Radhika G.SHALU ELIZABETH SIMON2020-09-072020-09-072018https://krishikosh.egranth.ac.in/handle/1/5810150905Goats, commonly called as ‘poor man’s cow’ forms the basis of livelihood for economically weaker sections of society. India has 23 well defined goat breeds, of which Kerala has two native breeds, Malabari and Attappady Black, which vary significantly in prolificacy. Double digest restriction associated DNA sequencing (ddRADseq) is a modern reduced representation sequencing technique which is a powerful and inexpensive approach for identification of Single Nucleotide Polymorphisms (SNP) across populations. In this study ddRADseq technique was applied to highly prolific Malabari and low prolific Attappady Black goats to unravel the genetic variations existing between them. ddRADseq discovered 4140 SNPs and 126 INDELS in Malabari and 2192 SNPs and 59 INDELS in Attappady Black goats of which 55 per cent variants were common between the groups. A panel of 38 candidate prolific genes were screened and 25 SNPs were discovered in 20 genes which included one exonic variant and 18 intronic variants. Another set of 11 genes were identified based on the difference in allelic distribution of SNPs between the two groups, which might have an effect on prolificacy. Based on in silico studies, variant c.614-32789C>T in BMP6 was chosen for validation studies in 100 Malabari and 50 Attappady Black goats. PCR-RFLP revealed all the three genotypes TT, TC and CC, thus confirming the robustness of SNPs discovered by ddRADseq. SERPIND1 of super family Serpins is reported to have a major role in placenta formation in humans. Variant c.1259T>C identified in exon three of SERPIND1, showed significant association with litter size with a mean value of 1.348±0.071 for TT genotype and 2.27 ±.0.132 for TC genotype. This emphasized the relevance of this polymorphism and usefulness of ddRADseq in identifying novel SNPs in unexplored genes.RGS 14 gene which affects early embryonic development, harboured a missense mutation c.1624G>A resulting in p.Pro542Ser, suggesting a variation in protein quality. Expression study of RGS 14gene in endometrial tissues revealed a 3.35 fold higher expression in Malabari than Attappady Black goats which was statistically significant. Current study emphasized the relevance of ddRADseq in identifying novel SNPs in candidate genes responsible for economic traits and unexplored genes affecting complex traits.enThesis