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A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content
Article

High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.)

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Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China
2
Shaanxi Key Laboratory of Chinese Jujube; College of Life Science, Yan’an University, Yan’an 716000, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(3), 1040; https://doi.org/10.3390/ijms21031040
Received: 27 December 2019 / Revised: 30 January 2020 / Accepted: 1 February 2020 / Published: 4 February 2020
(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)
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 (R2 > 10%) and novel QTLs (viz., qSW-1-1ZN and qSLT-20-1K3N). 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-13-3ZY, qSL-13-4ZY, and qSW-13-4ZY, 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). View Full-Text
Keywords: Soybean; seed shape; seed size; QTL mapping; high-density genetic map; QTL hotspot; epistatic interactions; candidate genes Soybean; seed shape; seed size; QTL mapping; high-density genetic map; QTL hotspot; epistatic interactions; candidate genes
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MDPI and ACS Style

Hina, A.; Cao, Y.; Song, S.; Li, S.; Sharmin, R.A.; Elattar, M.A.; Bhat, J.A.; Zhao, T. High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.). Int. J. Mol. Sci. 2020, 21, 1040. https://doi.org/10.3390/ijms21031040

AMA Style

Hina A, Cao Y, Song S, Li S, Sharmin RA, Elattar MA, Bhat JA, Zhao T. High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.). International Journal of Molecular Sciences. 2020; 21(3):1040. https://doi.org/10.3390/ijms21031040

Chicago/Turabian Style

Hina, Aiman, Yongce Cao, Shiyu Song, Shuguang Li, Ripa A. Sharmin, Mahmoud A. Elattar, Javaid A. Bhat, and Tuanjie Zhao. 2020. "High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.)" International Journal of Molecular Sciences 21, no. 3: 1040. https://doi.org/10.3390/ijms21031040

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