Yaks are multipurpose ruminants crucial for milk, meat, wool, fuel, and high-altitude transportation. Effective management of their genetic resources requires detailed knowledge of their genetic diversity, population structure, and genealogical parameters. SNP arrays offer a reliable and reproducible method for genotyping, overcoming limitations of other approaches. The present study focused on developing and validating a high-density SNP array tailored for Indian yak populations. In whole genome resequencing analysis, 31 million variants, including SNPs and InDels, were scored in the Indian yak populations. The identified variants underwent rigorous filtering based on various criteria such as minor allele frequency, removal of insertions and deletions, selection of biallelic SNPs, filtration of adjacent SNPs, and p-convert value. Finally, a total of 627,377 SNPs were selected and tiled using Affymetrix® Axiom® High Density genotyping array technology. Subsequently, the developed SNP array was validated using 338 Indian yak DNA samples using the Affymetrix GeneTitan platform. Further, the SNP array data analysis revealed a greater than 99

Cow’s milk is an essential part of the human diet as it provides vital nutrients and exhibits medicinal properties. It is rich in high-quality proteins, fats, sugars, vitamins, and minerals, with over 95% of its proteins consisting of caseins and whey proteins. Among these, ?-casein exists in several genetic variants, categorized into A1 and A2 types. During digestion, A1 milk releases a peptide called ?-casomorphin-7 (BCM-7), which has been linked to adverse health effects, including cardiovascular and neurological disorders. In contrast, A2 milk does not release BCM-7 and is considered a safer alternative. The aim of this study is to find out the effects of A1 and A2 milk on biochemical parameters in C57BL/6J mice fed a highfat diet (HFD). A total of 25 male mice were divided into five groups: control (standard chow), HFD, HFD + A1A1 milk, HFD + A2A2 milk, and HFD + A1A2 milk. The results showed that the HFD group had elevated levels of blood glucose, ALT, AST, triglycerides, and uric acid compared to the control group. While no significant differences were observed between the A1A1 and A1A2 groups. The A2A2 milk group exhibited significantly lower blood glucose, ALT and urea compared to the A1A1 and HFD groups. Other markers, such as albumin, total protein, and creatinine, did not significantly varied amongst the groups. Overall, the study indicates that A2 milk may offer health benefits in reducing liver enzymes and triglycerides in the context of a high-fat diet.

In this study, whole genome sequence data of Ladakhi cattle from high altitude region of Leh-Ladakh and Sahiwal cattle from arid, semi-arid tropical region were compared. To gain a deeper understanding of the selective footprints in the genomes of Ladakhi and Sahiwal cattle, two strategies namely run of homozygosity (ROH), and fixation index (FST) were employed. A total of 975 and 1189 ROH regions were identified in Ladakhi and Sahiwal cattle, respectively. Several genes associated with high-altitude adaptation were enriched in many of the ROH hot spots in genome of Ladakhi cattle such as; HIF1A, VEGFA, VEGFC, EPHB1, ZEB1, CAV3, TEK, SENP2, GATA6, RAD51 and ADAMTSL4 etc.. The FST value of 0.32 also indicated strong genetic differentiation between Ladakhi and Sahiwal cattle. A total of 3616 genomic regions were identified to be under selection in the two cattle breeds. The FST selection signature analysis led to identification of several genes such as HIF1A, VEGFC, ZEB1, SOD1, EGLN3, EPAS1, ZNF, DYSF, ADAM, SENP2, MMP16, and CDK2 etc., that could be associated with high altitude adaptation in Ladakhi cattle. Additionally, several signalling pathways found in Ladakhi cattle like HIF1A, VEGF, DNA repair, and angiogenesis, which are associated with adaptation to high-altitude hypoxic environments. The phylogenetic, PCA and admixture analysis separated the individuals of Ladakhi and Sahiwal cattle according to their geographic origin. In the present study, the WGS data has helped to identify key genes and genic regions that contribute to high altitude adaptation in Ladakhi cattle.

This study has identified 46 metabolites in colostrum, transition milk and mature milk of unique indigenous high altitude adapted Ladakhi cows using 1D 1H 800 MHz NMR spectroscopy. The multivariate analysis revealed that UDP-galactose, UDP-glucose, citrate, creatine phosphate, myo-inositol, lactose, 2-oxoglutarate, valine, maltose, leucine, dimethylamine, and choline with high VIP scores could differentiate the colostrum, transition and mature milk in separate clusters. Highly enriched metabolites in colostrum such as UDP-galactose, UDP-glucose play crucial roles in cell growth, differentiation, and defense responses. Similarly, the presence of branched chain amino acids in colostrum could be linked to mammary gland development, N-acetylglucosamine, N-acetyl carnitine, choline etc. in high concentration in colostrum l might be helping in growth and development of neonatal calves of Ladakhi cows under hypoxia environment. Overall, this study has helped to characterize the metabolomic signatures of milk/colostrum of Ladakhi cows adapted to high altitude and cold desert of Leh-Ladakh.

