Power of exclusion of 19 microsatellite markers for parentage testing in river buffalo (Bubalus bubalis)

In the present study, 19 microsatellite markers were assessed for their power of exclusion to test parentage in river buffalo. Microsatellite genotypes of 216 unrelated buffaloes belonging to five different breeds were utilized for the study. The probabilities of exclusion were calculated for three hypothetical situations viz. paternity testing (PE1), one parental genotype unavailable (PE2) and exclusion of both parents i.e. substituted offspring (PE3). The mean probability of exclusion across 19 investigated markers in buffalo was 0.578 (PE1), 0.405 (PE2) and 0.764 (PE3) respectively. The probability of exclusion for paternity (PE1) ranged between 0.297 and 0.814 across different markers. The exclusion probability for the cases one parent unavailable (PE2) and substituted offspring (PE3) varied from 0.143 to 0.688 and 0.465 to 0.946 respectively. Polymorphism information content and expected heterozygosity were found to have significantly high correlation with probability of exclusion of microsatellite markers. The cumulative PE1 of nine marker loci was estimated to be 0.9999 while in case of absence of one of the parental genotypes, a minimum of 11 markers were required to achieve a cumulative PE2 of 0.999. In conclusion, the present study proposes two multiplex sets with four and five markers respectively for routine parentage testing in buffalo and an additional set of four markers for doubtful cases of paternity.

Involvement of transcription factor GATA-4 in regulation of CYP19 gene during folliculogenesis and luteinization in buffalo ovary

CYP19 gene encode aromatase, the key enzyme of estrogen biosynthesis, is regulated in species- and tissue-specific manner by alternate use of different promoters. Previously, we have reported the cloning and characterization of tissue-specific promoter and transcripts in buffalo ovary and placenta. In human and rat ovary, FSH induces the phosphorylation of transcription factor CREB (cAMP response element binding protein) through PKA pathway which binds to cAMP response element like sequence (CLS) in CYP19 gene ovarian promoter. However, in buffalo as well as in bovine, in silico analysis of ovary specific promoter sequence identified a single base pair deletion in CLS site and is designated as CLS-like sequence. To understand if CLS with a point mutation is still a functional cis-element and is involved in FSH stimulated transactivation of CYP19 gene in buffalo ovary, the present study was thus aimed to functionally characterize the role of buffalo CLS in CYP19 gene transactivation. We also studied the involvement of GATA-4, having consensus binding sites in CYP19 gene ovarian promoter in the vicinity of CLS during different stages of the buffalo estrus cycle. Reporter construct analyses and EMSA results showed that CLS is playing no significant role in CYP19 gene regulation in buffalo ovary. Real time absolute quantification of GATA-4 showed the differential expression of GATA-4 mRNA during folliculogenesis and luteinization with significantly higher transcript abundance in large follicle in comparison to other tissues. Western blot analysis of granulosa cells nuclear protein isolated from different stage of follicular development (small and large follicles) and differentiation (corpus luteum) showed that abundance of phosphorylated GATA-4 (Ser261) was significantly higher in granulosa cell nuclear protein of large follicles as compared to small follicles and corpora lutea. Interestingly, binding studies using ChIP showed significantly enhanced binding to the CYP19 gene promoter in large follicle which was seen to be declined in the luteal tissue. Similar results were obtained in the in vitro experiments as well. Finally, RNAi experiments were performed to validate the involvement of GATA-4 in CYP19 gene regulation. Results of RNAi showed that knockdown of GATA-4 mRNA significantly declined CYP19 gene mRNA as well as 17β-estradiol contents. In conclusion, result of the present study indicated that that in the absence of consensus CRE (cAMP response element); GATA-4 could be a downstream effector of cAMP/PKA pathway in regulation of CYP19 gene during folliculogenesis and luteinization.

Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed

The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

Characterization of serum-free buffalo granulosa cell culture and analysis of genes involved in terminal differentiation from FSH- to LH-responsive phenotype

In the present study, buffalo granulosa cells were cultured under serum-free conditions and characterized to study the changes in gene expression associated with the transition of granulosa cells from estrogen- to progesterone-secreting phenotype. The cells were cultured in vitro under completely serum-free conditions for 8 d. Gene expression and hormone analysis showed that on day 4 granulosa cells exhibit FSH responsiveness with preovulatory phenotype having highest CYP19 gene expression and 17β-estradiol production, whereas a significant increase in transcript abundance of STAR, CYP11, and HSD3B genes accompanied with an increase in progesterone production was observed on day 8. Cells treated with LH on day 4 followed by gene expression analysis at 1, 2, 4, 6, 18, and 24 h showed significant increase in transcripts of LH-responsive genes. In conclusion, culture condition used in the present study showed that granulosa cells were FSH responsive and attained attributes of granulosa cells of dominant follicles at day 4 with highest CYP19 and LHR gene expression beyond which they acquired the ability to luteinize and thus were more LH responsive. In addition, after LH treatment, analysis of early LH-responsive genes (EGR2, RUNX1, and NR4A1) on day 4 showed that granulosa cells at this stage in culture exhibits phenotype similar to that of preovulatory follicles before LH surge in vivo and corresponds to the in vivo transition of well-orchestrated gene expression profile after LH surge. The characterized culture conditions represent a suitable in vitro model for analysis of genes involved in terminal differentiation of granulosa cells from FSH- to LH-responsive phenotype during folliculogenesis in buffalo.

Evaluation of ISSR markers for genetic diversity analysis in Anatolian water buffaloes

BACKGROUND

The utilisation of molecular markers has increased in molecular research recently. Inter-simple sequence repeat (ISSR) markers allow the analysis of genomes without preliminary sequence information, since random primers are used. The purpose of the present study was to evaluate ISSR markers for assessing the genetic diversity of indigenous Anatolian Water Buffaloes reared in Afyon, Konya and Sivas provinces of Turkey, with a view to conservation of the gene resources.

RESULTS

The 11 ISSR primers chosen for the analysis revealed a total of 110 bands, of which 76 (69.09%) were polymorphic. Also, genetic similarity, polymorphic information content (PIC), resolving power (R(p)) and mean resolving power (R(p)), heterozygosity (H) and Shannon index (I) were calculated as 0.9479-0.9562, 0.35 ± 0.20, 2.73, 0.27, 0.18 ± 0.07 and 0.28 ± 0.11, respectively.

CONCLUSION

The ISSR markers were found to be promising for assessing the genetic diversity in buffalo populations. Potential genetic parameters such as PIC, R(p), R(p), H and I were effectively used in this study.

A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo

The Illumina BovineSNP50 BeadChip features 54,001 informative single nucleotide polymorphisms (SNPs) that uniformly span the entire bovine genome. Among them, 52,255 SNPs have locations assigned in the current genome assembly (Btau_4.0), including 19,294 (37%) intragenic SNPs (i.e., located within genes) and 32,961 (63%) intergenic SNPs (i.e., located between genes). While the SNPs represented on the Illumina Bovine50K BeadChip are evenly distributed along each bovine chromosome, there are over 14,000 genes that have no SNPs placed on the current BeadChip. Kernel density estimation, a non-parametric method, was used in the present study to identify SNP-poor and SNP-rich regions on each bovine chromosome. With bandwidth = 0.05 Mb, we observed that most regions have SNP densities within 2 standard deviations of the chromosome SNP density mean. The SNP density on chromosome X was the most dynamic, with more than 30 SNP-rich regions and at least 20 regions with no SNPs. Genotyping ten water buffalo using the Illumina BovineSNP50 BeadChip revealed that 41,870 of the 54,001 SNPs are fully scored on all ten water buffalo, but 6,771 SNPs are partially scored on one to nine animals. Both fully scored and partially/no scored SNPs are clearly clustered with various sizes on each chromosome. However, among 43,687 bovine SNPs that were successfully genotyped on nine and ten water buffalo, only 1,159 were polymorphic in the species. These results indicate that the SNPs sites, but not the polymorphisms, are conserved between two species. Overall, our present study provides a solid foundation to further characterize the SNP evolutionary process, thus improving understanding of within- and between-species biodiversity, phylogenetics and adaption to environmental changes.

