Milk somatic cell DNA isolation and characterization of κ-casein gene in Halari donkey milk.

Halari donkey breed is one of the indigenous breeds of India and its population is rapidly decreasing. The Jenny milk is more similar to human milk, exhibits a wide range of probiotic diversity and hypo-allergenicity, especially among infants suffering from cow and buffalo milk protein allergy. Some studies indicated low levels of κ-casein fraction of casein protein in donkey milk. The k-casein gene was not amplified from the DNA derived from the milk somatic cells of Halari donkeys. The Halari donkey milk has low somatic cells count. We report the first isolation of DNA from milk somatic cells of Halari donkeys with subsequent characterization of k-casein gene. Through our work, we showed that the milk somatic cells can be used as a non-invasive source for DNA isolation towards molecular studies. It also proved the presence of k-casein gene in Halari donkey milk by its amplification from isolated DNA.

Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds.

The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.

Identification and characterization of single nucleotide polymorphisms in DMRT3 gene in Indian horse (Equus caballus) and donkey (Equus asinus) populations.

Equines' ability in racing and riding as well as gaitedness have influenced the human civilization. Aim of this study was to identify and characterize the novel polymorphisms or SNPs in DMRT3 gene in Indian horse and donkey breeds. In this study, the DMRT3 gene was sequenced and characterized in 72 Indian horses' and 33 Indian donkeys' samples. One SNP (A > C) at 878 was found in studied horses while identical SNPs (A > C) at two different nucleotide positions i.e., 878 and 942 in DMRT3 gene (chromosome 23) were observed in studied Indian donkey breeds. Horses and donkeys both have a non-synonymous mutation (A > C) at nucleotide 878 (codon 61) that converts a Stop codon (TAG > TCG) to coding codon Serine, whereas donkeys have a synonymous mutation at nucleotide 942 (codon 82) that converts Serine (TCA > TCC) into Serine. A phylogenetic tree indicated that the DMRT3 gene was equally distributed among the equine breeds. Most of the donkey breeds have been shown high levels of genetic diversity while horse breeds and Halari donkey showed the least genetic diversity. Mutation in DMRT3 has a major impact on gaitedness in horses and is presented at a high frequency in gaited breeds and in horses breed for harness racing.

Characterization of Partial Sequence of Myostatin Gene Exon 2 along with SNP detection in Indian Horse Breeds (Equus caballus).

India has well documented horse and pony breeds; however, the population is well diversified in different geographical regions. The Myostatin gene is one of the most profoundly studied genetic components for the detection of SNP's for the performance analysis in horses. In the present study, the MSTN exon 2 partial cds were amplified, sequenced and characterized in about 60 samples of eight different breeds of Indian horses. The results indicated the transition of Thymine to Cytosine (T>C) as single nucleotide polymorphisms in the partial sequence of exon 2 of the MSTN gene at two different codon positions (T12C, T13C) on chromosome 18. The haplotypes and phylogeny of the MSTN gene in the selected horse population were also analyzed. The overall and singleton haplotype are two different entities, indicating the variation among breeds is unique while the gene is equally distributed throughout the population. The phylogeny suggests that all the breeds are somehow equally distributed in their specific geographical tracts. It is the first study of MSTN gene variations in Indian horse breeds, which provides insight into predicting athletic performance as well as phylogeny. This study provides useful genetic information on Indian horses that can be used to model the racing performances of the breeds.