Plant genome resequencing and population genomics: Current status and future prospects

Song, B and Ning, W and Wei, D and Jiang, M and Zhu, K and Wang, X and Edwards, D and Odeny, D A and Cheng, S (2023) Plant genome resequencing and population genomics: Current status and future prospects. Molecular Plant (TSI), 16. pp. 1252-1268. ISSN 1674-2052

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Abstract

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.

Item Type:	Article
Divisions:	Research Program : East & Southern Africa
CRP:	UNSPECIFIED
Uncontrolled Keywords:	WGRS, WGS, resequencing, genome variation, adaptation
Subjects:	Others > Genetic Engineering Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	27 Oct 2023 10:47
Last Modified:	27 Oct 2023 10:47
URI:	http://oar.icrisat.org/id/eprint/12254
Official URL:	https://www.cell.com/molecular-plant/pdf/S1674-205...
Projects:	Science and Technology Major Project of Guangxi, Guangdong Innovation Research Team Fund
Funders:	National Key Research and Development Program of China
Acknowledgement:	We thank Professor Jeffrey J. Doyle at Cornell University and Dr. Xu Li in at Huazhong Agricultural University for his critical reads and comments. We thank Baizhi Chen, Wang Chen, Zhiyi Ye, and Shaojie Ye for their help in data collection and correction, and Yuchen Sun for his help in the preparation of figures. No conflict of interest is declared.
Links:	Google Scholar

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