T. K. Bhattacharya

Genetic variants of beta-lactoglobulin gene and its association with milk composition traits in riverine buffalo.

A study was carried out to determine genetic variants of beta-lactoglobulin gene and to explore associations between these and milk composition traits in riverine buffalo. Single strand conformation polymorphism was employed to detect the genetic variants of the gene. Two fragments of this gene i.e. 119 bp of exon I and 400 bp spanning exon IV and intron IV were included in the study. For 119 bp fragment, three alleles namely, A, B and C were observed in all the buffalo breeds whereas four alleles (A, B, C and D) were detected for 400 bp fragment. The frequency distribution of alleles was different in different breeds of buffaloes for both the fragments. For exon I fragment, the milk composition traits such as total SNF, protein, solid, fat and whey protein yield were found to be significantly (P<0.05) associated with genotypes in Murrah and Bhadawari buffalo whereas in Mehsana breed genotypes were significantly (P<0.05) co-related with total SNF, solid and fat yield. Genotypes of 400 bp fragment, only total fat yield in Mehsana buffalo was found to be significantly (P<0.05) associated with genotypes.

Estimation of inbreeding in cattle using RAPD markers

Inbreeding indicates the degree of homozygosity at a locus within a population. Normally inbreeding is estimated in terms of a coefficient calculated from the pedigree of an individual. If no history is available, however, there is no way to estimate the inbreeding coefficient. Sometimes, data on individuals are missing, and that too can prevent the estimation of the inbreeding coefficient, which is essential for formulation of a breeding programme at the farm level and for breed development.

Genetic Relationship Among Four Indian Breeds of Sheep Using RAPD-PCR

Abstract Kumar, K.G., Kumar, P., Bhattacharya, T.K., Bhushan, B., Patel, A.K., Choudhary, V. and Sharma, A. 2003. Genetic relationship among four Indian breeds of sheep using RAPD-PCR. J. Appl. Anim. Res., 24: 177–183. The study was carried out in four Indian sheep breeds namely, Marwari, Mandya, Madras Red and Muzaffarnagari maintained at different organised herds of the country. A total of six oligonucleotide primers were subjected to perform random amplified polymorphic DNA (RAPD) fingerprinting to estimate genetic relationship (relatedness) among different breeds of sheep. All the six primers showed polymorphism in producing bands. The average number of bands in different breeds ranged from 6 to 15 with size of 0.3 to 1.9 kb. Out of six primers, OPM-2 and ILO-17 produced comparatively large number of bands in agarose gel. The intrabreed relatedness in terms of band sharing ranged from 0.66 to 1.00, the highest being in Marwari, whereas, lowest in Muzaffarnagari breed. The interbreed relatedness in terms of mean average percentage difference (MAPD) was highest (9.44±1.66) between Marwari and Muzaffarnagari breed while lowest value (4.90±1.54) was found between Mandya and Mujaffarnagari. It may be concluded that the Mandya breed is closest to Marwari while Marwari breed is too distant from Muzaffamagari breed.

Polymorphism of ZuBeCa3 microsatellite and its association with mammary tumor in dogs

A study was conducted to explore the genetic polymorphism at ZuBeCa3 microsatellite and to estimate the association between microsatellite polymorphism and mammary cancer in dogs. Three genotypes namely AA, AB and BB were observed both in dogs affected by mammary cancer and in non‐affected dogs. In the affected group, the frequency of genotype and allele was 0.63 for AA, 0.25 for AB and 0.12 for BB genotype, and 0.76 for A and 0.24 for B allele. In the nonaffected group, the frequency of AA, AB and BB genotype was 0.39, 0.38 and 0.23 and the frequency of A and B allele was 0.58 and 0.42, respectively. Histopathological observation classified the cancer‐affected animals into three groups namely, malignant solid mammary carcinoma, malignant papillary adenocarcinoma and benign papillary adenoma in which the frequency of A allele was relatively more predominant in benign tumor group, which is more than 80%. Statistical tests showed significant differences (P < 0.01) of allelic distribution between tumor‐affected and non‐affected group, which reveals the effect of polymorphism on occurrences of mammary cancer in dogs. Besides, χ2 test also reflected the significant effect of genotypes on occurrences of three groups of mammary cancer in dogs.

Molecular Characterization and SNP Detection of CD14 Gene of Crossbred Cattle

CD14 is an important molecule for innate immunity that can act against a wide range of pathogens. The present paper has characterized CD14 gene of crossbred (CB) cattle (Bos indicus×Bos taurus). Cloning and sequence analysis of CD14 cDNA revealed 1119 nucleotide long open reading frame encoding 373 amino acids protein and 20 amino acids signal peptide. CB cattle CD14 gene exhibited a high percentage of nucleotide identity (59.3–98.1%) with the corresponding mammalian homologs. Cattle and buffalo appear to have diverged from a common ancestor in phylogenetic analysis. 25 SNPs with 17 amino acid changes were newly reported and the site for mutational hot-spot was detected in CB cattle CD14 gene. Non-synonymous substitutions exceeding synonymous substitutions indicate the evolution of this protein through positive selection among domestic animals. Predicted protein structures obtained from deduced amino acid sequence indicated CB cattle CD14 molecule to be a receptor with horse shoe-shaped structure. The sites for LPS binding, LPS signalling, leucine-rich repeats, putative N-linked glycosylation, O-linked glycosylation, glycosyl phosphatidyl inositol anchor, disulphide bridges, alpha helix, beta strand, leucine rich nuclear export signal, leucine zipper and domain linker were predicted. Most of leucine and cysteine residues remain conserved across the species.