Tissue-specific promoter methylation coincides with Cyp19 gene expression in buffalo (Bubalus bubalis) placenta of different stages of gestation

Aromatase is the key enzyme for estrogen biosynthesis and is encoded by Cyp19 gene. Placental cotyledons are the main site of Cyp19 gene expression during pregnancy. The present study was aimed to investigate if DNA methylation and thus epigenetic mechanisms play a potential role in stage-specific regulation of Cyp19 expression in placental cotyledons of pregnant water buffaloes (Bubalus bubalis). Significantly higher expression of Cyp19 gene (p<0.05) in placental cotyledons of early gestation period and post parturition period was found in comparison to mid-gestation placenta. Tissue-specific promoter driven transcript analyses showed that the change in expression was mainly due to change in the relative abundance of transcripts from exon I.1 while the transcripts from exon II showed comparatively less variation. Methylation analysis of 5 CpG dinucleotides of placenta-specific promoter I.1 and proximal promoter, PII showed hypo-methylation of PI.1 in early and term placenta while hyper-methylation in mid-placenta. However, PII was found to be hypomethylated in all the three tissues. In conclusion, result of the present study demonstrated that stage-specific methylation status of PI.1, the major promoter responsible for aromatase expression in buffalo placental cotyledons, coincides with the change in expression of Cyp19 gene in different stages of pregnancy.

Short tandem repeat based analysis of genetic variability in Kanarese buffalo of South India

The goal of the present study was assessing genetic diversity within Kanarese buffalo, the dual purpose breed of South India. A total of 48 unrelated animals were genotyped at 23 short tandem repeat (STR markers) loci. The total number of observed alleles was 180 with a mean of 7.83 per locus, which varied from 3 to 12 across different loci. The mean observed and expected heterozygosity in South Kanara buffaloes was estimated to be 0.518 and 0.712 respectively. Within population inbreeding estimate (F(IS)) was significantly positive in most of the investigated loci which resulted in significant deviation from Hardy-Weinberg equilibrium at 19 of 23 loci analyzed. Evaluation of South Kanara buffalo population for mutation drift equilibrium revealed no significant heterozygosity excess under three different models of evolution viz. infinite alleles model (IAM), stepwise mutation model (SMM) and two phase model (TPM), thus indicating the absence of any recent genetic bottleneck. The results of the present study will help in formulating rational breeding strategies as well as conservation of this important germplasm.

Study on the inter-subspecies nuclear transfer of river buffalo somatic cell nuclei into swamp buffalo oocyte cytoplasm

The objective of this study was to explore the feasibility of inter-subspecies somatic cell nuclear transfer (SCNT) of river buffalo (50 chromosomes) somatic cell nuclei into swamp buffalo (48 chromosomes) oocyte cytoplasm. The enucleated swamp buffalo oocytes were fused with four different types of river buffalo cells: freshly thawed ear fibroblasts, serum-starved ear fibroblasts, cumulus cells and ear fibroblasts from a cloned buffalo calf. As a result, the developmental competence of embryos reconstructed with freshly thawed ear fibroblasts was the poorest (P<0.01), while those of the other three types were not different from each other. Furthermore, the efficiency of swamp-swamp buffalo, swamp-river buffalo and bovine-buffalo SCNT were also compared. The results showed that the blastocyst rate of swamp-river reconstructed embryos was not different from swamp-swamp embryos, while significantly higher than that of bovine-buffalo embryos (P<0.01). A total of thirty cloned blastocysts derived from freshly thawed ear fibroblasts were transferred into thirteen recipient buffaloes, four recipients established pregnancy, while three of them aborted on Days 65, 75 and 90 of gestation, respectively. One cross-bred buffalo (Murrah x swamp, 49 chromosomes) receiving three embryos delivered a 39 kg female calf on Day 335 of gestation. These results indicate that the inter-subspecies SCNT is feasible to produce swamp-river buffalo embryos, and these can develop to full term and result in live buffalo calves.

