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The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/ .

The study aimed at identifying the best genotypes for important candidate PIT 1 gene and seasonality influencing the yield and quality of milk, in the Jersey and Crossbred HF cattle population maintained at an organized farm in Mountain Livestock Research Institute, Manasbal, Kashmir. The Jersey and Crossbred HF cows (60 each) were genotyped for quality and yield traits. Milk samples (50 ml) were collected on weekly basis for quality evaluation for the years 2016-18, among all the four seasons of Kashmir. The milk quality traits studied were fat%, lactose%, protein%, SNF, density and ash. The quantity traits were average monthly milk yield, protein yield and fat yield. Genomic DNA was extracted using Phenol-chloroform method and association analysis was done. The PIT 1 exon VI (451 bp) was screened for polymorphisms using PCR-RFLP using HinfI restriction enzyme, revealing two genotypes (Pp and pp) for both the breeds. Allele ‘p’ was most frequently present in Crossbred HF cows (0.95) and Jersey cows (0.82). The genotype Pp in crossbred HF cows and pp in Jersey cows showed higher values for yield traits in all four seasons under study. In crossbred HF cows, the effect of genotype Pp was significant on fat% and SNF. The genotype pp effect was significant on fat% in Jersey cows. Winter and autumn seasons had significant effect on fat% in both breeds under study. Based on the study, it was concluded that breed, season, and genotype of the PIT 1 gene are highly associated with the milk quality and yield in the dairy cattle of Kashmir. Genome wide association studies are recommended for better understanding the effects of all genes on milk quality and quantity.

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Background: Polymorphisms in candidate beta-lactoglobulin genes are associated with traits of economic importance in cows and are related to milk composition, quality, production as well as cheese-production. The objective of the study was to evaluate the effects of breed, season and polymorphism on milk quality and yield in Jersey and Crossbred Holstein Friesian cows. Methods: The quality traits studied were fat %, lactose %, protein %, SNF, density and ash while quantity traits were average monthly milk yield, protein yield and fat yield. The beta-lactoglobulin gene exon IV (262 bp) was screened for polymorphisms by PCR-RFLP using BsuRI (Hae III) enzyme. Result: Our investigation revealed only two patterns AA and AB in both the breeds under study. BB genotype was absent. AA genotype was most abundant in Jersey cows (0.68) and crossbred HF cows (0.56). A allele frequency was highest in Crossbred HF cows (0.72) and Jersey cows (0.66). In Jersey genotype AB was observed to be responsible for high milk yield, protein and fat yield in each season whereas it was genotype AA of crossbred HF cows affecting milk yield, protein and fat yield. In crossbred HF cow, genotype effect was observed to be non-significant (p greater than 0.05) on all quality traits and effect of season was significant on lactose % and fat %. In Jersey cows, genotype and season effects were significant (P less than 0.05) on fat % concluding that the breed, season and genotype affectmilk quality and yield.

PstI and TaqI restriction fragment length polymorphism (RFLP) of caprine DRB3.2 revealed three genotypes under each RFLP in Changthangi goat. The genotypic and allelic frequency in PstI RFLP was calculated as 0.07, 0.72 and 0.20 for PP, Pp and pp genotypes and 0.43 and 0.57 for P and p alleles. In TaqI RFLP the frequencies were observed as 0.11, 0.61 and 0.27 for TT, Tt and tt genotypes and 0.41, 0.59 for T and t alleles. Alignment study indicates variability of nucleotides and amino acids between alleles and different breeds of goats. The nucleotide sequences reported in this paper have been submitted to the European Molecular Biology Laboratory GenBank and the accession numbers were AY496935, AY496061 and AY496062. A significant affect (P

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A genetic polymorphism study on butyrophilin gene was carried out to explore variability of this gene and to estimate effects of such variability on milk quality traits in crossbred cattle. Polymorphism was unraveled by conducting Hae III PCR-RFLP of this gene. Three genotypes such as AA, BB and AB and two alleles namely A and B were observed in crossbred population. The frequencies of genotypes and alleles were 0.78, 0.17 and 0.04 for AA, AB and BB genotypes, respectively, and 0.87 and 0.13 for A and B alleles, respectively. The nucleotides, which have been substituted from allele A to B, were observed as C to G (71 st nucleotide), C to T (86 th nucleotide), A to T (217 th nucleotide), G to A (258 th nucleotide), A to C (371 st nucleotide) and C to T (377 th nucleotide). The nucleotide substitutions at 71 st , 86 th and 377 th position of the fragment were found as silent mutations whereas nucleotide changes at 217 th , 258 th and 371 st positions were detected as substitution of amino acid lysine with arginine, valine with isoleucine, and leucine with proline from allele A to B. The genotypes had significant effects (p≤0.05) on total milk solid%, fat%, SNF%, while showing nonsignificant impact on total protein%. AA genotype produced highest average yield for all the traits.