Plant pangenomics, current practice and future direction

Haifei Hu; Jian Wang; Shuai Nie; Junliang Zhao; Jacqueline Batley; David Edwards

Agriculture Communications (Jun 2024)

Plant pangenomics, current practice and future direction

Haifei Hu,
Jian Wang,
Shuai Nie,
Junliang Zhao,
Jacqueline Batley,
David Edwards

Affiliations

Haifei Hu: Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
Jian Wang: Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
Shuai Nie: Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
Junliang Zhao: Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
Jacqueline Batley: School of Biological Sciences, University of Western Australia, Perth 6009, Australia
David Edwards: School of Biological Sciences and Centre for Applied Bioinformatics, University of Western Australia, Perth 6009, Australia; Corresponding author.

Journal volume & issue: Vol. 2, no. 2
p. 100039

Abstract

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A pangenome encompasses the complete genetic diversity of a species, by assembling a range of representative individuals from various populations. This review describes the advances in plant pangenomics, tracing its evolution since the initial plant genome sequencing in 2000, and provides comprehensive best-practice advice to build a linear or graphical pangenome, delineating the strengths and limitations of different pangenome construction methods. The review also examines the challenges in pangenome data visualisation, the challenges of graph-based pangenomes and their utility in investigating the potential function of genome variation. Furthermore, we examine the application of pangenomes in plant breeding, including the identification of genetic diversity for crop improvement, and the integration of multi-omics data into pangenome databases to advance plant breeding.

Published in Agriculture Communications

ISSN: 2949-7981 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Agriculture
Website: https://www.sciencedirect.com/journal/agriculture-communications

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