Yak, an economically important bovine species considered as the lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. The Y chromosome is widely recognized for its role in male traits, characterized by paternal inheritance, high mutation rate, and minimal recombination rate or reverse mutation. So, we investigated the Y-chromosome-specific variants in four yak populations namely, Arunachali, Himachali, Ladakhi, and Jinchuan through whole genome resequencing, we identified nearly 274828, 243143, 283774, and 194 228 SNPs, respectively. The intergenic regions held the highest proportion of SNPs, with Jinchuan yaks showing fewer SNPs due to intense selective breeding for reproductive performance and product quality. The Ts/Tv ratios were 1.57, 1.67, 1.55, and 1.99 for Arunachali, Himachali, Ladakhi, and Jinchuan yaks, respectively. SnpEff annotation indicated that most SNPs were intergenic, followed by intronic regions. Key genes identified included ASMT, ASMTL, and SRY, with significant roles in melatonin biosynthesis and male sex determination. Interestingly, we performed Linkage disequilibrium (LD) pruning, which retained only about 20% of SNPs, underscored the complexity of genetic analyses and highlighted the importance of careful LD criteria selection to avoid losing loci under selection. This pioneering mapping of Y-chromosome SNPs in yaks provides essential insights into their genetic landscape and underscores the critical need for precise LD pruning parameters to accurately assess genetic diversity and population differentiation.

This study delves into the genomic foundations of high-altitude adaptation in Indian yaks, with a specific emphasis on the X chromosome and its role in traits related to production, reproduction, and immunity. Utilizing whole-genome resequencing, we identified 319,015 high-quality X chromosomal SNPs from 30 unrelated Indian yaks and 8 Jinchuan yaks. These SNPs were analyzed through various statistical methodologies, including composite likelihood ratio (CLR) statistics, Tajima’s D, iHS, FST, and XP-EHH. Our findings highlight several genes associated with high-altitude adaptation, such as AIFM1, APOOL, ATRX, CHST7, DACH2, DGAT2L6, DIAPH2, and EIF2S3B, identified through iHS, Tajima’s D, and CLR approaches. Additionally, genes including GPR119, HS6ST2, MAGED1, MOSPD1, PQBP1, SLC25A14, SLC35A2, TIMM17B, and WDR44 exhibited common selection signatures across FST and XP-EHH methods. Unique genes and loci specific to each yak population were uncovered on the X chromosome, which are critical for adaptability, immunity, reproduction, and production traits. Notably, our study identified selection regions containing the RLIM gene in Himachali yaks, which is crucial for Dosage Compensation on the X chromosome. This research offers new insights into X-linked selection across different yak populations, enhancing our understanding of the genomic mechanisms underlying high-altitude adaptation.

The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.

The study was carried out in Gir cattle for identification of genome wide SNPs and then to annotate the identified high-quality SNPs to the milk production traits. A total of 99 517 SNPs were identified with respect to the Bos indicus reference genome. Upon annotation of SNPs identified with respect to Bos indicus reference genome, 984 SNPs located in 175 candidate genes related with milk production traits, notably Acetyl-CoA carboxylase β gene, which affects milk composition traits by regulation of fatty acid oxidation in the mitochondria; Growth hormone receptor gene which have role in milk yield and its composition traits; LEP gene, involved in energy partitioning and metabolism, were among others. This study provides the first analysis of ddRAD sequences to discover SNPs in Indian Gir cattle breed, aligned to indicine reference genome. The variants mined in this study can be incorporated in existing SNP chips and thus, play an important role in understanding the genetic structure of our cattle in order to design appropriate breed improvement programmes.

This study explored the maternal genetic diversity of six indigenous Indian horse and pony breeds (Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari) using comprehensive mitochondrial genome (mitogenome) analysis. Blood samples from 53 horses across diverse agro-climatic zones of India were analyzed, revealing 36 distinct haplotypes, with a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices suggest significant maternal genetic diversity in Indian equines. A median-joining (MJ) network, based on the hypervariable region of the D-loop along with sequences of Indian equids retrieved from the NCBI, identified 55 haplotypes, including shared haplotypes across 2-5 breeds. Hierarchical AMOVA analysis revealed that 95.20% of genetic variation was within populations, while only 4.80% was among different groups, indicating minimal genetic structuring based on geographic distribution. Phylogenetic analysis of these mitogenomes, alongside global sequences, revealed significant genetic variability without clear geographic clustering, highlighting extensive gene flow and interbreeding across regions. Median-Joining network based on D-loop sequence revealed that Indian horses conform to seven of the 18 globally recognized haplogroups (A, B, G, J, L, M, and P), with haplogroup A being the most frequent. This research contributes to the broader understanding of equine genetic diversity, aligning with global patterns of extensive maternal haplotype diversity, and underscores the intricate genetic backgrounds resulting from historical breeding practices.

