Soumen Naskar

Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): evidence for duplication.

The genetic diversity of MHC class II DQ genes was investigated in riverine buffalo (Bubalus bubalis) by PCR-RFLP and sequencing. Highly variable regions (exons 2-3) of DQ genes were amplified from 152 buffaloes and genotyped by PCR-RFLP. Alleles identified by differential restriction patterns were sequenced for the characterization. PCR-RFLP was a rapid method to discriminate between DQA1 and duplicated DQA2 genes in buffalo, however, the method appeared to be inadequate for determining the more complicated DQB genotypes. A total of 7 and 10 alleles were identified for DQA and DQB loci, respectively. Nucleotide as well as amino acid variations among DQ alleles particularly at peptide binding regions were high. Such variations were as expected higher in DQB than DQA alleles. The phylogenetic analysis for both genes revealed the grouping of alleles into two major sub-groups with higher genetic divergence. High divergence among DQ allelic families and the isolation of two diverse DQA and DQB sequences from individual samples indicated duplication of DQ loci was similar in buffalo to other ruminants.

Strategies to Improve Livestock Genetic Resources to Counter Climate Change Impact

Global diversity of livestock in the form of many different species and breeds in a variety of production environments is indicative of the fact that it has developed over time in sync with the ecosystem. The developing world is particularly enriched with livestock breed portfolio. Natural selection has mainly acted on fitness including adaptability and reproductive success, whereas selection practised by livestock keepers and animal breeders has been need based. As against highly structured breeding programmes and intensive selection in developed world, livestock of developing world have largely been subjected to differential selection pressures in the form of their ability to survive in harsh production environments and challenged inputs. The last few decades have witnessed large-scale erosion of livestock genetic diversity. Climate change (CC) through its direct and indirect effects including its mitigation measures is believed to have influenced the erosion. Faster loss of animal genetic diversity poses greatest threat to the sustainability of the sector. The presence of varied livestock species and their breeds with widely variable performances offers the opportunity for genetic improvement. In the absence of it, we risk progress in this sector. Reorientation of livestock breeding is required to address the issues of CC. Although resource-use efficiency is imperative, careful trade-off between livestock production, productivity and adaptability will be required. Breeding strategies for livestock genetic resources to counter CC impact will not be fundamentally different in the future. Natural stratification of species and breeds of livestock shall be an important guide in the design. Appropriate policy framework, large-scale cooperation in knowledge and resources and awareness will be crucial.

Genetic Adaptability of Livestock to Environmental Stresses

The concept of adaptability revolves around fitness describing relative ability of an individual to survive and reproduce next generation to ensure continued survival of the population and is the result of natural selection over many generations. Current trend in genetic selection has severely eroded the genetic base ignoring the diversity of the production milieu, importance of adaptation, production of multiple products and social value of the livestock. The problem has been compounded with non-capturing of environmental costs though animal genetic resources (AnGR) on extensive and intensive scale are affected by direct impacts of climate change. Unplanned genetic introgression and crossbreeding has contributed to the greatest extent toward the loss of indigenous breeds. The genetic mechanism influencing fitness and adaptation is not well explored and adaptation traits are usually characterized by low heritability. Further, it may be difficult to combine the adaptation traits with high production potential as there seem to be different physiological and metabolic processes involved. Though decision regarding matching genotypes with environment or vice versa will be situation specific, the low and intermediate level of animal production in many parts of the world suggests that increased yields and efficiency will be more environmentally sustainable than extensive goals ensuring genetic diversity, environmental soundness, animal health and welfare, and social viability. Breeding for climate change adaptation or mitigation will not be necessarily different from existing programs. However, the problems associated with measuring the phenotypes relevant to adaptation have to be overcome. Breeding indices should be balanced to include traits associated with heat resilience, fertility, feed conversion efficiency, disease tolerance and longevity in addition to higher productivity, and give more consideration to genotype by environment interactions (GxE) to identify animals most adapted to specific conditions and natural stratification of breeds and species by climatic zones. Favorable correlation suggests that if major importance is placed on performance traits in stressful environments, adaptability traits would not be compromised and thus the most productive and adapted animals for each environment need to be identified for breeding purposes. Recent successes like slick hair gene in cattle, halothane gene in pig asks for extensive efforts for finding significant quantitative trait loci (QTL) for stress and exploitation of heat shock proteins (HSP). Implementation of marker-assisted breeding value estimation (MA-BVE) using dense genome map for highest possible accuracy will be a welcome step. There is a need of extensive study of interaction among the drivers of changes of climate and livestock, studying it in a composite manner. Appropriate organizational structures and adequate funding to support a climate resilient animal agriculture will be vital.

