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Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

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Relation http://oar.icrisat.org/11835/
https://doi.org/10.3389/fpls.2021.666342
doi:10.3389/fpls.2021.666342
 
Title Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain
 
Creator Ruperao, P
Thirunavukkarasu, N
Gandham, P
Selvanayagam, S
Govindaraj, M
Nebie, B
Manyasa, E
Gupta, R
Das, R R
Odeny, D A
Gandhi, H
Edwards, D
Deshpande, S P
Rathore, A
 
Subject Plant Breeding
Sorghum
Genetics and Genomics
 
Description Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production
ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart
crop to overcome the food and nutritional insecurity in the developing world. The
development and characterisation of the sorghum pan-genome will provide insight
into genome diversity and functionality, supporting sorghum improvement. We built
a sorghum pan-genome using reference genomes as well as 354 genetically diverse
sorghum accessions belonging to different races. We explored the structural and
functional characteristics of the pan-genome and explain its utility in supporting genetic
gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome
of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes
are enriched with environment responsive genes and classify the sorghum accessions
according to their race.We show that 53%of genes display presence-absence variation,
and some of these variable genes are predicted to be functionally associated with drought
adaptation traits. Using more than two million SNPs from the pan-genome, association
analysis identified 398 SNPs significantly associated with important agronomic traits, of
which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that
are functionally linked to different conditions, of which 79 were absent from the reference
genome assembly. This study provides comprehensive genomic diversity resources in
sorghum which can be used in genome assisted crop improvement.
 
Publisher Frontiers Media
 
Date 2021-06
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11835/1/Sorghum%20Pan-Genome%20Explores%20-Frontiers%20in%20plant%20sci.%202021.pdf
Ruperao, P and Thirunavukkarasu, N and Gandham, P and Selvanayagam, S and Govindaraj, M and Nebie, B and Manyasa, E and Gupta, R and Das, R R and Odeny, D A and Gandhi, H and Edwards, D and Deshpande, S P and Rathore, A (2021) Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. Frontiers in Plant Science (TSI), 12. ISSN 1664-462X