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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]

Twenty-four polymorphic and ubiquitously distributed microsatellite loci were utilized to genotype four populations of indigenous Mallard ducks in India using Khaki campbell as an out-group. The data was used to establish population parameters and genetic relationship among the populations. All the selected loci exhibited high polymorphic information content and gene diversity. F-statistics revealed population structure in four indigenous duck populations. There was not much differentiation among the duck populations along coastline, while land birds were found to be distinct from coastline ducks. The data presented here will be useful for undertaking duck improvement programmes in future. [ABSTRACT FROM AUTHOR]

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]

Background: Indian domesticated chickens have a wide variety of phenotypes. Unlike other chicken breeds, Kadaknath chicken has black meat and is used by indigenous tribal people for its invigorating and therapeutic properties. To look for the functional traits that might be contributing towards the acclaimed benefits, free radical scavenging capacity and metal chelating ability of Kadaknath meat were explored for the first time in comparison to the commercial Cobb broiler. Methods: During the period 2018-2020, breast and thigh meat were collected from chickens (n=20/ group) at their commercial slaughter age. Meat extract was used for qualitative evaluation of protein as well as the antioxidant capacity utilizing diverse in vitro methods corresponding to different antioxidation mechanisms. Result: Protein concentration (g/100g of tissue) in Kadaknath breast (25.25 ± 0.31) and thigh (19.98 ± 0.29) meat was significantly (P<0.05) higher than the Cobb. Breast meat had better scavenging capacity than the thigh. The superiority of the antioxidant capacity of Kadaknath meat was explicitly established by more than one in vitro assay. Free radical scavenging assays viz. 2,2-azinobis (3- ethyl-benzothiazoline-6-sulfonic acid) (ABTS); 1,1-diphenyl-2-picrylhydrazyl (DPPH) and Cupric reducing antioxidant capacity (CUPRAC) had significantly (P<0.05) higher values for Kadaknath in comparison to the Cobb broiler meat. Ferric reducing antioxidant power (FRAP) values (mM Fe2+/g of tissue) were also more in breast meat of Kadaknath (26.97±0.37) than the Cobb (15.24±0.40). Similarly, FRAP values were higher in Kadaknath (33.85±0.47) than the Cobb (19.2±0.31) thigh meat. Kadaknath had higher antioxidant capacity as reflected by metal chelation inhibition value. These findings help to explain the unique nutritional and functional characteristics of Kadaknath black-bone chicken and provide basic research data for exploring the commercial potential of its meat in the fields of functional foods, cosmeceuticals and nuutraceuticals. [ABSTRACT FROM AUTHOR]

Background: Indian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation. Sadly, the population of indigenous cattle (Bos indicus) is declining (8.94 % in last decade) and needs immediate scientific management. Genetic characterization is the first step in the development of proper management strategies for preserving genetic diversity and preventing undesirable loss of alleles. Thus, in this study we investigated genetic diversity and relationship among eleven Indian cattle breeds using 21 microsatellite markers and mitochondrial D loop sequence. Results: The analysis of autosomal DNA was performed on 508 cattle which exhibited sufficient genetic diversity across all the breeds. Estimates of mean allele number and observed heterozygosity across all loci and population were 8.784 ± 0.25 and 0.653 ± 0.014, respectively. Differences among breeds accounted for 13.3 % of total genetic variability. Despite high genetic diversity, significant inbreeding was also observed within eight populations. Genetic distances and cluster analysis showed a close relationship between breeds according to proximity in geographic distribution. The genetic distance, STRUCTURE and Principal Coordinate Analysis concluded that the Southern Indian Ongole cattle are the most distinct among the investigated cattle populations. Sequencing of hypervariable mitochondrial DNA region on a subset of 170 cattle revealed sixty haplotypes with haplotypic diversity of 0.90240, nucleotide diversity of 0.02688 and average number of nucleotide differences as 6.07407. Two major star clusters for haplotypes indicated population expansion for Indian cattle. Conclusions: Nuclear and mitochondrial genomes show a similar pattern of genetic variability and genetic differentiation. Various analyses concluded that the Southern breed 'Ongole' was distinct from breeds of Northern/ Central India. Overall these results provide basic information about genetic diversity and structure of Indian cattle which should have implications for management and conservation of indicine cattle diversity. [ABSTRACT FROM AUTHOR]

Background: Indian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation. Sadly, the population of indigenous cattle (Bos indicus) is declining (8.94 % in last decade) and needs immediate scientific management. Genetic characterization is the first step in the development of proper management strategies for preserving genetic diversity and preventing undesirable loss of alleles. Thus, in this study we investigated genetic diversity and relationship among eleven Indian cattle breeds using 21 microsatellite markers and mitochondrial D loop sequence. Results: The analysis of autosomal DNA was performed on 508 cattle which exhibited sufficient genetic diversity across all the breeds. Estimates of mean allele number and observed heterozygosity across all loci and population were 8.784 ± 0.25 and 0.653 ± 0.014, respectively. Differences among breeds accounted for 13.3 % of total genetic variability. Despite high genetic diversity, significant inbreeding was also observed within eight populations. Genetic distances and cluster analysis showed a close relationship between breeds according to proximity in geographic distribution. The genetic distance, STRUCTURE and Principal Coordinate Analysis concluded that the Southern Indian Ongole cattle are the most distinct among the investigated cattle populations. Sequencing of hypervariable mitochondrial DNA region on a subset of 170 cattle revealed sixty haplotypes with haplotypic diversity of 0.90240, nucleotide diversity of 0.02688 and average number of nucleotide differences as 6.07407. Two major star clusters for haplotypes indicated population expansion for Indian cattle. Conclusions: Nuclear and mitochondrial genomes show a similar pattern of genetic variability and genetic differentiation. Various analyses concluded that the Southern breed ‘Ongole’ was distinct from breeds of Northern/ Central India. Overall these results provide basic information about genetic diversity and structure of Indian cattle which should have implications for management and conservation of indicine cattle diversity. [ABSTRACT FROM AUTHOR]