 pairs of QTLs showing epistatic effects were also detected. However, except three epistatic QTLs, viz., qSL-13-3(ZY), qSL-13-4(ZY), and qSW-13-4(ZY), all the remaining QTLs depicted no main effects. Hence, the present study is a detailed and comprehensive investigation uncovering the genetic basis of seed size and shape in soybeans. The use of a high-density map identified new genomic regions providing valuable information and could be the primary target for further fine mapping, candidate gene identification, and marker-assisted breeding (MAB).
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