J Integr Plant Biol.

• Research Article • Previous Articles    

Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China

Xiaoshuai Hao1, Xinyang Hu1, Yongpeng Pan1, Qi Zhang1, Ran Ou1, Fenfen Jiang1, Fangdong Liu1,2,3,4,5,6, Jiaoping Zhang1,2,3,4,5,6, Wubin Wang1,2,3,4,5,6, Guangnan Xing1,2,3,4,5,6, Junyi Gai1,2,3,4,5,6* and Jianbo He1,2,3,4,5,6*   

  1. 1. MARA National Center for Soybean Improvement (General), Nanjing Agricultural University, Nanjing 210095, China
    2. Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing 210095, China
    3. MARA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing 210095, China
    4. National Innovation Platform for Industry‐Education Integration of Soybean Bio‐breeding, Nanjing Agricultural University, Nanjing 210095, China
    5. State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
    6. Jiangsu Key Laboratory of Soybean Biotechnology and Intelligent Breeding, Nanjing Agricultural University, Nanjing 210095, China
    *Correspondences: Jianbo He (hjbxyz@gmail.com, Dr. He is fully responsible for the distribution of all materials associated with this article); Junyi Gai (sri@njau.edu.cn)
  • Received:2025-10-10 Accepted:2026-02-12 Online:2026-03-16
  • Supported by:
    This work was supported by the National Key Research and Development Program of China (2024YFD1201400), the Local Science and Technology Development Fund Guided by the Central Government of Shandong Province (YDZX2023102), the Zhongshan Biological Breeding Laboratory (ZSBBL‐KY2023‐03), the Key Science & Technology Project of Anhui Province (202423l10050012), the MOE 111 Project (B08025), the MOA CARS‐04 program, and the Sanya institute of NAU (NAUSY‐ZZ02).

Abstract: The subgenus Soja, including annual wild (Glycine soja) and cultivated soybean (Glycine max), is the primary germplasm source of soybeans. We analyzed the genome constitution of 750 wild and cultivated accessions from the Chinese Soybean Germplasm Population (CSGP), covering ~20.42% genic and ~79.58% intergenic regions. Most previous genomic studies focused on gene compositions and functions, with intergenic regions being non‐emphasized yet. Our results showed: (i) We defined 48,465 gene blocks (2–23 alleles/gene block) in the genic region. For intergenic region partitioning, the linkage‐disequilibrium (LD) confidence interval (CI) method performed the best, identifying 137,104 SNP LD blocks (SNPLDBs, 2–24 haplotypes/SNPLDB). (ii) Wild and cultivated accessions shared 98.5%/80.9% genes/alleles and 88.0%/80.8% SNPLDBs/haplotypes, indicating high wild genomic contribution to the cultivated genome; genic and intergenic regions exhibit distinct allele/haplotype dynamics during domestication. (iii) We proposed the three‐case restricted two‐stage multi‐locus multi‐allele genome‐wide association study (three‐case RTM‐GWAS), identifying 82 day‐to‐flowering (DTF) main‐effect genes and 47 intergenic‐SNPLDB‐impacted genes (by 34 SNPLDBs) (total 129 genes, 746 alleles). These explained 98.87% of phenotypic variance (PV), with main‐effect and SNPLDB‐impacted genes accounting for 68.61% and 30.26% PV, respectively; gene‐allele(s) impacted by SNPLDB‐haplotype (one/both sides) were also identified. (iv) Domestication process excluded more large‐effect positive alleles that shorten DTF in cultivated accessions, enhancing DTF's transgressive recombination potential in earliness. This study provides insights into genic/intergenic genome regions, offering a novel understanding of soybean functional genomics.

Key words: annual wild soybean Glycine soja Sieb. & Zucc, cultivated soybean Glycine max (L.) Merr, days to flowering, gene function, intergenic impact, linkage disequilibrium, three‐case RTM‐GWAS

Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
No. 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: +86 10 6283 6133 Fax: +86 10 8259 2636 E-mail: jipb@ibcas.ac.cn
Copyright © 2026 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q
备案号:京ICP备16067583号-22