Using species-specific repeat and PCR-RFLP in typing of DNA derived from blood of human and animal species

Species determination of tissue specimens, including blood, is an important component of forensic analysis to distinguish human from animal remains. DNA markers based on a method of species-specific PCR and amplifying the 359-base pair (bp) fragment of the mitochondrially encoded cytochrome-b gene and then digestion with the TaqI restriction enzyme were developed for detection and discrimination of human, cattle, buffalo, horse, sheep, pig, dog, cat and chicken blood samples. The results reveal that PCR-amplification of the gene encoding the species-specific repeat (SSR) region generated 603 bp in cattle and buffalo, 221 bp in horse, 374 bp in sheep, <or=100 bp in pig, 808 bp in dog, 672 bp in cat and 50 bp in chicken. Restriction analysis of the amplified 359-bp portion of the cytochrome-b gene using the TaqI restriction enzyme results in species-specific restriction fragment length polymorphism (RFLP) between buffalo, cattle and human. Two different bands were generated in buffalo (191 and 168 bp) and human (209 and 150 bp), with no digestion in cattle (359 bp). Cytochrome-b is a highly conserved region and consequently a good molecular marker for diagnostic studies. Therefore, the two complementary techniques, SSR-PCR and PCR-RFLP, could be used successfully as routine methods in forensics for sensitive, rapid, simple and inexpensive identification of the species in bloodstains.

Molecular cloning and characterization of β-defensin cDNA expressed in distal ileum of buffalo (Bubalus bubalis)

Defensins play a prominent role in protection of various epithelial surfaces. In this study, we have cloned and characterized the mRNA from the distal ileum of Bubalus bubalis. Total RNA after isolation from ileal epithelium was reverse transcribed to synthesize cDNA using primers designed by taking conserved region of cattle enteric beta-defensin (EBD) mRNA, goat beta-defensin 2 (BD 2) and cattle lingual antimicrobial peptide (LAP) mRNA sequences. The PCR amplified cDNA of 254 bp was ligated to pDrive cloning vector and transformed into XL-blue strain of E coli. The sequence analysis indicated 29 nucleotide substitutions with reported cattle EBD mRNA sequence sharing 86.2% homology, 92.1% with cattle LAP, 81.6% with cattle tracheal antimicrobial peptide and 84.6% with goat BD 2. The deduced amino acid sequence encodes for a 64 amino acid precursor peptide. Both nucleotide and amino acid sequence homology shows that the cloned sequence is closer to cattle LAP.

Different promoter usage for CYP19 gene expression in buffalo ovary and placenta

Aromatase is the key enzyme for estrogen biosynthesis and is coded by CYP19 gene. The expression of CYP19 gene is regulated in tissue-specific manner by alternate use of different promoters. In this study, we have analyzed tissue-specific expression and their regulation of CYP19 gene in preovulatory and postovulatory stages of buffalo (Bubalus bubalis) ovary and placenta. RT-PCR analysis showed that the CYP19 gene expression was significantly (p<0.05) higher in granulosa cells of large follicles as compared to the other tissues. The transcript analysis and transcriptional start site identified by 5'-RLM RACE for CYP19 expression indicated different transcriptional start sites within the different sized follicles during folliculogenesis. Sequence analysis showed that the transcription start site of transcript isolated from buffalo granulosa cells of small follicles was 37 bases upstream of the transcript isolated from granulosa cells of large follicles. However, both the transcripts were found to be derived from proximal promoter II. Difference in the transcriptional start site indicates the different promoter sequence usage in granulosa cells of different sized follicles. Further, in silico analysis of the difference in promoter sequence based on the 5'-UTRs isolated from granulosa cells of small follicles (151 bases) and large follicles (114 bases) showed that consensus sequence for certain important trans-elements (viz., TATA binding protein, E2F and CAAT binding protein) would lie in the promoter sequence isolated from the granulosa cells of large follicles. These transcription factors may be involved in regulation of CYP19 gene expression in ovary, either directly or indirectly. The difference in the size of 5'-UTR among the granulosa cells of ovary reflects the possible mechanism for the differential regulation of CYP19 gene during development. The transcripts isolated from buffalo corpus luteum and placental cotyledons were having same 5'-UTR comprises of 168 bases and found to be derived from PI.1. Estimates of CYP19 gene transcript concentration in the different tissues revealed that the CYP19 gene expression in granulosa cells is predominantly regulated by PII and to a minor extent by PI.1. However, PI.1 is almost exclusively responsible for CYP19 gene expression in placenta and residual expression in corpus luteum. In order to understand the complex CYP19 gene regulation in these tissues, further studies are needed to elucidate the activity of different promoters and define regulatory elements for binding of transcription factors.

