Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources

Ruperao, Pradeep; Gandham, Prasad; Odeny, Damaris A.; Mayes, Sean; Selvanayagam, Sivasubramani; Thirunavukkarasu, Nepolean; Das, Roma R.; Srikanda, Manasa; Gandhi, Harish; Habyarimana, Ephrem; Manyasa, Eric; Nebie, Baloua; Deshpande, Santosh P.; Rathore, Abhishek

doi:10.3389/fpls.2023.1143512

Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources

Ruperao, Pradeep; Gandham, Prasad; Odeny, Damaris A.; Mayes, Sean; Selvanayagam, Sivasubramani; Thirunavukkarasu, Nepolean; Das, Roma R.; Srikanda, Manasa; Gandhi, Harish; Habyarimana, Ephrem; Manyasa, Eric; Nebie, Baloua; Deshpande, Santosh P.; Rathore, Abhishek

Authors

Pradeep Ruperao

Prasad Gandham

Damaris A. Odeny

Dr SEAN MAYES SEAN.MAYES@NOTTINGHAM.AC.UK
ASSOCIATE PROFESSOR

Sivasubramani Selvanayagam

Nepolean Thirunavukkarasu

Roma R. Das

Manasa Srikanda

Harish Gandhi

Ephrem Habyarimana

Eric Manyasa

Baloua Nebie

Santosh P. Deshpande

Abhishek Rathore

Abstract

Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.

Citation

Ruperao, P., Gandham, P., Odeny, D. A., Mayes, S., Selvanayagam, S., Thirunavukkarasu, N., Das, R. R., Srikanda, M., Gandhi, H., Habyarimana, E., Manyasa, E., Nebie, B., Deshpande, S. P., & Rathore, A. (2023). Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources. Frontiers in Plant Science, 14, Article 1143512. https://doi.org/10.3389/fpls.2023.1143512

Journal Article Type	Article
Acceptance Date	Feb 22, 2023
Online Publication Date	Mar 17, 2023
Publication Date	Mar 17, 2023
Deposit Date	Apr 29, 2023
Publicly Available Date	May 2, 2023
Journal	Frontiers in Plant Science
Electronic ISSN	1664-462X
Publisher	Frontiers Media
Peer Reviewed	Peer Reviewed
Volume	14
Article Number	1143512
DOI	https://doi.org/10.3389/fpls.2023.1143512
Keywords	Sorghum race, deep learning, deep variant calling, k-mer analysis, selection pressure, gene enrichment, positive and negative selection
Public URL	https://nottingham-repository.worktribe.com/output/20008306
Publisher URL	https://www.frontiersin.org/articles/10.3389/fpls.2023.1143512/full