A comparative study of SINE insertion together with a mutation in the first intron of follicle stimulating hormone beta gene in indigenous pigs of India

The Follicle stimulating hormone beta polypeptide (FSHβ) gene has been investigated as a candidate gene for litter size because of its role in maturation of small and medium follicles into ovulating large follicles. Genes coding follicle stimulating hormone have been found to have significant effects on litter size in pigs. The aim of the study was to investigate the polymorphism of the first intron of FSH-β gene present in Ghungroo, Niang Megha and Nagaland local pigs of India. PCR based short interspersed nuclear elements (SINE) detection method and PCR–RFLP were carried out to identify the polymorphism in FSHβ gene. Significantly higher frequencies of SINE−/− and SINE+/− genotypes were observed in Ghungroo pigs as compared to Niang Megha and Nagaland local pigs. PCR–RFLP study also showed higher frequency of T allele in all the three breeds even though there existed difference in genotypes among breeds. Association studies clearly demonstrated that SINE−/− genotypes have significantly higher litter size and weight at birth as well as at weaning. SINE −/− genotypes have higher number of live births too. Moderately high D′ value indicates that haplotypic pattern within the two loci can be utilized for marker assisted selection for litter traits in pigs.

cDNA characterization and molecular analysis of buffalo MHC class II gene, DRA (Bubu-DRA).

Abstract Sakaram, D., Niranjan, S.K., Kumar, S., Naskar, S., Deb, S.M., Mitra, A., Sharma, A. and Sharma, D. 2010. cDNA characterization and molecular analysis of buffalo MHC class II gene, DRA (Bubu-DRA). J. Appl. Anim. Res., 37: 73–76. Full cDNA of DRA gene was amplified in Murrah buffalo (Bubalus bubalis) and analysed to identify the genetic variability. Buffalo DRA (Bubu-DRA) sequence showed highest similarity with cattle (98%) followed by goat (96.5%) and sheep (96.1%). DRA gene was highly conserved among all the species especially ruminants. The residues involved in antigen binding at peptide binding site (PBS), N-linked glycosylation and heterodimer formation were highly conserved across the species. Unlike other MHC molecules, PBS sites of Bubu-DRA were highly conserved in al domain among all species. The absence of much variation in Bubu-DRA supports the notion that gene is mostly conserved among all mammalian species. However, highly conserved DRA gene among ruminants including buffalo may be attributed to its recent separation in evolutionary process.

Molecular characterization of MHC-DRB cDNA in water buffalo (Bubalus bubalis)

In the present study, water buffalo MHC (Bubu)-DRB cDNA was cloned and characterized. The 1022 base long-amplified cDNA product encompassed a single open reading frame of 801 bases that coded for 266 amino acids. The Bubu-DRB sequence showed maximum homology with the BoLA-DRB3*0101 allele of cattle. A total of seven amino acid residues were found to be unique for the Bubu-DRB sequence. The majority of amino acid substitutions was observed in the β1 domain. Residues associated with important functions were mostly conserved. Water buffalo DRB was phylogenetically closer to goat DRB*A.

Genetic characterisation of buffalo MHC (Bubu)-DQB cDNA molecule

A 771 nucleotide long cDNA molecule corresponding to major histocompatibility complex (MHC)-DQB gene was amplified, cloned and sequenced from water buffalo (Bubalus bubalis). Open reading frame of the Bubu-DQB sequence was short by three nucleotides from the DQB genes of the other ruminants. Nucleotide similarity of Bubu-DQB was highest with cattle DQB alleles (84–97%), followed by goat (88.8%) and sheep (87.5%). The sequence comparison revealed that the DQB gene was highly variable in buffalo particularly, in exon 2 (β1 domain). A total of 45 amino acid substitutions were identified in Bubu-DQB compared to cattle DQB*0101 sequence, with a maximum (27) in β1 domain. The residues involved in antigen binding and heterodimer formation were found to be different in buffalo DQB sequence compared to other species. Phylogenetic study showed that the Bubu-DQB has evolved prior to the diversification of common DQB alleles in ruminants. Our study revealed the high genetic variation in the DQB gene in buffalo, which might have generated to recognise species specific antigens.