Genetic diversity and bottleneck analysis of Nagpuri buffalo breed of India based on microsatellite data

In this study, 25 heterologous bovine microsatellite markers have been used for the assessment of genetic diversity in Nagpuri buffalo, an important breed of Central India. For this, 48 DNA samples of unrelated individuals of Nagpuri buffalo were PCR amplified and microsatellite alleles were resolved in 6% denaturing, silver stained Urea-PAGE gel. Genotypic status of individuals at each locus was identified manually and data analysis carried out using POPGENE software. Observed number of alleles varied from 2 (ILSTS073 locus) to 8 (HEL13 & ILSTS058 loci) with a mean of 5.24 alleles per locus. Moderate level of heterozygosity (0.45) indicated sufficient genetic diversity existing in this buffalo population. PIC values for the microsatellite loci analysed, ranged from 0.10 (ILSTS019 locus) to 0.81 (ILSTS058 locus) with a mean of 0.53. No shift in the frequency distribution of alleles and a normal L-shaped curve indicated non-existence of any bottleneck in Nagpuri. The study thus highlights the usefulness of heterologous bovine microsatellite markers to assess the genetic variability in buffalo breeds as well. Also various diversity indices suggest sufficient genetic variability within Nagpuri buffalo that can be utilized as initial guidelines for future breeding strategies and conservation.

Water buffalo (Bubalus bubalus Arnee) allotypes: identification of a multiple allelic system

This paper describes two allotypes of water buffalo controlled by two codominant allelic genes. The third allele is a null allele and behaves as a recessive one. The two detectable serum antigens are termed A1 and A2 and the third one (as yet undetectable) A0. The A1 antigen was recovered in the third peak and A2 antigen in the first peak following gel filtration through Sephadex G-200. The A1 antigen is common to water buffalo and cattle; the frequency of the corresponding gene (A1) was the same in both species.

Water buffalo (Bubalus bubalus arnee) allotypes: identification of two specificities controlled by independent genes

Two water buffalo allotypes (B1 and C1) are described, which are located on distinct low molecular weight molecules. B1 is common to water buffalo and cattle. These two markers are inherited in a simple Mendelian manner and controlled by two independent genes.

Sequence variation and molecular evolution of hormone-sensitive lipase genes in species of bovidae

The partial sequences of exon I of hormone-sensitive lipase (HSL) genes in yak (Bos grunniens), cattle (Bos taurus), zebu (Bos indicus), and buffalo (Bubalus bubalis) were analyzed. Comparisons of these sequences and the deduced amino acid sequences with the homologous HSL gene and protein sequences in other mammalian species including pig (Sus scrofa), human (Homo sapiens), mouse (Mus musculus), and rat (Rattus sp.) retrieved from the GenBank were carried out and finally a phylogenetic tree was constructed using the partial DNA sequences of the HSL genes in all species. The results showed that the homologies of the partial exon I sequences of the HSL genes between yak and cattle, zebu, buffalo, pig, human, mouse, and rat were as high as 99.8%, 99.6%, 97.4%, 90.6%, 88.4%, 83.5%, and 82.3%, respectively. This was accompanied by highly homologous amino acid sequences of the HSLs: 100%, 100%, 98.2%, 94.0%, 92.2%, 89.8%, and 89.8% identity, respectively. There are more transitions, less transversions, and no insertion or deletion in variable nucleotides of the HSL genes between the yak and other species. The majority of the variable mutations was synonymous and was found most frequently at the third codon, followed by the first and second codons, a finding that was in accordance with the neutralism hypothesis for molecular evolution. In the phylogenetic tree, the cattle and zebu were clustered together first, followed by the yak, buffalo, pig, human, mouse, and rat. This was in agreement with taxonomy suggesting that the partial sequences of exon I of the HSL genes were useful in constructing the phylogenetic tree of mammalian species. Among the four species of Bovidae, genetic differentiation in the HSL genes between yak and buffalo is equivalent to that between buffalo and cattle and between buffalo and zebu. Furthermore, the genetic distances in the HSL genes are much smaller between yak, cattle, and zebu than those between each of the three species and the buffalo. Therefore, it is reasonable to consider yak as an independent species of the genus Bos.

