Background: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH 5000 ) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here,

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 genetic diversity in two buffalo populations of northern India, the Bhadawari and the Tarai was assessed using a set of 22 heterologous (bovine) microsatellite markers. The average number of alleles across all loci in both populations was found to be 4.7, indicating that this set of 22 bovine microsatellite markers could be used to study genetic variation in buffalo species also. The overall polymorphic information content (PIC) value for these markers was 0.54. The average observed and expected heterozygosities for both populations were 0.59 and 0.64, respectively. Common alleles with varying allele frequencies in both populations also represented the genetic variability existing between Bhadawari and Tarai buffaloes. However the h estimates for population differentiation indicated low levels of differentiation between the two populations. This was further supported by the low genetic distance (0.155) between Bhadawari and Tarai, which was calculated using Nei's standard genetic distance method. The present study on Bhadawari and Tarai populations represents a much-needed preliminary effort that could be extended to other local buffalo populations of India as well. Zusammenfassung Genetische Diversita¨tsstudie von zwei nordindischen Büffelpopulationen mit MikrosatellitenmarkernDie genetische Diversität in zwei nordindischen Bü ffelpopulationen, Bhadawari und Tarai wurde mit 22 heterologen-(bovinen) Mikrosatellitenmarkern geschätzt. Die durchschnittlich geschätzte Allelzahl ü ber alle Genorte in beiden Populationen betrug 4,7 und zeigt, dass diese 22 bovine Mikrosatellitenmarker auch benutzt werden kö nnen, um die genetische Variabilität von Bü ffeln zu studieren. Der gesamte ÔÔPolymorphic Information ContentÕÕ (PIC) fü r diese Marker war 0,54. Die durchschnittlichen beobachteten und erwarteten Heterozygotiewerte fü r beide Populationen waren 0,59 beziehungsweise 0,64. Gemeinsame Allele mit unterschiedlichen Frequenzen in beiden Populationen stellten auch die genetische Variabilität dar, die zwischen Bhadawari und Tarai Bü ffeln besteht. Jedoch zeigten die Schätzungen fü r die Populationsdifferenzierung (h) niedrige Werte zwischen den zwei Populationen an. Dies wird auch gestü tzt durch den niedrigen genetischen Abstand (0,155) zwischen Bhadawari und Tarai, der mit Nei's-Standard genetischer Distanzmethode (Ds) berechnet wurde. Die vorliegenden Untersuchungen anhand von Bhadawari-und Tarai-Populationen stellen eine dringend benö tigte Basis dar, die auch auf andere lokale indische Bü ffelpopulationen ausgeweitet werden kö nnte.

The expression of genes and their regulation during lactation in buffaloes remains less understood. To understand the interplay of various genes and pathways, the milk transcriptome from three lactation stages of Murrah buffalo was analyzed by RNA sequencing. The filtered reads were mapped to the Bubalus bubalis as well as Bos taurus reference assemblies. The average mapping rate to water buffalo and Btau 4.6 reference sequence, was 75.5% and 75.7% respectively. Highly expressed genes (RPKM > 3000), throughout lactation included CSN2, CSN1S1, CSN3, LALBA, SPP1 and TPT1. A total of 12833 transcripts were common across all the stages, while 271, 205 and 418 were unique to early, mid and late lactation respectively. Majority of the genes throughout lactation were linked to biological functions like protein metabolism, transport and immune response. A discernible shift from metabolism in early stage to metabolism and immune response in mid stage, and an increase in immune response functions in late lactation was observed. The results provide information of candidate genes and pathways involved in the different stages of lactation in buffalo. The study also identified 14 differentially expressed and highly connected genes across the three lactation stages, which can be used as candidates for future research.

This study describes the muscle transcriptome profile of Bandur breed, a consumer favoured, meat type sheep of India. The transcriptome was compared to the less desirable, unregistered local sheep population, in order to understand the molecular factors related to muscle traits in Indian sheep breeds. Bandur sheep have tender muscles and higher backfat thickness than local sheep. The longissimus thoracis transcriptome profiles of Bandur and local sheep were obtained using RNA sequencing (RNA Seq). The animals were male, non-castrated, with uniform age and reared under similar environment, as well as management conditions. We could identify 568 significantly up-regulated and 538 significantly down-regulated genes in Bandur sheep (p≤0.05). Among these, 181 up-regulated and 142 down-regulated genes in Bandur sheep, with a fold change ≥1.5, were considered for further analysis. Significant Gene Ontology terms for the up-regulated dataset in Bandur sheep included transporter activity, substrate specific transmembrane, lipid and fatty acid binding. The down-regulated activities in Bandur sheep were mainly related to RNA degradation, regulation of ERK1 and ERK2 cascades and innate immune response. The MAPK signaling pathway, Adipocytokine signaling pathway and PPAR signaling pathway were enriched for Bandur sheep. The highly connected genes identified by network analysis were CNOT2 , CNOT6 , HSPB1 , HSPA6 , MAP3K14 and PPARD , which may be important regulators of energy metabolism, cellular stress and fatty acid metabolism in the skeletal muscles. These key genes affect the CCR4-NOT complex, PPAR and MAPK signaling pathways. The highly connected genes identified in this study, form interesting candidates for further research on muscle traits in Bandur sheep.

Three buffalo populations viz. Bhadawari, Tarai and local buffaloes of Kerala were genotyped using 24 heterologous polymorphic microsatellite loci. A total of 140 alleles were observed with an average observed heterozygosity of 0.63. All the loci were neutral and 18 out of the 24 loci were in Hardy Weinberg Equilibrium. The F IS values (estimate of inbreeding) for 16 loci in all the three populations were negative. This indicated lack of population structure in the three populations. The effective number of immigrants was 5.88 per generation between the Tarai and Bhadawari populations which was quite high suggesting substantial gene flow. The genetic distances revealed closeness between the Tarai and Bhadawari populations which was expected from geographical contiguity. The F ST values were not significantly different from zero showing no population differentiation. The Correspondence Analysis based on the allelic frequency data clustered the majority of the Tarai and Bhadawari individuals as an admixture.

Estimation of genetic variability and relationship among different livestock breeds is important for management of genetic resources for their sustainable utilization and conservation. This is more important when the livestock species, like camel, have shown a sharp decline in head count during the last decade. In the present study we estimated genetic variability and relationship among four camel breeds of India using 23 microsatellite loci. A total of 252 alleles were observed across all the four populations with mean number of alleles per locus as 8.04, 7.30, 6.39, and 7.43 for Bikaneri, Jaisalmeri, Kutchi, and Mewari breeds, respectively. The mean observed heterozygosity of the four breeds were 0.58, 0.57, 0.56, and 0.60 for Bikaneri, Jaisalmeri, Kutchi, and Mewari breeds, respectively and were lower than expected heterozygosity values. The mean estimates of F statistics were 0.227+/-0.044 (F(IT)), 0.157+/-0.038 (F(IS)), and 0.082+/-0.019 (F(ST)). The values were significantly different from zero for all the three measures and point towards the existence of population structure and moderate differentiation in four camel breeds. The exact test also indicated significant population differentiation (P < 0.001). The analysis of molecular variance revealed 12% of the variation attributed to among populations and 88% within populations. Sixty-nine percent of the individuals could be correctly assigned using "leave one out" procedure. All the individuals of Mewari and 42 out of 44 Jaisalmeri were correctly assigned. The existence of strong population structure in Jaisalmeri and Mewari camel was further substantiated by Nei's standard genetic distance as well as interindividual allele sharing distance. Thus these two breeds owing to selection for specific traits are distinct from other camel breeds.

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