Background: HSP70 (Heat Shock Protein 70), plays a crucial role in nascent protein folding; the added challenges due to physiological factors demand stringent role-playing of such chaperones for tropical livestock such as water buffalo (Bubalus bubalis). Therefore to evaluate the variations at nucleotide level in HSP70 that could potentially unravel the molecular basis of thermal adaptation in the riverine buffalo breeds of India, the current study was targeted to sequence the CDS (Coding Sequence) and UTR (Untranslated Region) of the gene in a panel of 16 Indian riverine buffalo breeds. Methods: Blood samples were collected and genomic DNA was isolated followed by PCR standardized for the amplification of different fragments of the HSP70 gene using different sets of primer pairs covering the entire coding region and 5’UTR. Multiple amplicons generated to cover the entire gene were sequenced. Sequences were further analyzed manually for the identification of heterozygous animals to detect the polymorphic nucleotide sites and variation between breeds documented. Result: The HSP70 results suggest, the highly conserved nature of gene in buffalo. The only non-synonymous polymorphic site was found in the Toda buffalo breed (g.SNPC greater than T at position 14), resulting in amino acid change 5M greater than T. A total of 7 polymorphic sites were found in the 5’UTR flanking region. Additionally, two insertion/deletions (INDEL) of 30 and 1 nucleotide length were found in the 5’UTR.

A stop-gain mutation (rs715966442; BTA11: 1,02,463,944 nucleotide position) in transcription termination factor, RNA polymerase I (TTF1) gene causes abortion in Holstein Friesian (HF) cattle. A PCR-restriction fragment length polymorphism (PCR-RFLP)-based genetic test has been developed and validated to screen the TTF1 mutation locus in HF cattle. The mutation locus was screened in 80 HF and HF crossbreds using the protocol, which revealed two animals as carriers of the mutant TTF1 allele. The test employed is cost-effective, rapid and precise and can be utilized as an effective tool for the screening of TTF1 mutation carriers in HF cattle population.

Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.

The unique horse and pony breeds of India are declining at an alarming rate. These horses have been integral to the Indian culture and customs for centuries and represent a valuable genetic resource. It is imperative to harness the potential of this equine genetic resource that urgently needs conservation. The study highlights the design and development of a high density SNP array, the Axiom_Ashwa to aid in the genetic analysis and conservation efforts for Indian horse and pony breeds. With 613,950 SNPs, this chip offers extensive genome coverage having an average inter-marker distance of 4 kb. The Axiom_Ashwa has been validated on a larger set of diverse indigenous samples as well as Thoroughbreds, demonstrating a high call rate of 99.4

The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.

Indian yaks (Bos grunniens) have experienced a significant decline in their population in recent years, primarily due to reduced economic returns from bovid products and the lack of mainstream markets for yak milk and meat. This decline has led to a decreased interest among younger generations in continuing the tradition of nomadic yak herding. To establish effective conservation strategies and improvement plans, it is imperative to conduct in-depth studies on these animals, uncovering their genetic intricacies and identifying key genomic variants associated with adaptive traits. The present study focuses on whole-genome sequencing data from diverse Indian yak populations to elucidate the genomic adaptations associated with high-altitude hypoxia tolerance, physiological resilience, coat color variations, and skeletal modifications. Despite the critical role of yaks in these regions, the comprehensive genetic structure and evolutionary dynamics of these animals remain largely unexplored. Through comparative analyses using interpopulation statistical methodologies, including Fixation Index (FST) and Nucleotide Diversity Ratio (θπ), we examined the genetic makeup of Arunachali, Himachali, and Ladakhi yak populations alongside the Chinese Jinchuan yak. This analysis identified genomic loci subjected to selective pressures, revealing a suite of candidate genes indicative of adaptation to distinct environmental niches. Our integration of FST and θπ analyses highlighted substantial genetic signatures of selection, particularly in the Ladakhi yak, which exhibits enhanced adaptation to high-altitude environments. Notably, Ladakhi yaks demonstrated enriched pathways associated with altitude adaptation, underscoring their superior resilience compared to other Indian yak breeds. Comparative analyses between Indian and Chinese yaks unveiled distinctive genetic profiles, with Chinese yaks showing enrichment in pathways associated with tameness and domestication. These findings provide valuable insights into the molecular underpinnings of high-altitude adaptation and the diverse selective forces shaping the genomes of yak populations. Our study will contribute crucial knowledge on the genetic relationships between Indian yak populations, which is essential for the conservation of this native germplasm.

