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Journal of Integrative Agriculture  2022, Vol. 21 Issue (7): 1886-1902    DOI: 10.1016/S2095-3119(21)63653-5
Special Issue: 油料作物合辑Oil Crops
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses
PAN Wen-jing1*, HAN Xue2*, HUANG Shi-yu1, YU Jing-yao1, ZHAO Ying1, QU Ke-xin1, ZHANG Ze-xin1, YIN Zhen-gong1, QI Hui-dong1, YU Guo-long1, ZHANG Yong3, XIN Da-wei1, ZHU Rong-sheng1, LIU Chun-yan1, WU Xiao-xia1, JIANG Hong-wei1, HU Zhen-bang1, ZUO Yu-hu2, CHEN Qing-shan1, QI Zhao-ming1
1 College of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.China
2 Heilongjiang Bayi Agricultural University, Daqing 163000, P.R.China
3 Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161300, P.R.China
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本研究从历史数据以及公开文章中收集了57个与大豆种子可溶性糖含量相关的数量性状位点(QTLs)。通过meta、overview和共线性分析来细化QTL区间,共得到8个共有QTL。使用染色体片段代换系(CSSLs)群体对这些共有QTL进行验证,选择了两个包含共有QTL和有导入片段的品系:其中一个与共有QTL区间相关的一个品系可溶性糖含量较高,另一个品系可溶性糖含量较低。在种子发育的早期、中期和晚期对这两个品系进行转录组测序,分别鉴定出158个、109个和329个差异表达基因。通过重测序数据和共有QTL区间分析,在野生大豆遗传导入片段中鉴定出3个候选基因Glyma.19G146800Glyma.19G122500Glyma.19G128500。通过对两个CSSL亲本SN14和ZYD00006的序列比对,发现Glyma.19G122500编码序列发生单核苷酸多态性(SNP)突变,导致氨基酸序列发生非同义突变,影响了蛋白质结构。基于这一SNP,我们开发了竞争性等位基因特异性PCR (KASP)标记,并将其用于CSSL品系的鉴定。这些结果为进一步鉴定大豆可溶性糖相关基因及进一步育种奠定了基础

Abstract  Soluble sugar content in seeds is an important quality trait of soybean.  In this study, 57 quantitative trait loci (QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers.  After meta-overview-collinearity integrated analysis to refine QTL intervals, eight consensus QTLs were identified.  To further verify the consensus QTLs, a population of chromosome segment substitution lines (CSSLs) was analyzed.  Two lines containing fragments covering the regions of consensus QTLs and the recurrent parent were selected: one line showed high soluble sugar contents associated with a consensus QTL fragment, and the other line showed low soluble sugar contents.  Transcriptome sequencing was conducted for these two lines at the early, middle, and late stages of seed development, which identified 158, 109 and 329 differentially expressed genes, respectively.  Based on the analyses of re-sequencing data of the CSSLs and the consensus QTL region, three candidate genes (Glyma.19G146800, Glyma.19G122500, and Glyma.19G128500) were identified in the genetic fragments introduced from wild soybean.  Sequence comparisons between the two CSSL parents SN14 and ZYD00006 revealed a single nucleotide polymorphism (SNP) mutation in the coding sequence of Glyma.19G122500, causing a non-synonymous mutation in the amino acid sequence that affected the predicted protein structure.  A Kompetitive allele-specific PCR (KASP) marker was developed based on this SNP and used to evaluate the CSSLs.  These results lay the foundation for further research to identify genes related to soluble sugar contents in soybean seeds and for future soybean breeding.
Keywords:  soybean soluble sugar contents        consensus QTL        meta-overview-collinearity integrated analysis        population validation        RNA-seq and candidate gene mining  
Received: 15 October 2020   Accepted: 19 February 2021
Fund: This study was financially supported by the National Natural Science Foundation of China (31701449, 31971968, 31971899, and 31501332), the Natural Science Foundation of Heilongjiang, China (QC2017013), the National Key R&D Program of China (2016YFD0100500, 2016YFD0100300 and 2016YFD0100201-21), the Special Financial Aid to Post-Doctor Research Fellow in Heilongjiang, China (LBH-TZ1714), the International Postdoctoral Exchange Fellowship Program of China Postdoctoral Council (20180004), the China Post Doctoral Project, China (2015M581419), the Post-Doctoral Project of Northeast Agricultural University, China (NEAUBH-19002), the Heilongjiang Funds for Distinguished Young Scientists, China (JC2016004 and JC2017006), the Dongnongxuezhe Project, China (to Chen Qingshan), and the the Backbone of Young Talent Scholar Project (to Qi Zhaoming, 18XG01) of Northeast Agricultural University, China.

About author:  Correspondence CHEN Qing-shan, Tel: +86-451-55191945, E-mail:; ZUO Yu-hu, E-mail:; QI Zhao-ming, Tel: +86-451-55191945, E-mail: * These authors contributed equally to this study.

Cite this article: 

PAN Wen-jing, HAN Xue, HUANG Shi-yu, YU Jing-yao, ZHAO Ying, QU Ke-xin, ZHANG Ze-xin, YIN Zhen-gong, QI Hui-dong, YU Guo-long, ZHANG Yong, XIN Da-wei, ZHU Rong-sheng, LIU Chun-yan, WU Xiao-xia, JIANG Hong-wei, HU Zhen-bang, ZUO Yu-hu, CHEN Qing-shan, QI Zhao-ming. 2022. Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses. Journal of Integrative Agriculture, 21(7): 1886-1902.

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