Andaman local goat: mitochondrial genome characterization and lineage analysis

Abstract

Andaman local goat (ALG) is an endemic goat germplasm of Andaman and Nicobar Islands, notable for its adaptability to the hot and humid climate of these islands. Due to lack of a proper breeding plan and indiscriminate crossbreeding, the breed is under threat and its population is on a declining trend. Designing and implementation of a proper breeding plan necessitates the genetic characterization of the breed. Moreover, origin, evolution and phylogeography of the breed is still not well understood. Therefore, the present study deals with next generation sequencing based whole mitochondrial genome characterization of Andaman local goat and its evolutionary relationship with different goat breeds all over the world. The mitogenome was 16,640 bp in length containing 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNA subunits (rRNAs) and a non-coding region. Nucleotide composition and AT-GC skewness indicated that the mitogenome had a biasedness towards A + T over G + C. Incomplete or truncated stop codon was detected in ND1, ND2, COX3, ND3 and ND4. Presence of 16 intergenic spacer regions of length ranging from1 bp to 7 bp and 8 overlapping regions ranging from 1 to 40 bp were also detected. Phylogenetic analysis indicated that ALG is included under haplogroup or lineage A of Capra. Moreover, evolutionary analysis revealed that ALG formed a separate cluster and was phylogenetically close to some Chinese goat breeds and Jamnapari goat breed of Bangladesh. The findings of the study throw light on the evolution of the breed and will be vital for sketching a suitable breeding programme for the conservation of the breed.