Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China.
Mol Plant. 2023 Aug 7;16(8):1252-1268. doi: 10.1016/j.molp.2023.07.009. Epub 2023 Jul 26.
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
DNA 测序技术的进步引发了基因组学革命，推动了植物遗传学和作物育种的突破。最近，研究重点已经从对植物遗传多样性的编目转向探索其功能意义，并为作物改良提供有益的等位基因。这一转变得益于全基因组重测序的广泛采用。在这篇综述中，我们总结了基于群体的基因组重测序研究的最新进展，以及这些研究如何影响作物育种。已经对来自 163 个国家的 187 种陆地植物进行了重测序，包括 54413 个样本。作为重测序工作的一部分，已经调查了 367 个性状，并进行了 86 项全基因组关联研究。经济上重要的作物，特别是谷类、蔬菜和豆类，主导了重测序工作，留下了 49 个目（包括石松目、百合目、水鳖目、泽泻目和鸭跖草目）的缺口。重测序的种质资源分布在不同的地理位置，提供了植物基因组学的全球视角。我们强调了在驯化过程中选择的基因，或与农艺性状相关的基因，并形成了一个候选基因库，供未来的研究和应用。尽管有进行跨物种比较基因组学的机会，但许多群体基因组数据集无法访问，阻碍了二次分析。我们呼吁采取更加开放和协作的群体基因组学方法，促进数据共享，并鼓励基于贡献的信用政策。随着 DNA 测序成本的降低，以及分析和计算技术的进步，植物基因组重测序研究的数量将继续增加。无论是在规模还是质量方面，这种扩展都有望更深入地了解植物性状遗传学和育种设计。
