Abstract
Keratin-associated proteins (KAPs) are among the main structural components of the animal fibers and form semi-rigid matrix wherein the keratin intermediate filaments (KIFs) are embedded. Variation in the KAP genes has been reported to affect the structure of KAPs and hence fiber characteristics. As no information is available on this gene in Capra hircus therefore, present work was undertaken to characterize and explore the different polymorphic variants of KAP1.4 gene at DNA level in different breeds/genetic groups of goats of Kashmir. Cashmere (Changthangi, 30 animals) and non-Cashmere (Bakerwal and Kargil goats, 20 animals each) goats formed the experimental animals for the study. Single strand conformation polymorphism technique was employed for exploring variability at gene level. On exploring the size variability in KAP1.4 gene between Ovine and Caprine, it was concluded that sheep KAP1.4 gene has a deletion of 30 nucleotides. In comparison to published nucleotide sequences of sheep, goat sequences explored are differing at positions 174, 462 and 568 and at these positions “G”, “T” and “T” nucleotides are present in sheep, but are replaced by “A”, “C” and “C” respectively, in goats. By SSC studies, two genotypes were observed in each genetic group and in Bakerwal goats the genotypes were designated as A1A1 (0.40) and A1A2 (0.60) and were formed by two alleles A1 (0.70) andA2 (0.30). The different SSC patterns observed in Kargil goats were designated as B1B1 (0.35) and B1B2 (0.65) genotypes with frequencies of B1 and B2 alleles as 0.675 and 0.325, respectively. Similarly, two genotypes C1C1 (0.60) and C1C2 (0.40) were observed in Changthangi goats and the frequencies of C1 and C2 alleles were 0.80 and 0.20, respectively. These alleles were later confirmed by sequencing. The sequences of these alleles are available in NCBI under Acc. No's. JN012101.1, JN012102.1, JN000317.1, JN000318.1, JQ436929 and JQ627657. It was concluded that all the alleles observed in a breed were unique to the breed. The designated A1 and A2 alleles of Bakerwal goats differ from each other at positions 245 and the nucleotides observed were “C” or “A” and at position 605 of the nucleotide sequence “T” or “C”, were observed. The designated B1 and B2 alleles of Kargil goats differed from each other at positions 224, 374, 375 and 521. The nucleotides observed in two SSC pattern were C→G, A→G, G→A and T→C, respectively. The designated C1 and C2 alleles of Changthangi goats differed from each other at one position 440 with the change of “A”→“C”.
Only two mutations C224G and G375A in Kargil goats resulted in change of the Cysteine (C)→Serine (S) and Alanine (A)→Threonine (T), respectively. The nucleotide sequences of KAP 1.4 gene in Bakerwal, Kargil and Changthangi goats showed 99.7% similarity with each other and 96.7% with sheep and 74.4% with mice. Average guard fiber length and diameter were 81.02±0.16mm and 67.53±0.97μm, respectively, and average down fiber length and diameter was 48.38±0.70mm and 13.32±0.29μm, respectively for Changthangi goats. Average guard fiber length and diameter were 63.51±4.52mm and 105.31±4.48μm, respectively for Bakerwal goats and 62.60±5.03mm and 107.18±2.30μm, respectively for Kargil goats. The effects of the observed genotypes on Cashmere fiber diameter, Cashmere fiber length in Changthangi goats and guard fiber length and guard fiber diameters in Changthangi, Kargil and Bakerwal goats were found to be non-significant (P>0.05).The nonsignificant association between the polymorphism and fiber attributes reported herein may be due to small sample size.
► Molecular characterization of KAP1.4 gene of goats ► DNA polymorphism in Bakerwal, Kargil and Changthangi breeds of goats ► PCR-SSCP analysis to explore polymorphism ► Gene sequencing to confirm the allelic variants of KAP1.4 gene as observed in SSCP ► Nucleotide phylogenetic analysis of goat breeds