Identification of long InDels through whole genome resequencing to fine map qIF05-1 for seed isoflavone content in soybean (Glycine max L. Merr.)

doi:10.1016/j.jia.2023.08.011

Journal of Integrative Agriculture

2025, Vol. 24

Issue (1): 85-100 DOI: 10.1016/j.jia.2023.08.011

Crop Science

Advanced Online Publication | Current Issue | Archive | Adv Search

Identification of long InDels through whole genome resequencing to fine map qIF05-1 for seed isoflavone content in soybean (Glycine max L. Merr.)

Jia Jia^{1, 2, 3*}, Huan Wang^{1, 2, 3*}, Ximeng Yang^{1, 2, 3}, Bo Chen^{1, 2, 3}, Ruqian Wei^{1, 2, 3}, Qibin Ma^{1, 2, 3}, Yanbo Cheng^{1, 2, 3#}, Hai Nian^{1, 2, 3#}

¹Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China

²State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China

³Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China

Highlights
● This study identified a novel bHLH transcription factor gene, GmEGL3, as a potential candidate gene of the qIF05-1 locus for seed isoflavone content through comprehensive genetic and functional analysis.

Abstract
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摘要

大豆异黄酮是一种次生代谢物，可以为人体提供丰富的营养保健价值。在本实验室前期的研究中，利用一个由“华春2×瓦窑黄豆”杂交衍生的一个重组自交系群体，在大豆5号染色体上鉴定到一个控制大豆籽粒异黄酮含量的主效位点qIF05-1。本研究利用Illumina Solexa测序系统对大豆双亲亲本进行了深度的全基因组重测序分析，最终在华春2号和瓦窑黄豆基因组间共鉴定出63099个长片段InDel变异（≥15 bp），这些InDels不均匀地分布大豆的20条染色体上，数量从12号染色体的1826个到18号染色体4544个不等。鉴定到10002个（占总数量的15.85%）长片段InDel变异位于基因区，其中有1139个大效应长InDel变异能够导致蛋白质序列的截断或延长从而影响基因的功能。为了进一步应用长片段InDels进行大豆的遗传分析，在qIF05-1定位区间内检测到68个长InDel变异位点。通过子代重组实验结合基因型分析研究，将qIF051位点的基因组区间缩小到了102.2 kb的基因组区域，该区间包含12个基因。进一步结合RNA-seq数据分析、基因组序列比较和拟南芥异位表达功能验证，一个bHLH转录因子家族基因Glyma.05G208300（简称GmEGL3）被推测为可能是qIF05-1位点的候选基因。综上，通过鉴定和开发长长片段InDel标记再一次说明这是一种重要性状精细定位

Abstract

Soybean seed isoflavones are a type of secondary metabolites that can provide health and nutrition benefits for humans. In our previous study, a stable quantitative trait locus (QTL) qIF05-1 controlling the seed isoflavone content in soybean was detected on chromosome (Chr.) 05 in a recombinant inbred line (RIL) population from a cross of Huachun 2×Wayao. In this study, the parental lines were re-sequenced using the Illumina Solexa System with deep coverage. A total of 63,099 polymorphic long insertions and deletions (InDels) (≥15 bp) were identified between the parents Huachun 2 and Wayao. The InDels were unevenly distributed on 20 chromosomes of soybean, varying from 1,826 in Chr. 12 to 4,544 in Chr. 18. A total of 10,002 long InDels (15.85% of total) were located in genic regions, including 1,139 large-effect long InDels which resulted in truncated or elongated protein sequences. In the qIF05-1 region, 68 long InDels were detected between the two parents. Using a progeny recombination experiment and genotype analysis, the qIF05-1 locus was mapped into a 102.2 kb genomic region, and this region contained 12 genes. By RNA-seq data analysis, genome sequence comparison and functional validation through ectopic expression in Arabidopsis thaliana, Glyma.05G208300 (described as GmEGL3), which is a basic helix-loop-helix (bHLH) transcription factor in plants, emerged as the most likely confirmed gene in qIF05-1. These long InDels can be used as a type of complementary genetic method for QTL fine mapping, and they can facilitate genetic studies and molecular-assisted selection breeding in soybean.

Keywords: soybean seed isoflavone content whole genome re-sequencing long InDels fine map

Received: 10 May 2023 Accepted: 12 July 2023

Fund:

This work was supported by the China Agriculture Research System of MOF and MARA (CARS-04-PS12), the Research and Development Program in the Key-Areas of Guangdong Province, China (2020B020220008), and the Guangdong Agricultural Research System, China (2023KJ136-03).

About author: #Correspondence Yanbo Cheng, E-mail: ybcheng@scau.edu.cn; Hai Nian, E-mail: hnian@scau.edu.cn * These authors contributed equally to this study.

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Jia Jia, Huan Wang, Ximeng Yang, Bo Chen, Ruqian Wei, Qibin Ma, Yanbo Cheng, Hai Nian. 2025. Identification of long InDels through whole genome resequencing to fine map qIF05-1 for seed isoflavone content in soybean (Glycine max L. Merr.) . Journal of Integrative Agriculture, 24(1): 85-100.

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