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

OAR@ICRISAT

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Relation http://oar.icrisat.org/12052/
https://doi.org/10.3389/fpls.2023.1143512
 
Title Exploring the sorghum race level
diversity utilizing 272 sorghum
accessions genomic resources
 
Creator 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
 
Subject Sorghum
 
Description 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.
 
Publisher Frontiers
 
Date 2023-03-23
 
Type Article
NonPeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/12052/1/fpls-14-1143512.pdf
Ruperao, P and Gandham, P and Odeny, D A and Mayes, S and Selvanayagam, S and Thirunavukkarasu, N and Das, R R and Srikanda, M and Gandhi, H and Habyarimana, E and Manyasa, E and Nebie, B and Deshpande, S P and Rathore, A (2023) Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources. Plant Science (TSI), 14 (114351). pp. 1-15. ISSN 1664-462X