DOUBLE DIGEST RESTRICTION ASSOCIATED DNA SEQUENCING FOR IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN GOATS

Abstract

Goat rearing is considered as an Animal husbandry activity which promptly supplements economy of the rural poor. India, with its vast animal genetic resources is blessed with 28 goat breeds which vary in different quantitative traits. Malabari and Attappady Black are two native goat breeds of Kerala, which differ significantly in several economic traits like prolificacy, milk production, milk quality and disease resistance. In this study, a novel reduced representation sequencing technique called double digest restriction associated DNA sequencing (ddRADseq) is applied on Malabari and Attappady Black goats, for identification of genetic variants which can be used for exploring many complex economical traits and to serve as markers for selection. DNA samples were isolated from 10 animals of each breed and were pooled into two samples to represent Malabari and Attappady Black goats. These two samples were digested using SphI and MlucI Restriction enzymes which resulted in 26,77,648 reads in Malabari and 17,40,350 reads in Attappady Black goats. A total of 66299, 28859 and 4266 variants were identified in Malabari in read depths of 2, 5 and 10, respectively. In case of Attappady Black, it was 61241, 21230 and 2251. Variants in read depth 10, were considered as high confidence variants. In Read depth 10, Malabari had 4140 SNPs which included 14 missense SNPs, 24 synonymous SNPs, 58 SNPs in untranslated regions and 4044 SNPs in noncoding regions. In Attappady Black groups, 29 missense SNPs, 30 synonymous SNPs, 82 SNPs in untranslated region and 2051 SNPs in non coding regions were present in 2192 high confidence SNPs discovered.

Keywords

• double digest restriction associated dna sequencing
• prolificacy
• malabari and attappady black goats