Microsatellite and Mitochondrial Diversity Analysis of Native Pigs of Indo-Burma Biodiversity Hotspot

ABSTRACT Assessment of genetic diversity in indigenous animals is an important and essential task for animal genetic improvement studies as well as conservation decision-making. The genetic diversity and evolutionary relationships among geographically and phenotypically distinct three pig breeds/types native to Indo-Burma and Eastern Himalayan global biodiversity hotspots were determined by genotyping with a panel of 22 ISAG recommended microsatellite loci as well as sequencing partial MTRNR1gene. The mean number of alleles per locus, effective number of alleles and observed heterozygosity were found to be 11.27 ± 0.85, 5.29 ± 0.34, and 0.795 ± 0.01, respectively. The moderate FST value (0.115 ± 0.01) indicated a fair degree of genetic differentiation among the native breeds. The Nei’s unbiased genetic identity estimates indicated less genetic distance (0.2909) between Niang Megha and Tenyi Vo pigs than the both individually with Ghoongroo breed. The divergence time was also estimated from the microsatellite analysis. Analysis of MTRNR1gene revealed distinct clustering of native Indian pigs with Chinese pigs over European pigs. The study revealed the abundance of genetic variation within native Indian pigs and their relationships as well as genetic distances.

Evaluation of pig rearing farmers of north east India as prospective breeder: a retrospective analysis.

The present study was conducted for objective evaluation of the pig rearing farmers of north east India as breeder. Preliminary survey of persons engaged in pork production and processing were made, and reproductive tracts of slaughtered animals were collected from organized (ORG-) and unorganized (UNORG-) slaughter houses in and around Guwahati for assessing their reproductive status through morphometric examination and maturation potential of oocytes. The survey revealed that male pigs, sourced from organized farms, were mostly slaughtered at 8–12 months of age, whereas female pigs were slaughtered after third or fourth farrowing, at ORG-slaughter houses. Pigs slaughtered at UNORG-slaughter houses were mostly sourced from primary producers and household enterprises, and stage of reproductive life was not an important factor influencing the decision to selling. Organometry of female genital organs showed higher values (P<0.05) for pigs slaughtered in ORGslaughter houses. Further, higher numbers (P<0.05) of corpus luteum were found in ORG-ovaries. However, higher number (P<0.05) of surface follicles, in-vitro matureable oocytes and in-vitro matured oocytes were found in UNORG-ovaries. The results of present study suggest that female pigs of unorganized production system are more likely to be sold and slaughtered before realizing their (re) production potential.

Molecular Characterization of Bubaline Integrin β2 (ITGB2) cDNA

Abstract Sharma, D., Niranjan, S.K., Kumar, S., Deb, S.M., Naskar, S., Sharma, A. and Mitra, A. 2010. Molecular characterization of bubaline integrin β2 (ITGB2) cDNA. J. Appl. Anim. Res., 37: 217–220. A 2310-bp long buffalo (Bubalus bubalis) cDNA sequence of Integrin b2 (ITGB2) gene was characterized. At nucleotide sequence level, buffalo ITGB2 exhibited 96–98% homologies with other ruminants like cattle, bison, sheep, goat and deer. In coding region, total thirty two nucleotide differences have been observed between buffalo and cattle sequences including 15 non-homologous substitutions. Importantly, a conserved site (22) in PSI domain of the ruminants (Thr) was substituted in buffalo (Ala) indicating normal function of the integrin unless the second mutation in CD lie molecule coexists. Buffalo ITGB2 has seven differences in I-like domain region as compared to cattle. The transmembrane and cytoplasmic regions were highly conserved among buffalo and other ruminants. High homology and close phylogenetic association among ITGB2 sequences of the ruminants including buffalo indicates highly conserved nature of the gene.