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

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

doi:10.1016/j.jgg.2025.03.015

Volume 52 Issue 6

Jun. 2025

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Article Navigation > Journal of Genetics and Genomics > 2025 > 52(6): 774-785

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

doi: 10.1016/j.jgg.2025.03.015

a. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518100, China;
b. College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China;
c. State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, No. 379 Mingli Road (North Section), Zhengzhou, Henan 450046, China

Funds:

This work was supported by the National Key Research and Development Program of China (2023YFF1000100 and 2023YFA0914601) and the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (PT202101-01).

Received Date: 2024-11-28
Accepted Date: 2025-03-27
Rev Recd Date: 2025-03-25

Available Online: 2025-07-11

Publish Date: 2025-04-04

Abstract

Abstract

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.
- Wheat,
- Pangenome,
- Structural variation,
- Centromere plasticity,
- Growth habit

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