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

Frontiers in Plant Science

Plant Science

Pradeep Ruperao¹  Sean Mayes¹  Damaris A. Odeny¹  Manasa Srikanda²  Abhishek Rathore³  Nepolean Thirunavukkarasu⁴  Santosh P. Deshpande⁵  Ephrem Habyarimana⁶  Roma R. Das⁶  Baloua Nebie⁷  Harish Gandhi⁸  Prasad Gandham⁹  Eric Manyasa^1,10  Sivasubramani Selvanayagam^1,11 

[1] Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India;Department of Statistics, Osmania University, Hyderabad, India;Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India;Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research (ICAR) - Indian Institute of Millets Research, Hyderabad, India;Hytech Seed India Private Limited, Hyderabad, India;International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India;International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal;International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya;School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, LA, United States;Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya;Wageningen University and Research, Wageningen, Netherlands;

关键词: sorghum race;    deep learning;    deep variant calling;    k-mer;    selection pressure;    gene enrichment;    positive and negative selection;   

DOI  :  10.3389/fpls.2023.1143512

 received in 2023-01-16, accepted in 2023-02-22,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

Unknown   
Copyright © 2023 Ruperao, Gandham, Odeny, Mayes, Selvanayagam, Thirunavukkarasu, Das, Srikanda, Gandhi, Habyarimana, Manyasa, Nebie, Deshpande and Rathore