Empowering canine genomics: design and validation of a high-density SNP array for Indian dogs.

India harbors a substantial population of 9.43 million dogs, showcasing diverse phenotypes and utility. Initiatives focusing on awareness, conservation, and informed breeding can greatly enhance the recognition and welfare of the unique Indian canine heritage.

Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids.

Camels play a crucial socio-economic role in sustaining the livelihoods of millions in arid and semi-arid regions. They possess remarkable physiological attributes which enable them to thrive in extreme environments, and provide a source of meat, milk and transportation. With their unique traits, camels embody an irreplaceable source of untapped genomic knowledge.

Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations.

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.

Design and validation of high-density SNP array of goats and population stratification of Indian goat breeds.

Goats are the supporting pillars of rural economy contributing significantly to meat and milk production in India. It is a species targeted for fulfilling the interdependent goals of poverty reduction and creation of employment for supporting the rural income. The increased demand for goat products necessitates their genetic characterization and improvement to augment the production of native breeds.

Transcriptomics reveals key genes responsible for functional diversity in muscles of native black Kadaknath and broiler chicken.

Unlabelled: RNA sequencing-based expression profiles from muscles of black meat (Kadaknath) and white meat (broiler) chicken were compared to identify differentially expressed genes. A total of 156 genes with log fold change ≥  ± 2.0 showed higher expression in Kadaknath and 68 genes were expressed at a lower level in comparison to broiler.

Validation of stable reference genes in peripheral blood mononuclear cells for expression studies involving vector-borne haemoparasitic diseases in bovines.

Normalization of gene expression data using appropriate reference genes is critical to diminish any technical bias in an experiment involving quantitative real-time PCR (qPCR). To the best of our knowledge, this is the first report offering a systematic assessment of 14 potential reference genes (RPLP0, ACTB, RPS28, YWHAZ, SDHA, PPIA, RPS9, RPS15, UXT, GAPDH, B2M, BACH1, HMBS, and PPIB) for the identification of the most stable normalizers for qPCR of target genes in peripheral blood mononuclear cells (PBMCs) of bovines for vector-borne haemoparasitic diseases such as anaplasmosis, babesiosis, theileriosis, and trypanosomiasis. A total of 38 blood samples were collected from healthy as well as diseased cattle and buffaloes representing different haemoparasitic diseases.

Expression profiling of cytokine genes in peripheral blood mononuclear cells from infected and healthy cattle.

In this study, changes in expression profiles of genes encoding 14 cytokines (1, and ) were investigated amongst six infected and six healthy crossbred cattle. Health status of the animals was determined based on clinical signs, blood smear examination and molecular detection using -specific primers. Total RNA was isolated from the peripheral blood mononuclear cells of the infected animals as well as the healthy controls, which was further reverse transcribed to cDNA.

Comparative expression profiling of cytokine genes in Theileria annulata-infected and healthy cattle.

Theileriosis is one of the top ten economically important diseases in cattle in India. Cytokines are considered important mediators and regulators of the immune response to an infection. In the present study, the gene expression profiles of fourteen cytokines (IL1A, IL1B, IL2, IL4, IL6, IL8, IL10, IL12A, IL12B, IL16, TGFB1, TNFA, IFNA and IFNB) were compared in Theileria annulata-infected and healthy crossbred cattle.

First report on delineation of differentially expressed genes and pathways in milk somatic cells of mastitic and healthy Murrah buffaloes.

Despite immense contribution of buffaloes as dairy species, limited studies have addressed the bubaline mastitis as compared to cattle. This was the first differential transcriptomic study investigating the alterations induced by clinical mastitis in buffalo milk relative to healthy controls. Comparative gene expression profiling of three biological replicates of each group identified 1014 up-regulated and 999 down-regulated genes in the diseased buffaloes (Fold change > 2, FDR < 0.

Muscle transcriptome provides the first insight into the dynamics of gene expression with progression of age in sheep.

