Genomic clues of the evolutionary history of Bos indicus cattle

Abstract

SummaryTogether with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro‐Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian‐Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole‐genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.

Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

“…For diversity analysis, the existing number of samples in each breed greater than 12 was adequate and in consonance with other studies (Upadhyay et al, 2017;Colli et al, 2018). It has also been indicated that sample size as small as 4 -6 (Willing et al, 2012) and polymorphic SNP filtration (Colli et al, 2018;Utsunomiya et al, 2019) can mitigate ascertainment bias as long as the number of markers is sufficiently large as those under the current investigation. Earlier, in Indian dairy cattle breeds, we also tested bovine high-density genotyping array to assess its feasibility for Zebu cattle genomic studies (Dash et al, 2018).…”

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

“…in the 50k SNP chip discovery panel, recorded the highest p-values (S2 Table), confirming that the strategy implemented here removed those SNPs having the largest ascertainment bias impact. Importantly, the H o values of the reference breeds obtained using our SNP selection approach were comparable with those of the Illumina BovineHD array, which is still today considered the most robust SNP array for cattle [24,42]. Further, the population structure analyses performed using the reduced dataset provided results in line with the know relationship among the reference populations in our dataset, whereas the same analysis performed using the full SNP was distorted by the percentage of taurine ancestry in a given breed (S6 Fig).…”

Evolution and domestication of the Bovini species

“…About the same number of zebus lives in the tropical regions (Utsunomiya et al . 2019). Both taurine cattle and zebu descend from the extinct aurochs.…”

“…A more detailed account of the domestication of zebu has been presented by Utsunomiya et al . (2019).…”

“…2018; Utsunomiya et al . 2019). On the basis of molecular evidence, additional domestication sites have been proposed in Africa for taurine cattle and in south‐east China for zebus.…”