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.

Mithun, a semidomesticated and autochthonous bovine species of northeastern India, is reared under a free-range forest system.The 20 th livestock census shows an increase of 29.5% (3-3.9 lakhs) mithun over the previous census (20 th Livestock census, DAHD, Government of India, 2019). However, in recent times, denuding forest cover, commercialization of cropping systems, cross-breeding and sacrifice of potential elite mithun bulls have significantly decreased its habitat and the elite mithun population. The diminished population of superior breedable mithun bulls has increased the inbreeding within the population resulting in various reproductive problems including infertility. Therefore, elite bull selection, semen collection and artificial breeding programme need to be taken to overcome the inbreeding depression and to conserve and propagate this precious mountain bovine species.To have germplasm conservation, there is a need for an effective semen collection method from free-range mithun bulls. The rectal massage (Bhattacharyya et al., 2005) and artificial vagina (AV) (Bhattacharyya et al., 2009) methods have been used in collecting ejaculates from the farm mithun. Semen collected from the rectal massage method is poor in quality and quantity, resulted in

Background Mithun ( Bos frontalis ), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun. Results We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle. Conclusion Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5980-y) contains supplementary material, which is available to authorized users.

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The study aimed to evaluate follicular dynamics and concentrations of estradiol-17β (E2), progesterone (P4), follicle stimulating hormone (FSH) and luteinizing hormone (LH) during the oestrous cycle and to determine ovulation time in Mithun cows. Ovaries of experimental cows (n = 7) were examined daily by transrectal-ultrasonography for three consecutive oestrous cycles (n = 21). The characteristics of follicular waves, dominant follicle, largest subordinate follicle and corpus luteum and ovulation time were evaluated. The plasma samples were analysed throughout the interovulatory interval to determine the differences in the hormonal profiles (E2, P4, FSH and LH) between different follicular wave cycles. Out of eighteen oestrous cycles analysed, three-wave follicular cycles were maximum (n = 12: 66.66%) followed by two (n = 4: 22.22%) and four waves (n = 2: 11.11%). The two and three waves were statistically compared, and no significant (p > .05) differences were observed in day of wave emergence, number of follicles (≥3 mm) recruited, maximum diameter of the ovulatory dominant follicle, growth rates of ovulatory and anovulatory dominant follicles and maximum diameter of corpus luteum. The diameter of dominant follicles was significantly (p < .05) greater than subordinate follicles in both ovulatory and anovulatory waves. No significant differences were observed in peak concentrations of estradiol-17β and follicle stimulating hormone between ovulatory and anovulatory waves in all wave cycles. A preovulatory luteinizing hormone surge was observed a day before ovulation in all wave cycles. Progesterone concentrations were lower than 0.5 ng/ml during oestrus and increased sharply to the maximum levels of ≥3.8 ng/ml in all wave cycles. Ovulation time (mean ± SEM), irrespective of follicular waves was 10.5 ± 0.64 h after the end of oestrus. It was concluded that Mithun cows have a preponderance of three follicular waves with little difference between the two-and three-follicular waves and ovulation occurred 10.5 h after the end of oestrus.