基于k-mer的pangenome方法,对小麦种子贮藏蛋白基因进行编目,以促进基因型到表型的预测和最终使用质量的改善。

IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Molecular Plant Pub Date : 2024-07-01 Epub Date: 2024-05-24 DOI:10.1016/j.molp.2024.05.006
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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引用次数: 0

摘要

小麦(Triticum aestivum L.)是世界上 35% 以上人口的主食,其面粉用于制作数百种烘焙食品。卓越的最终使用品质是一个主要的育种目标,然而,提高最终使用品质尤其费时费力。此外,编码种子贮藏蛋白(SSP)的基因组成了多基因家族,并且具有重复性,在多个基因组组装中普遍存在空白。为了克服这些障碍并高效鉴定优良的小麦 SSP 等位基因,我们开发了 "PanSK"(Pan-SSP k-mer),用于基于 SSP 的泛基因组资源进行基因型到表型的预测。PanSK 使用在泛基因组水平上代表每个 SSP 基因的 29-mer 序列来揭示陆地品种和现代栽培品种之间尚未开发的多样性。利用 k-mer 进行的全基因组关联研究发现了 23 个与最终使用质量相关的 SSP 基因,这些基因代表了新的改良目标。我们评估了黑麦secalin基因对最终使用质量的影响,发现从1BL/SRS小麦易位系中移除ω-secalins与最终使用质量的提高有关。最后,受 PanSK 的启发,我们利用基于机器学习的预测方法,仅从基因型就能高精度地预测出品质表型。这项研究为基于 SSP 基因的基因组设计提供了一种有效的方法,从而能够培育出加工能力更强、最终使用品质更好的小麦品种。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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.

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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来源期刊
Molecular Plant
Molecular Plant 植物科学-生化与分子生物学
CiteScore
37.60
自引率
2.20%
发文量
1784
审稿时长
1 months
期刊介绍: Molecular Plant is dedicated to serving the plant science community by publishing novel and exciting findings with high significance in plant biology. The journal focuses broadly on cellular biology, physiology, biochemistry, molecular biology, genetics, development, plant-microbe interaction, genomics, bioinformatics, and molecular evolution. Molecular Plant publishes original research articles, reviews, Correspondence, and Spotlights on the most important developments in plant biology.
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