Bawri or Garri, a non-descript cattle population managed under an extensive system in Madhya Pradesh state of India, was identified and characterized both genetically and phenotypically to check whether or not it can be recognised as a breed. The cattle have white and gray colour and are medium sized with 122.5 ± 7.5 cm and 109.45 ± 0.39 cm height at withers in male and female, respectively. Double-digest restriction site associated DNA (ddRAD) sequencing was employed to identify ascertainment bias free SNPs representing the entire genome cost effectively; resulting in calling 1,156,650 high quality SNPs. Observed homozygosity was 0.76, indicating Bawri as a quite unique population. However, the inbreeding coefficient was 0.025, indicating lack of selection. SNPs found here can be used in GWAS and genetic evaluation programs. Considering the uniqueness of Bawri cattle, it can be registered as a breed for its better genetic management.

Genome-wide deleterious mutations were identified in zebu cattle (Bos indicus) using in silico approach. The ddRAD sequence data of Sahiwal cattle were annotated and aligned with the cattle reference genome (ARS-UCD1.2). A total of 279,383 SNPs were identified at Read Depth10, which were further filtered to 692 missense SNPs. These SNPs were further analyzed, for functional consequences, by using Variant Effect Predictor, PolyPhen, PROVEAN, and PANTHER tools. A total of 18 SNPs, were finally identified as deleterious, and among these, 12 SNPs were mapped on nine different genes. ERRAT, ProSA-web, Project HOPE, TM-Align, and YASSARA tools, further confirmed the protein malfunctioning of one missense (L290V) mutation of Retinoblastoma binding protein-5 (RBBP5) gene, transcribing a cell cycle regulatory protein and associated with Retinoblastoma in human. This derived bioinformatics pipeline may be useful for preliminarily identifying the deleterious DNA mutations in livestock, specifically in absence of any genetic disease records.

Background: Milk is essential part of diet across the globe and is a rich source of protein and calcium. Major protein component of milk is casein with beta-casein (β-casein) as the second most prevalent protein in cow milk. β-casein has 15 different genetic variants and of these A1 and A2 have gained research focus. All livestock as well as well human have proline at amino acid position 67 of β-casein, which is referred as A2 variant, but in cattle breeds, other genetic variant called A1 with histidine at amino acid position 67 is also present. This A1 type variant of â-casein or A1 type milk has been implicated as a potential etiological factor in several pathologies. Methods: The objective of the present study was to evaluate the A1and A2 β-casein variants of cow milk as factors affecting different hematological parameters and other parameters like glucose and insulin in streptozotocin (STZ)-induced diabetic C57/BL6 mice after the induction of diabetes. Diabetes was induced by injecting STZ intraperitoneally at dose of 45mg per kg of body weight for consecutive 5 days. Milk powder prepared from milk with A1A1 and A2A2 genotypes was used for feeding for three months. Result: After 3 months of feeding trial, it was observed that diabetic mice fed with A1A1 milk (STZ+A1A1) exhibited significantly elevated levels of glucose and insulin. Similarly, the levels of white blood cells, lymphocytes and neutrophils showed significant changes in STZ+A1A1 group compared to control and STZ+A2A2 group indicating the probable association A1A1 milk with inflammatory reaction. However, no significant changes were observed in parameters like red blood cells, hemoglobin, hematocrit or mean cell volume. In the mice group fed with A2A2 milk powder-based diet, no significant change was observed in the observed parameters except lymphocyte percentage which was lower compared to control group. In summary, our results show that A1 form of cow milk might have a proinflammatory effect.

The present study was aimed to identify the genome-wide SNPs associated with production and reproduction traits in 96 Indian Murrah buffalo genotyped based on ddRAD approach using Genome-Wide Association Study (GWAS) along with phenotypes of contemporary animals using mixed linear model for production and reproduction traits. A total of 27,735 SNPs identified using ddRAD approach in 96 Indian Murrah buffaloes were used for GWAS. A total of 28 SNPs were found to be associated with production and reproductive traits. Among these, 14 SNPs were present in the intronic region of AK5, BACH2, DIRC2, ECPAS, MPZL1, MYO16, QRFPR, RASGRF1, SLC9A4, TANC1, and TRIM67 genes and one SNP in long non-coding region of LOC102414911. Out of these 28 SNPs, 9 SNPs were found to have pleiotropic effect over milk production traits and were present in chromosome number BBU 1, 2, 4, 6, 9, 10, 12, 19, and 20. SNPs in the intronic region of AK5, TRIM67 genes were found to be associated with milk production traits. Eleven and five SNPs in the intergenic region were associated with milk production and reproduction traits respectively. The above genomic information may be used for selection of Murrah animals for genetic improvement.

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.