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Genetic variants cause changes in genetic composition and are accountable for uniqueness of genomes of individuals. Copy number variations (CNVs) cause genetic variations due to loss or gain of DNA segments varying from 50 bp to several mega base pairs (Mb) compared with a reference genome. These unbalanced structural variants are heritable and have potentially greater effect than SNPs. The present study was conducted on whole genome resequencing (WGS) data of swamp buffalo for identification of CNVs. Sample of swamp buffalo was collected from Manipur and karyotyped and confirmed to be of swamp type. After quality and quantity checking it was sent for sequencing with Illumina Hiseq 2000 platform. Paired end reads of WGS data were analysed using Read depth (RD) based approach aligning to the reference Mediterranean riverine buffalo assembly. CNVs were identified using CNVnator with standardized parameters and total 587 CNVs were found in swamp buffalo. Among CNV events, 405 deletions and 182 duplications were identified. These variations comprised of 5.82% of reference genome. This was the first Genome-wide CNV study in indigenous swamp buffalo with reference to buffalo genome using Read Depth based approach. [ABSTRACT FROM AUTHOR]

The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise FSTvalue among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034–0.00555, and the net divergence (Da) was 0–0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks. [ABSTRACT FROM AUTHOR]