Abstract
The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.
Highlights
Mithun are traditionally raised as a meat animal in a free-range system in the sub-tropical rain forest with almost zero input
Observed (Ho) and expected (He) heterozygosities estimated in the Indian mithun population ranged from 0.25 to 0.17, and 0.25 to 0.18, respectively (Table 2)
Treemix results indicated there was considerable genetic similarity between Indian mithun and gaur, and consistently placing mithun and gaur in the same clade. This is first study aiming to assess the genetic structure of Indian mithun and population diversity using the BovineHD BeadChip SNP array
Summary
Mithun are traditionally raised as a meat animal in a free-range system in the sub-tropical rain forest with almost zero input. The mithun population may suffer from inbreeding Under these circumstances, the genetic diversity of the mithun population needs to be described. The genetic diversity of the mithun population needs to be described This will assist ongoing mithun conservation and genetic improvement programme and for devising a suitable breeding policy. Other bovine species including indigenous cattle, yak and gaur are found in the North Eastern parts of India along with mithun. Forest cover and natural habitats of mithuns in the North Eastern Hill States of India have shrunk over the years. This raises concerns about possible introgression of local cattle with mithun, sharing the same habitat. We used the unsupervised clustering analysis (carried out with the ADMIXTURE software)[18] to estimate individuals’ ancestries from SNP genotypes to assess the extent of admixture in mithun with other cattle species (Table 1)
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