Molecular cloning and characterization of buffalo αs1-casein gene

Buffaloes in Indian subcontinent play an important role as the producer of milk and milk products. The αs1-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 αs1-casein cDNA was synthesized by RT-PCR, then cloned using pDRIVE-cloning vector and sequenced. The sequencing revealed that the size of αs1-casein cDNA was of 645 bp with GC content of 45.58%. The αs1-casein gene coded 214 amino acids precursor with a signal peptide of 15 amino acid residues. The similarity of buffalo αs1-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 αs1-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.

Cloning and characterization of αs2-casein gene of Riverine buffalo

The present study was carried out to characterize the αs2-casein gene in Riverine buffalo. Total RNA was extracted from the mammary tissue of buffalo and αs2-casein cDNA were synthesized by RT-PCR, then cloned using pDRIVE-cloning vector and sequenced. The sequencing revealed that the size of αs2-casein was 669 bp with GC content of 41.11%. The gene encoded for 222 amino acid precursors and that it possessed 15 amino acids signal peptide. The similarity of buffalo αs2-casein mRNA sequence with that of cattle, sheep, goat, pig and camel were estimated as 97.9, 93.6, 93.4, 73.5 and 73.0%, respectively. In the phylogenetic trees, constructed from the data of the αs2-casein mRNA sequences as well as protein sequences, it has been observed that the cattle and buffalo were in the same group whereas sheep and goat formed another group. The camel and swine were placed in two separate groups.

SNPs in minimal promoter of myostatin (GDF-8) gene and its association with body weight in broiler chicken

Myostatin (MSTN), a transforming growth factors β (TGF-β) family member, is an important regulator of muscle mass. While polymorphism in the coding region of MSTN is extensively studied, the genetic causes of transcriptional regulation are poorly understood. This study is targeted to identify variations in the promoter region of MSTN. This study revealed that the promoter region of the growth differentiation factor 8 (GDF-8) is highly polymorphic and the identified nucleotide variations were attributed to transition mutations in sequence. Out of three genotypes observed, the frequency of AA was significantly higher (0.63) followed by the frequencies of AB (0.28) and BB (0.09). Genotype BB had a significant effect on body weight at hatching implicating the role of the identified single nucleotide polymorphisms (SNPs) in the chicks muscle development.

Cloning and characterization of DGAT1 gene of Riverine buffalo

The present study was carried out to characterize the DGAT1 gene of Riverine buffalo. Total RNA was extracted from the mammary tissue of buffalo and DGAT1cDNA were synthesized by RT-PCR, then cloned using pDRIVE cloning vector and sequenced. The sequencing revealed that the size of DGAT1 gene was 1470 bp with GC content of 62.30%. The gene encoded for 489 amino acid precursors and that it possessed 32 amino acids signal peptide. The similarity of buffalo DGAT1 mRNA sequence with that of cattle, pig, monkey, human, mice and rat were determined as 98.4, 90.7, 85.4, 85.0, 77.4 and 77.1%, respectively. Phylogenetic tree constructed from the derived DGAT1 protein sequences of 15 different species illustrated a unique branches for mammals, fly, nematode and plants. Among mammals, cattle and buffalo grouped together, whereas swine formed another group in the same branch. Four motifs were predicted in buffalo DGAT1 peptide sequence, one N-linked glycosylation site (246th position), two putative tyrosine phosphorylation site (316 and 261), one putative diacylglycerol binding site (382–392 amino acid position) and a conserved domain MBOAT (membrane bound acyl transferase from 150 to 474 amino acids) with a histidine as an active residue.

DRB3.2 gene polymorphism and its association with pashmina production in Changthangi goat

PstI and TaqI restriction fragment length polymorphism (RFLP) of caprine DRB3.2 revealed three genotypes under each RFLP in Changthangi goat. The genotypic and allelic frequency in PstI RFLP was calculated as 0.07, 0.72 and 0.20 for PP, Pp and pp genotypes and 0.43 and 0.57 for P and p alleles. In TaqI RFLP the frequencies were observed as 0.11, 0.61 and 0.27 for TT, Tt and tt genotypes and 0.41, 0.59 for T and t alleles. Alignment study indicates variability of nucleotides and amino acids between alleles and different breeds of goats. The nucleotide sequences reported in this paper have been submitted to the European Molecular Biology Laboratory GenBank and the accession numbers were AY496935, AY496061 and AY496062. A significant affect (P ≤ 0.05) of MHC DRB3.2 PstI polymorphism was found on the first and second year of pashmina production.