Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia

Scientists have identified high within-breed genetic diversity in indigenous cattle populations from Tigray region in northern Ethiopia, representing an opportunity for breeding improvement programs.

The study, which is published in Frontiers in Genetics (July 2023), also identified significant novel variants that could increase the number of known cattle variants.

The members of the research team were from Addis Ababa University, the Chinese Academy of Agricultural Sciences, the International Livestock Research Institute, Mekelle University, the University of Edinburgh and the University of Nottingham.

Their findings represent important contributions to the body of knowledge on domestic cattle genetic diversity.

The Tigray region, home to around 8% of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations of the Fertile Crescent and the Indian subcontinent.

The researchers used whole genome sequencing data to characterize the genomic diversity, relatedness and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia.

They detected 28 to 29 million single nucleotide polymorphisms (SNPs) and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel.

Functional annotation of the variants showed around 0.01% SNPs and 0.22%–0.27% indels in coding regions.

Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds.

They included important genes associated with

• morphology (SCN4A, TAS1R2 and KCNG4),
• milk yield (GABRG1),
• meat quality (MMRN2, VWC2),
• feed efficiency (PCDH8 and SLC26A3),
• immune response (LAMC1, PCDH18, CELSR1, TLR6 and ITGA5),
• heat resistance (NPFFR1 and HTR7), and genes belonging to the olfactory gene family, which may be related to adaptation to harsh environments.

Tigray indigenous cattle are very diverse. Their genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036.

The number of heterozygous SNPs was about 0.6–0.7 times higher than homozygous ones.

The within-breed average number of runs of homozygosity (ROHs) ranged from 777.82 to 1000.45, with the average sum of the length of ROHs ranging from 122.01 Mbp to 163.88 Mbp.

The genomic inbreeding coefficients differed among animals and breeds, reaching up to 10% in some Begait and Raya animals.

Tigray indigenous cattle shared a common ancestry with Asian indicine (85.6%–88.7%) and African taurine (11.3%–14.1%) cattle, with very small, if any, European taurine introgression.

Citation
Zegeye, T., Belay, G., Vallejo-Trujillo, A., Han, J. and Hanotte, O. 2023. Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Frontiers in Genetics 14: 1050365.

Photo credit: Boy feeding cow In Ethiopia’s Tigray region (Apollo Habtamu/Africa Rising)