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Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security
Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going ‘beyond a reference genome’ should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
crop improvement, food security, genomics, pangenome, population genomics, reference genome, underutilized crops
0028-646X
1583–1597
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
He, Yuqi
b7260ec0-4a95-49f1-a341-ba6e6364d2d2
Zhou, Meiliang
d9044cc6-9c6c-4483-be2b-030b0ab04cbf
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
He, Yuqi
b7260ec0-4a95-49f1-a341-ba6e6364d2d2
Zhou, Meiliang
d9044cc6-9c6c-4483-be2b-030b0ab04cbf

Chapman, Mark, He, Yuqi and Zhou, Meiliang (2022) Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. New Phytologist, 234 (5), 1583–1597. (doi:10.1111/nph.18021).

Record type: Review

Abstract

Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going ‘beyond a reference genome’ should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.

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More information

Accepted/In Press date: 22 January 2022
e-pub ahead of print date: 22 March 2022
Published date: June 2022
Additional Information: Funding Information: This research was supported by grants from the National Key R&D Program of China (2019YFD1001300/2019YFD1001302) and National Natural Science Foundation of China (31871536 and 32161143005) to MZ and from the Natural Environment Research Council and Biotechnology and Biological Sciences Research Council (NE/S002022/1) to MAC. We thank our lab groups for ongoing discussions into these crops as well as three anonymous reviewers who gave insightful comments and suggestions on a previous version of this review. Publisher Copyright: © 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.
Keywords: crop improvement, food security, genomics, pangenome, population genomics, reference genome, underutilized crops

Identifiers

Local EPrints ID: 457534
URI: http://eprints.soton.ac.uk/id/eprint/457534
ISSN: 0028-646X
PURE UUID: 13835713-68bc-4216-b3f1-4e1e485aca97
ORCID for Mark Chapman: ORCID iD orcid.org/0000-0002-7151-723X

Catalogue record

Date deposited: 10 Jun 2022 16:38
Last modified: 22 Jan 2023 05:01

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Contributors

Author: Mark Chapman ORCID iD
Author: Yuqi He
Author: Meiliang Zhou

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