Molecular characterization of cDNA encoding B. taurus cathelicidin-7 like antibiotic peptide from bone marrow cells of Bubalus bubalis

Cathelicidins represent a diverse family of endogenous cationic antibiotic peptide present in all mammalian species. In the present study, a novel cathelicidin cDNA was identified and characterized from bone marrow cells of buffalo (Bubalus bubalis) using RT-PCR based approach. The cDNA encodes a propeptide of 1.18 kDa with net positive charge at neutral pH. The precursor peptide possesses a signal peptide of 29 amino acids and a biologically active peptide of 34 residues. Comparison of sequences indicates only 66.1 and 64.1% identity at nucleotides and amino acids level respectively, with the already reported cathelicidin congener from the same species. However, high degree of similarity (92.8% nucleotides and 81.9% amino acids) was noticed with cathelicidin 7 sequence of Bos taurus suggesting interspecies conservation of cathelicidin peptides rather than intra-species within bovidae family. Phylogenetic trees analyses also support these data. Our findings, further justify the cloned cDNA as a unique cathelicidin member of B. bubalis, and may reasonably considered to be another example of structural diversity exhibited by cathelicidin-derived peptides as reported from other mammals.

Molecular characterization of follicle stimulating hormone receptor (FSHR) gene in the Indian river buffalo (Bubalus bubalis)

Follicle stimulating hormone (FSH) plays a central role in regulation of ovarian function in mammals. The actions of follicle stimulating hormone are mediated through receptors present on the granulosa cells of the ovary. In the present study we have cloned and characterized the FSHR gene of buffalo. Sequence analysis indicated that the buffalo FSHR cDNA sequence comprised of an open reading frame of 2085bp encoding a 695 amino acid protein. Its nucleotide sequence showed more than 80% similarity to the homologous genes of mammalian species. At amino acid level buffalo FSHR exhibited a high percentage (84-96.7%) of identity with the corresponding mammalian homologs. This is the first isolation and characterization of FSHR cDNA from buffalo ovary.

The high resolution G- and R-banding pattern in chromosomes of river buffalo (Bubalus bubalis L.)

High resolution G- and R-banding patterns in chromosomes of river buffalo (Bubalus bubalis L.) were obtained by using early (G-bands) and late (R-bands) BrdU-incorporation in synchronized cell cultures. To better characterize the river buffalo chromosomes, GTG-, GBG-, and RBG-techniques were used. The total number of bands achieved were 490 (207 G-positive, 207 R-positive, 45 variable, and 31 centromeric regions). Only one common G- and R-banding nomenclature was reported. The number, position and intensity of G bands were highly similar by the structural GTG and the replicating GBG-techniques. However, the replicating G- and R-bands appeared to be more distinct and reproducible than the structural G-bands. Some changes in chromosome nomenclature (chromosomes 1p, 2p, 5p, and 21) were made when referred to the cattle homologues.

Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis

BACKGROUND

Simple sequence repeats (SSRs) of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in the best characterized organisms including human, remains unclear. The main objective of this study was to explore the buffalo transcriptome for its association with GACA/GATA repeats, and study the structural organization and differential expression of the GACA/GATA repeat tagged transcripts. Moreover, the distribution of GACA and GATA repeats in the prokaryotic and eukaryotic genomes was studied to highlight their significance in genome evolution.

