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Volume 23
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10.3390/ijms23052671
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Review

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

by
Cassandria Geraldine Tay Fernandez
,
Benjamin John Nestor
,
Monica Furaste Danilevicz
,
Mitchell Gill
,
Jakob Petereit
,
Philipp Emanuel Bayer
,
Patrick Michael Finnegan
,
Jacqueline Batley
and
David Edwards
*
School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2022, 23(5), 2671; https://doi.org/10.3390/ijms23052671
Submission received: 1 February 2022 / Revised: 21 February 2022 / Accepted: 21 February 2022 / Published: 28 February 2022
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)
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Abstract

Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
Keywords: pangenome assembly; graph pangenomes; presence absence variation; QTLs; trait discovery pangenome assembly; graph pangenomes; presence absence variation; QTLs; trait discovery

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MDPI and ACS Style

Tay Fernandez, C.G.; Nestor, B.J.; Danilevicz, M.F.; Gill, M.; Petereit, J.; Bayer, P.E.; Finnegan, P.M.; Batley, J.; Edwards, D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int. J. Mol. Sci. 2022, 23, 2671. https://doi.org/10.3390/ijms23052671

AMA Style

Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. International Journal of Molecular Sciences. 2022; 23(5):2671. https://doi.org/10.3390/ijms23052671

Chicago/Turabian Style

Tay Fernandez, Cassandria Geraldine, Benjamin John Nestor, Monica Furaste Danilevicz, Mitchell Gill, Jakob Petereit, Philipp Emanuel Bayer, Patrick Michael Finnegan, Jacqueline Batley, and David Edwards. 2022. "Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species" International Journal of Molecular Sciences 23, no. 5: 2671. https://doi.org/10.3390/ijms23052671

APA Style

Tay Fernandez, C. G., Nestor, B. J., Danilevicz, M. F., Gill, M., Petereit, J., Bayer, P. E., Finnegan, P. M., Batley, J., & Edwards, D. (2022). Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. International Journal of Molecular Sciences, 23(5), 2671. https://doi.org/10.3390/ijms23052671

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