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Article

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

by
Tengfei Zhang
1,†,
Tingting Wu
1,†,
Liwei Wang
1,†,
Bingjun Jiang
1,
Caixin Zhen
1,
Shan Yuan
1,
Wensheng Hou
1,2,
Cunxiang Wu
1,
Tianfu Han
1 and
Shi Sun
1,*
1
Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2
National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(23), 5915; https://doi.org/10.3390/ijms20235915
Submission received: 26 September 2019 / Revised: 21 November 2019 / Accepted: 21 November 2019 / Published: 25 November 2019
(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)
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Abstract

Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10−4). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis.
Keywords: soybean; protein content; oil content; quantitative trait loci (QTL); linkage analysis; genome-wide association study (GWAS); candidate genes soybean; protein content; oil content; quantitative trait loci (QTL); linkage analysis; genome-wide association study (GWAS); candidate genes

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MDPI and ACS Style

Zhang, T.; Wu, T.; Wang, L.; Jiang, B.; Zhen, C.; Yuan, S.; Hou, W.; Wu, C.; Han, T.; Sun, S. A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content. Int. J. Mol. Sci. 2019, 20, 5915. https://doi.org/10.3390/ijms20235915

AMA Style

Zhang T, Wu T, Wang L, Jiang B, Zhen C, Yuan S, Hou W, Wu C, Han T, Sun S. A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content. International Journal of Molecular Sciences. 2019; 20(23):5915. https://doi.org/10.3390/ijms20235915

Chicago/Turabian Style

Zhang, Tengfei, Tingting Wu, Liwei Wang, Bingjun Jiang, Caixin Zhen, Shan Yuan, Wensheng Hou, Cunxiang Wu, Tianfu Han, and Shi Sun. 2019. "A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content" International Journal of Molecular Sciences 20, no. 23: 5915. https://doi.org/10.3390/ijms20235915

APA Style

Zhang, T., Wu, T., Wang, L., Jiang, B., Zhen, C., Yuan, S., Hou, W., Wu, C., Han, T., & Sun, S. (2019). A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content. International Journal of Molecular Sciences, 20(23), 5915. https://doi.org/10.3390/ijms20235915

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