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The present investigation was focused to study genomic diversity of Indian swamp buffalo populations through reduced representation approach (ddRAD). The heterozygosity (F ST ) among the swamp buffaloes was 0.11 between Assam and Manipuri; 0.20 between swamp (Manipuri) and riverine buffaloes; 0.30 between swamp (Manipuri) and cattle. The average observed and expected heterozygosity in swamp buffalo populations was 0.254 and 0.221 respectively. The Inbreeding coefficient (F IS ) value was 0.02 among the swamp buffaloes. PCA and structure analysis revealed Manipuri swamp buffalo was genetically distinct and closely related to Nagaland swamp buffalo and least to Assam swamp buffalo. Identification of selective sweeps revealed 1087 regions to have undergone selection related to immune response, adaptation and nervous system. A total of 3451 SSRs were identified in the genome of swamp buffaloes. The study evidenced the genomic diversity in the swamp buffalo populations and its uniqueness in comparison with riverine buffalo and cattle., Competing Interests: Declaration of Competing Interest The author(s) declare that there are no competing interests., (Copyright © 2020. Published by Elsevier Inc.)

The present study was carried out to identify and annotate the genome wide SNPs in Murrah buffalo genome. A total of 21.2 million raw reads from 4 pooled female Murrah buffalo samples were obtained using restriction enzyme digestion followed by sequencing with Illumina Hiseq 2000. After quality filtration, the reads were aligned to Murrah buffalo genome (ICAR-NBAGR) and Water buffalo genome (UMD_CASPUR_WB_2.0) which resulted in 99.37% and 99.67% of the reads aligning, respectively. A total of 130,688 high quality SNPs along with 35,110 indels were identified versus the Murrah bufffalo genome. Similarly 219,856 high quality SNPs along with 15,201 indels were identified versus the Water buffalo genome. We report 483 SNPs in 66 genes affecting Milk Production, 436 SNPs in 38 genes affecting fertility and 559 SNPs in 72 genes affecting other major traits. The average genome coverage was 13.4% and 14.8% versus the Murrah and Water buffalo genomes, respectively., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The aim of this Research Communication was to contribute to the knowledge of milk sialic acid concentration of bovines with specific focus on India. Sialic acids (SA) are important constituents of mammalian milks. Buffaloes are the main milk producing species in India, therefore, our research focused on both cow and buffalo. Two Indian cattle (Bos indicus) breeds (Sahiwal, Tharparkar), one cross bred cattle - Karan Fries (Tharparkar × Holstein Friesian) and a buffalo breed (Murrah) were selected. Systematic comparisons of the total, free and bound form of SA and also its distribution over the course of lactation- colostrums and mature milk (120-140 d) was generated. Animal management, sample collection and methodology of SA estimation were identical for the different groups. Colostrum had the highest concentration of SA, which declined with the progress of lactation in all the groups. Majority of the SA existed in bound form. No significant (P < 0.05) difference was recorded in the total, bound or free SA across all the groups. However, differences were obvious in the total and bound SA level in the mature milk. Indian cattle, Sahiwal and Tharparkar were equivalent, but had higher concentration of total and bound SA than crossbred cattle. Milk of buffalo had SA equivalent to that of crossbred cattle. The mean (se) levels of total SA was 23.4 (0.8), 25.8 (2.4), 20.3 (0.6) and 20.2 (1.2) in Sahiwal, Tharparkar, cross bred and Murrah buffalo, respectively. The findings suggested that milk of indigenous cattle may be a potential source of SA, a bioactive compound with beneficial effect on human health and a potential functional ingredient in foods. Results add value to the currently declining indigenous cattle of India.

The buffalo population of Uttar Pradesh (UP) constitutes 26.1% of the total buffalo population of India, yet this population has not been classified into distinct breeds or subpopulations due to lack of systematic study. Genetic variation at 30 microsatellite loci was examined and statistical analysis was carried out to reveal genetic diversity, demographic parameters of these buffaloes and to investigate the existence of population substructures underlying geographical distribution. The mean number of alleles per locus was 13.26 and mean effective number of alleles was 3.74, whereas mean observed and expected heterozygosities were found to be 0.57 and 0.67 in UP buffaloes. Principal component analysis (PCA) based on allele frequency data revealed subclustering of UP buffalo population. Bayesian analysis result also revealed clear membership of individuals into five clusters indicating a genetic subdivision within the UP buffalo population. The buffaloes of Western and Central regions of UP were subtly separated while buffaloes of Tarai area and Bhadawari buffaloes revealed distinctive population structure. The buffaloes of Mau, Ballia and Ghazipur districts of Eastern region also had a distinctive genetic structure. The analysis of data on buffaloes of Indo-Gangetic plains revealed that population was in mutation drift equilibrium. The observed mean M ratio in the population was above the critical significance value (Mc) suggesting that it has not suffered any severe reduction in effective population size. The statistical tests revealed a historical constancy of size of buffalo in this geographical area. The high level of genetic variability indicates UP buffalo population is a vast reservoir of genetic diversity and this shall help in taking informed conservation decisions and sustainable utilization.

Background: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species., Results: A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0)., Conclusion: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.

The water buffalo (Bubalus bubalis) is an important dairy animal on the Indian subcontinent and in Southeast Asian countries. The diversity and differentiation among 12 populations or breeds of buffalo were studied. Data were generated and analyzed from 527 animals belonging to 10 recognized breeds and 2 additional populations of Indian buffalo by using 22 microsatellite loci. Relationships among buffalo breeds and populations were estimated based on genetic distances. The Bayesian analysis grouped 12 populations into 8 distinctive clusters. Geographically close breeds clustered together, except for the Jaffarabadi and Murrah, which were not in geographic contiguity. The Mantel test revealed nonsignificant correlations between genetic and geographic distances. This supports the hypothesis that buffaloes have been domesticated at different places for specific purposes. The phylogenetic relationship based on microsatellite loci supported the breed classification based on body size. The Toda breed, which is considered to be endangered, had genotypes similar to those of the surrounding buffalo populations.

The sequence of myostatin gene (growth differentiation factor 8 [GDF 8]) in Indian riverine buffalo (Bubalus bubalis) is reported. The genomic DNA as well as mRNA were sequenced. The sequence is conserved across all the livestock species. Five nonsynonymous changes as compared to cattle were found in this study and were also confirmed by mRNA sequence. Two intronic single nucleotide polymorphisms (SNPs) were identified in buffalo.

Background: Indian cattle (Bos indicus) and riverine buffalo (Bubalus bubalis) give a poor yield of milk but it has a high fat and protein percentage compared to taurine cattle. The identification of QTLs (Quantitative Trait Loci) on BTA14 and BTA6 and its subsequent fine mapping has led to identification of two non conservative mutations affecting milk production and composition. Our objective was to estimate the frequency of K232A (DGAT1--diacylglycerol-acyltransferase 1) and Y581S (ABCG2--ATP binding cassette sub family G member 2) polymorphisms in diverse cattle and buffalo breeds of India having large variation in terms of milk production., Results: We screened the reported missense mutations in six cattle and five buffalo breeds. The DGAT1K and ABCG2Y alleles were found to be fixed in Indian cattle and buffalo breeds studied., Conclusion: This study provides an indirect evidence that all the Indian cattle and buffalo breeds have fixed alleles with respect to DGAT1 and ABCG2 genes reported to be responsible for higher milk fat yield, higher fat and protein percent.