The dynamic synergy of genes and pathways in muscles in relation to age affects the muscle characteristics. Investigating the temporal changes in gene expression will help illustrate the molecular mechanisms underlying muscle development. Here we report the gene expression changes in skeletal muscles through successive age groups in Bandur, a meat type sheep of India.

Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India.

The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats.

Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits.

The study presents the miRNA profiles of two Indian sheep populations with divergent carcass and muscle traits. The RNA sequencing of longissimus thoracis muscles from the two populations revealed a total of 400 known miRNAs. Myomirs or miRNAs specific to skeletal muscles identified in our data included oar-miR-1, oar-miR-133b, oar-miR-206 and oar-miR-486.

Milk somatic cell derived transcriptome analysis identifies regulatory genes and pathways during lactation in Indian Sahiwal cattle (Bos indicus).

Background: The present study is an effort to understand the genomic drivers of lactation in Sahiwal (Bos indicus), the best milch cattle breed of the tropics.

Methods: RNA sequencing of four animals from early, mid and late lactation stages was performed using milk somatic cells as source of RNA.

Results: The genes encoding the milk casein and whey proteins showed highest expression in early and mid lactation, with a declining trend towards the late stage.

Comparative gene expression profiling of milk somatic cells of Sahiwal cattle and Murrah buffaloes.

India is the world's largest milk producing country because of massive contribution made by cattle and buffaloes. In the present investigation, comprehensive comparative profiling of transcriptomic landscape of milk somatic cells of Sahiwal cattle and Murrah buffaloes was carried out. Genes with highest transcript abundance in both species were enriched for biological processes such as lactation, immune response, cellular oxidant detoxification and response to hormones.

Skin transcriptome profiling of Changthangi goats highlights the relevance of genes involved in Pashmina production.

Pashmina, the world's finest natural fiber is derived from secondary hair follicles of Changthangi goats which are domesticated in Ladakh region of Jammu and Kashmir by nomadic pastoralists. Complex epithelial-mesenchymal interactions involving numerous signal molecules and signaling pathways govern hair follicle morphogenesis and mitosis across different species. The present study involved transcriptome profiling of skin from fiber type Changthangi goats and meat type Barbari goats to unravel gene networks and metabolic pathways that might contribute to Pashmina development.

Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India.

This study describes the muscle transcriptome profile of Bandur breed, a consumer favoured, meat type sheep of India. The transcriptome was compared to the less desirable, unregistered local sheep population, in order to understand the molecular factors related to muscle traits in Indian sheep breeds. Bandur sheep have tender muscles and higher backfat thickness than local sheep.

Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation.

The expression of genes and their regulation during lactation in buffaloes remains less understood. To understand the interplay of various genes and pathways, the milk transcriptome from three lactation stages of Murrah buffalo was analyzed by RNA sequencing. The filtered reads were mapped to the Bubalus bubalis as well as Bos taurus reference assemblies.

Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India.

Red Junglefowls (RJFs), the wild progenitor of modern day chickens (DCs), are believed to be in genetic endangerment due to introgression of domestic genes through opportunistic matings with domestic or feral chickens. Previous studies from India reported rare hybridization of RJFs in the wild. However, RJF population genetic structure, pattern of gene flow and their admixture with DC populations are poorly understood at the landscape level.

Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India.

The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed.

Molecular characterization of RNA binding motif protein 3 (RBM3) gene from Pashmina goat.

Pashmina goat inhabits the high altitude cold arid desert of Ladakh, India. This goat is known for its finest and costliest under fiber. Though the under fiber may be a part of its complex thermoregulation mechanism, the genetics of its adaptability under cold conditions is not known.

Development of parthenote following in vivo transfer of embryos in Capra hircus.

The aim of this study is to generate parthenogenetic embryos from chemically activated in vitro matured caprine oocytes and to study the in vivo developmental potency of such embryos. The parthenogenetic embryos (2-8 and 16 cells to morula stage) were surgically transferred in 26 recipients. Pregnancy in recipients following embryo transfer was monitored by ultrasonography.