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

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

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Abstract

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.

Item Type:	Article
Divisions:	Research Program : Asia Research Program : East & Southern Africa Research Program : West & Central Africa
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Sorghum, Pan-genome, Diversity, SNP, gPAV, GWAS, Drought Genes
Subjects:	Others > Plant Breeding Mandate crops > Sorghum Others > Genetics and Genomics
Depositing User:	Mr Arun S
Date Deposited:	04 Jun 2021 08:19
Last Modified:	04 Jun 2021 08:19
URI:	http://oar.icrisat.org/id/eprint/11835
Official URL:	https://doi.org/10.3389/fpls.2021.666342
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The authors thank Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA and Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA for providing the sorghum WGRS, RNASeq data, and phenotype data. The authors also acknowledge the supporting funds from AVISA (OPP1198373) and ICAR-BMGF (101165).
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