数字农科院2.0

A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality

文献类型： 外文期刊

作者： Zhaoheng Zhang;Dan Liu;Binyong Li;Wenxi Wang;Jize Zhang;Mingming Xin;Zhaorong Hu;Jie Liu;Jinkun Du;Huiru Peng;Chenyang Hao;Xueyong Zhang;Zhongfu Ni;Qixin Sun;Weilong Guo;Yingyin Yao

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关键词： end-use quality;genomic prediction;k-mer;pangenome;seed-storage protein;wheat

期刊名称： Molecular Plant

ISSN： 1674-2052

年卷期： 2024 年 17 卷 7 期

页码：

收录情况： SCIE（2024版） ; ; CSCD（2023-2024年度） ; ; 科技核心（2024版）

摘要： Wheat is a staple food for more than 35% of the world's population, with wheat flour used to make hundreds of baked goods. Superior end-use quality is a major breeding target; however, improving it is especially time-consuming and expensive. Furthermore, genes encoding seed-storage proteins (SSPs) form multi-gene families and are repetitive, with gaps commonplace in several genome assemblies. To overcome these barriers and efficiently identify superior wheat SSP alleles, we developed “PanSK” (Pan-SSP k-mer) for genotype-to-phenotype prediction based on an SSP-based pangenome resource. PanSK uses 29-mer sequences that represent each SSP gene at the pangenomic level to reveal untapped diversity across landraces and modern cultivars. Genome-wide association studies with k-mers identified 23 SSP genes associated with end-use quality that represent novel targets for improvement. We evaluated the effect of rye secalin genes on end-use quality and found that removal of ω-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use quality. Finally, using machine-learning-based prediction inspired by PanSK, we predicted the quality phenotypes with high accuracy from genotypes alone. This study provides an effective approach for genome design based on SSP genes, enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.

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