Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle.

Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.

Genetic structure, population diversity and ancestry of Nicobari fowl based on mtDNA complete D-loop sequences.

Nicobari fowl constitute an endemic poultry germplasm of Andaman and Nicobar Islands, India. Genetic diversity, population structure and ancestry of Nicobari fowl were analysed with mitochondrial D-loop sequences. Analysis of complete D-loop sequences (1231-1232 bp) showed 46 polymorphic sites resulting in 26 haplotypes with overall haplotype diversity of 0.895 and nucleotide diversity of 0.0064. Analysis of molecular variance of spatial populations (sampling sites) of Nicobari fowl revealed that the estimated FST value as 0.229 among the populations. Tajima's D and Fu's FS tests indicated nonsignificant deviation from neutrality and the multimodal pattern of mismatch distribution in demographic expansion suggested that Nicobari fowl populations are in equilibrium. The median-joining (MJ) network of D-loop sequences with reference haplogroup sequences identifies the presence of haplogroups A, B, E1, E2, F and I in Nicobari fowl. The major haplogroup in Nicobari fowl was E (60%), which is otherwise found mainly in the Indian subcontinent. Phylogenetic analysis of Nicobari fowl with junglefowl by maximum likelihood method showed Gallus gallus murghi and G. g. spadiceus as maternal progenitors. Grouping of Nicobari fowl with their primary ancestor, Indian red Junglefowl (G. g. murghi) and the presence of Indian subcontinent-specific haplogroups (E2 and I) support the independent domestication of chickens in India. This study will help to design breeding strategy for conservation of Nicobari fowl in its island habitat.

Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers.

For proteome analyses, the tissue samples are mostly preserved either snap frozen or formalin-fixed, paraffin-embedded form. Use of RNAlater-a non-toxic solution primarily used to stabilize the RNA content of samples-in tissue preservation for proteome analysis recently described equally reliable with snap-frozen preservation in human tissues. Even though RNALater storage has great potential in the preservation of Peripheral Blood Mononuclear Cells (PBMC), its impact on the results of proteome analysis is poorly described at qualitative and quantitative measures. The present study investigated protein profiles of RNAlater preserved and fresh PBMCs using three extraction buffers viz. Triton X-100, RIPA and SDS. Proteins are separated in SDS-PAGE and quantified using densitometry. On an average 19.3 bands from fresh and 15.6 bands from RNAlater storage cells were obtained with a molecular weight ranging from 25 to > 250 kDa. RNAlater storage generated a fewer number and lesser quantity of low molecular weight proteins while yielded a similar or high quantity of high molecular weight protein fractions. The principal component analysis showed that Triton X-100 is inferior as compared to SDS and RIPA with respect to their protein bands and quantity yielded. While RNAlater is effective in preserving PBMC for proteome analysis, our findings warrant caution in its use in proteomics experiments especially if the target is low molecular weight proteins.