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; Huan Wang; Ximeng Yang; Bo Chen; Ruqian Wei; Qibin Ma; Yanbo Cheng; Hai Nian

doi:10.1016/j.jia.2023.08.011

Journal of Integrative Agriculture (Jan 2025)

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,
Huan Wang,
Ximeng Yang,
Bo Chen,
Ruqian Wei,
Qibin Ma,
Yanbo Cheng,
Hai Nian

Affiliations

Jia Jia: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
Huan Wang: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
Ximeng Yang: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
Bo Chen: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
Ruqian Wei: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
Qibin Ma: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
Yanbo Cheng: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China; Correspondence Yanbo Cheng, Hai Nian
Hai Nian: Key Laboratory of Plant Molecular Breeding of Guangdong Province/College of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China; Correspondence Yanbo Cheng, Hai Nian

DOI: https://doi.org/10.1016/j.jia.2023.08.011
Journal volume & issue: Vol. 24, no. 1
pp. 85 – 100

Abstract

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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.

Published in Journal of Integrative Agriculture

ISSN: 2095-3119 (Print); 2352-3425 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Agriculture: Agriculture (General)
Website: https://www.journals.elsevier.com/journal-of-integrative-agriculture

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