RESULTS

We explored several genomes and transcriptomes, and observed total absence of these repeats in the prokaryotes, with their gradual accumulation in higher eukaryotes. Further, employing novel microsatellite associated sequence amplification (MASA) approach using varying length oligos based on GACA and GATA repeats; we identified and characterized 44 types of known and novel mRNA transcripts tagged with these repeats from different somatic tissues, gonads and spermatozoa of water buffalo Bubalus bubalis. GACA was found to be associated with higher number of transcripts compared to that with GATA. Exclusive presence of several GACA-tagged transcripts in a tissue or spermatozoa, and absence of the GATA-tagged ones in lung/heart highlights their tissue-specific significance. Of all the GACA/GATA tagged transcripts, approximately 30% demonstrated inter-tissue and/or tissue-spermatozoal sequence polymorphisms. Significantly, approximately 60% of the GACA-tagged and all the GATA-tagged transcripts showed highest or unique expression in the testis and/or spermatozoa. Moreover, approximately 75% GACA-tagged and all the GATA-tagged transcripts were found to be conserved across the species.

CONCLUSION

Present study is a pioneer attempt exploring GACA/GATA tagged transcriptome in any mammalian species highlighting their tissue, stage and species-specific expression profiles. Comparative analysis suggests the gradual accumulation of these repeats in the higher eukaryotes, and establishes the GACA richness of the buffalo transcriptome. This is envisaged to establish the roles of integral simple sequence repeats and tagged transcripts in gene expression or regulation.

Isolation and sequence characterization of mammary derived growth inhibitor gene of riverine buffalo (Bubalus bubalis)

In this study, attempts have been made to identify and characterize water buffalo (Bubalus bubalis) mammary derived growth inhibitor (MDGI) gene, isolated from a mammary gland cDNA library of lactating buffalo. The complete MDGI cDNA was of 698 nucleotides, consisting 61 nucleotides in 5' UTR, coding region of 402 nucleotides, and 235 nucleotides representing the 3' UTR. Comparison of nucleotide and deduced amino acid sequence data with that of MDGI/fatty acid binding protein (FABP) of other species shows three buffalo specific nucleotide changes while seven nucleotide changes were common to cattle and buffalo. Buffalo and cattle MDGI had 100% amino acid sequence similarity, which also shared three amino acid changes: 34 (Ala-Gly), 109 (Leu-Met), and 132 (Glu-Gln) as compared to other species. Comparison with FABPs reported from other cattle tissues revealed highest amino acid sequence similarity with FABP-heart (100%) and least with FABP-liver (20.5%). Phylogenetic analysis revealed cattle MDGI to be closest to buffalo, while mouse MDGI was distantly placed, whereas different tissue derived FABPs of cattle showed FABP-heart closest and FABP-epidermis most distantly placed from buffalo MDGI. This report also differs from the earlier findings that MDGI is intermediate of FABP-heart and adipose.

Molecular cloning and characterization of buffalo alpha(s1)-casein gene

Buffaloes in Indian subcontinent play an important role as the producer of milk and milk products. The alpha(s1)-casein constitutes 38% of the total milk proteins. The present study was carried out to characterize the gene in Murrah breed of Riverine buffalo. Buffalo alpha(s1)-casein cDNA was synthesized by RT-PCR, then cloned using pDRIVE-cloning vector and sequenced. The sequencing revealed that the size of alpha(s1)-casein cDNA was of 645 bp with GC content of 45.58%. The alpha(s1)-casein gene coded 214 amino acids precursor with a signal peptide of 15 amino acid residues. The similarity of buffalo alpha(s1)-casein mRNA sequence with that of cattle, goat, sheep, pig, camel, equine and human were estimated as 97.2, 93, 92.3, 57.2, 59.5, 55.9 and 46.6%, respectively. A similar trend was observed when compared amino acid sequences of these species. In the phylogenetic trees, constructed from the data of the alpha(s1)-casein mRNA as well as protein sequences, it has been observed that buffalo, cattle, goat and sheep formed a cluster with a closer relationship between cattle and buffalo followed by goat and sheep.