Background: In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip.Result: De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent.Conclusion: The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.

Bos indicus breed Sahiwal, famous for its optimum performance, has so far been genetically improved for performance traits based on phenotypic records and the genomic knowhow regarding genes, regions and biological processes underlying the complex quantitative traits is lacking. In this context, a Genome-wide Association Study was performed for fertility and growth traits in Sahiwal cattle to shed light on its genomic profile. A total of 46 SNPs were found associated with the traits at genome-wide suggestive threshold of P ≤ 10⁻⁴. USP32, LRPPRC, PLA2G10, RRN3 and ASAP1 were identified as putative candidate genes for body weight at different ages. However, several genes mapped for growth traits like GREB1, PLA2G10, RAD51C, BIRC6, TEX14 and PEBP4 had significant physiological underpinnings in determining fertility of the animals. Moreover, Quantitative trait loci (QTL) identification revealed potential overlaps with the already reported QTLs for both fertility and growth for most of the traits. Further, candidate SNP enrichment analysis revealed an enriched biological process for birth weight with a significant reproductive role. Based on the findings, genetic linkages underlying fertility and growth could be discerned in Sahiwal population and may be utilized for improving fertility traits in future.

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. 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. 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.

Mithun (Bos frontalis) or gayal and Indian Bison or wild gaur (Bos gaurus) are listed among the rare and endangered bovine species of India. The remote location of mithun in four North Eastern Hill states (Arunachal Pradesh, Nagaland, Manipur, and Mizoram), scattered population size, and non-availability of genetic diversity status are major limitations towards devising a suitable breeding and conservation policy of these species. Since several studies have demonstrated the successful applicability of microsatellite/SSR markers across related genera/families in both crop plants and animal species, 30 FAO recommended cattle microsatellites were utilized for the assessment of the genetic diversity of Indian mithun, bison, and local Tho-tho cattle. Mitochondrial transmembrane protein coding cytochrome B (CYTB) complete sequence data of 71 bovine samples from India were also used to reinforce the study. Population structuring clustered the all bovines into three subgroups as per geographical location and species. Bottleneck analysis indicated a mode shift in the allelic frequency distribution of gaur, indicating minor genetic bottleneck events in the past, while no bottleneck was found in mithun and Tho-tho cattle. To our knowledge, this study represents the first report of molecular genetic characterization showing the population structure and status of genetic diversity in rare Indian bovines, namely, Mithun, Gaur, and Tho-tho cattle.

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the longterm sustainability of these breeds.Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes.Results: The average LD between single nucleotide polymorphisms (SNPs) was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based Ne of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for Ne estimation), respectively.Conclusion: KF cattle have an Ne exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for longterm sustainable development.