Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia
文献类型： 外文期刊
作者： Zegeye, Tsadkan 1 ; Belay, Gurja 2 ; Vallejo-Trujillo, Adriana 4 ; Han, Jianlin 3 ; Hanotte, Olivier 3 ;
作者机构： 1.Tigray Agr Res Inst, Mekelle Agr Res Ctr, Mekelle, Ethiopia
2.Addis Ababa Univ, Dept Microbial, Cellular & Mol Biol, Addis Ababa, Ethiopia
3.Int Livestock Res Inst ILRI, Live Gene CTLGH, Addis Ababa, Ethiopia
4.Univ Edinburgh, Roslin Inst, Ctr Trop Livestock Genet & Hlth CTLGH, Edinburgh, Scotland
5.Chinese Acad Agr Sci CAAS, Inst Anim Sci, ILRI Joint Lab Livestock & Forage Genet Resources, CAAS, Beijing, Peoples R China
6.Univ Nottingham, Sch Life Sci, Cells Organism & Mol Genet, Nottingham, England
关键词： Abergelle; Arado; Begait; Erob; private missense variants; Raya; runs of homozygosity; Tigray cattle
期刊名称：FRONTIERS IN GENETICS （ 影响因子：3.7； 五年影响因子：4.3 ）
ISSN：
年卷期： 2023 年 14 卷
页码：
收录情况： SCI
摘要： The Tigray region, where we found around eight per cent 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. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million 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 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. This study identified high within-breed genetic diversity representing an opportunity for breeding improvement programs and, also, significant novel variants that could increase the number of known cattle variants, an important contribution to the knowledge of domestic cattle genetic diversity.
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