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Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat

文献类型： 外文期刊

作者： Cheng, Hong 1 ; Kong, Lingpeng 1 ; Zhu, Kun 3 ; Zhao, Hang 1 ; Li, Xiuli 1 ; Zhang, Yanwen 1 ; Ning, Weidong 1 ; Jiang, Mei 1 ; Song, Bo 1 ; Cheng, Shifeng 1 ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Genome Anal Lab,M, Shenzhen 518100, Guangdong, Peoples R China

2.Northwest A&F Univ, Coll Grassland Agr, Yangling 712100, Shaanxi, Peoples R China

3.Henan Univ, Sch Life Sci, State Key Lab Crop Stress Adaptat & Improvement, 379 Mingli Rd North Sect, Zhengzhou 450046, Henan, Peoples R China

关键词： Wheat; Pangenome; Structural variation; Centromere plasticity; Growth habit

期刊名称：JOURNAL OF GENETICS AND GENOMICS （ 影响因子：7.1； 五年影响因子：6.4 ）

ISSN： 1673-8527

年卷期： 2025 年 52 卷 6 期

页码：

收录情况： SCI

摘要： Increasing number of structural variations (SVs) have been identified as causative mutations for diverse agronomic traits. However, the systematic exploration of SVs quantity, distribution, and contribution in wheat was lacking. Here, we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size, gene number, and TE component, which indicates their representativeness of wheat genetic diversity. Pan-gene analyses uncover 140,261 distinct gene families, of which only 23.2 % are shared in all accessions. Moreover, we build a-16.15 Gb graph pangenome containing 695,897 bubbles, intersecting 5132 genes and 230,307 cis-regulatory regions. Pairwise genome comparisons identify-1,978,221 non-redundant SVs and 497 SV hotspots. Notably, the density of bubbles as well as SVs show remarkable aggregation in centromeres, which probably play an important role in chromosome plasticity and stability. As for functional SVs exploration, we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups. Additionally, several reported functional genes in wheat display complex structural graphs, for example, PPD-A1, VRT-A2, and TaNAAT2-A. These findings deepen our understanding of wheat genetic diversity, providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat. Copyright (c) 2025, The Authors. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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