Genome diversity and adaptations of indigenous Sudanese livestock Breeds

Genome diversity and adaptations of indigenous Sudanese livestock Breeds

Genome diversity and adaptations of indigenous Sudanese livestock Breeds

Hassan H. Musa1, 2*, Taha H. Musa2, Abdelkareem A. Ahmed2, Jaafar S. Fedail2, Ibrahim H. Musa2

1Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan

2BRI, Darfur University College, Nyala, Sudan

*Corresponding email:hassantahir70@hotmail.com

 

Abstract

The geography of Sudan offers diversified ecological conditions and climate types that had influenced notably the distribution of today’s existence Sudanese livestock breeds. In this study, we carried out whole genome resequencing for Sudanese indigenous cattle comprising of three dairy breeds (Kenana, Butana and Aryshai) and three beef breeds (Baggara, Gash and Fulani). Eleven Sheep breeds comprising Sudan Desert ecotype (Kabbashi, Hammari,
Meidobe, Dubasi, Ashgar, Watish, Beja and Riverine wool), Arid land ecotype (Zaghawi), West African Fulani ecotype (Fallata or Um bororo) and Sudanese fused ecotype (Garage). Three goat breeds (Nubain, Desert and Tiggar). In addition, five camel breeds comprising three packing camel (Arabian Kenani, Lahawi) and two riding (racing) camel (Bishari and Anafi) were genotyped using the pair-end GBS technology.

The aim was to investigate their genome diversity, population structure and signature of positive selection. Genomic DNA was extracted from whole blood using Qiagen DNeasy extraction kit (Qiagen, Valencia, CA, USA). Whole genome re-sequencing and GBS were performed on the Illumina HiSeq 2000 platform by Novogene (Novogene Co., Ltd, Tianjin, China).

Genomic diversity and population structure were assessed among the Sudanese livestock breeds compared with other African and non-African livestock breeds. Genomic signatures of positive selection were assessed using pooled heterozygosity (Hp) approach for within breed analysis and genetic differentiated (Fst) test between the dairy and beef breeds and/or between backing and riding camels. The common candidate selected genes are related to growth and conformation traits, skeletal muscles development and functionality, immunity, residual feed intake, heat stress response and tick resistance. This study for the first time report the valuable genetic resources for Sudanese indigenous animal breeds and provide insights into their genomic features. The variants discovered will pave way for further research into the genetic basis of economically important traits.

 

Keywords: Genomic diversity, genomic signatures, livestock breeds, Sudan

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