TY - JOUR
T1 - Plant genome resequencing and population genomics
T2 - Current status and future prospects
AU - Song, Bo
AU - Ning, Weidong
AU - Wei, Di
AU - Jiang, Mengyun
AU - Zhu, Kun
AU - Wang, Xingwei
AU - Edwards, David
AU - Odeny, Damaris A.
AU - Cheng, Shifeng
N1 - Funding Information:
This work was supported by the National Key Research and Development Program of China ( 2020YFE0202300 ), Science and Technology Major Project of Guangxi ( GuiKeAA20108005-2 ), Guangdong Innovation Research Team Fund (grant number: 2014ZT05S078 ), and National Key Research and Development Program of China ( 2019YFA0707000 ). No conflict of interest declared.
Publisher Copyright:
© 2023 The Author
PY - 2023/8/7
Y1 - 2023/8/7
N2 - 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.
AB - 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.
KW - adaptation
KW - genome variation
KW - resequencing
KW - WGRS
KW - WGS
UR - http://www.scopus.com/inward/record.url?scp=85168115125&partnerID=8YFLogxK
U2 - 10.1016/j.molp.2023.07.009
DO - 10.1016/j.molp.2023.07.009
M3 - Review article
C2 - 37501370
AN - SCOPUS:85168115125
SN - 1674-2052
VL - 16
SP - 1252
EP - 1268
JO - Molecular Plant
JF - Molecular Plant
IS - 8
ER -