Background: A population is continuously facing the changing environment and its directly influencing the production of animal so to adopt these changes population must be flexible and have sufficient variability to overcome the adverse affects of environment. The evaluation of animals in terms of production performance traits along with impact of inbreeding coefficient is essential to formulate breeding and selection strategies for higher genetic improvement. Methods: Genealogy data of 6429 animals maintained at ICAR-NDRI, Karnal, India was analyzed by web-based POPREP application tool (http:// poprep.tzv.fal.de) and ENDOG V5.8 used to study the population structure and genetic diversity and regression model to study the effect of inbreeding on first lactation productive traits in Murrah buffaloes. Result: The result indicated that 91.91% of the individuals had known pedigree. The maximum generation traced was 13 with mean, full and equivalent complete generation as 5.93, 1.67 and 3.25 respectively. The average generation interval was 8.28 years and longer for the sire-son pathway and 2.16% was average inbreeding in whole population. The average genetic diversity loss was 2.10% indicated that the population has been stable with sufficient diversity. The study also revealed non significant effect of inbreeding on all first lactation traits. The low inbreeding was firstly due to introduction of new genetic variant and culling of animals avoiding mating of related ones and secondly due to incompleteness of pedigree in earlier years. This can be used as a base line information of phenomic needs to be generated before applying genomics tools in particular herd to be used as reference population in future for genomic selection.
PCR-RFLP analysis of PCR products were carried out using Sph I /Pae1enzyme for 100 Sahiwal cattle and 115 Karan Fries animals. In Sahiwal cattle the 448 bp have three genotype AA (448), AB (448+313+135bp), BB (313+135 bp) having genotype frequencies 0.20, 0.45, 0.35 and gene frequencies are 0.42 (A) and 0.58 (B) and in Karan Fries cattle genotype frequencies 0.29, 0.21, 0.50 respectively and gene frequencies are 0.39 (A) and 0.61 (B). These genotypes of 448 bp are highly significant for FL305DMY, FLTMY, FL305DSNFY and non significant for FL305 DFY and FL305DPY in Sahiwal and In Karan Fries cattle these genotypes are highly significant for FL305DMY, FLTMY, FL305DSNFY and FL305DPY and non significant for FL305DFY. AB genotype was superior for FL305DMY, FLTMY, FL305DSNFY traits and AA genotype was superior for FL305DFY and BB genotype was superior for FL305DPY trait in Sahiwal cattle and In Karan Fries Cattle AB genotype was superior for all traits.
Background: Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh.However, the origin of this species is still disputed and information on its genomic architecture is scanty so far.We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun.Recently, the first genome assembly of gayal, mithun of Chinese origin, was published.However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly.We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun.
Background: Neuropeptide Y (NPY), a 36-AA neurotransmitter involved in the control of appetite, feeding and energy homeostasis. The bovine NPY gene is located on chromosome 4 and consists of four exons. Earlier studies have reported that genes involved in feed intake regulation, energy production and energy regulation may affect different growth and production traits in cattle. Information associating NPY SNP to reproduction and production traits in dairy cattle is, however, limited. Hence, the present study was planned to explore SNPs in NPY gene and its possible association with reproduction and first lactation production traits in Sahiwal cattle. Methodology: DNA samples were isolated from blood that has collected from hundred and three Sahiwal cows. Three regions of NPY were amplified using designed primer pairs. The sequencing of the targeted regions was done in 103 Sahiwal cows. Least squares analysis of variance was carried out for unequal and non-orthogonal data using the technique described by Harvey (1990) to study effect of non-genetic factors. Significance of differences based on genotypes effect of growth, reproduction and production traits were tested by general linear models.Result: Sequence data analysis revealed two transversions in NPY gene. For these identified nucleotide variations, positions were A72073973C (intron 3) and C72068620A (intron 3). This is the first report of the presence of NPY gene polymorphism in purebred Bos indicus of Indian origin. For SNP A72073973C, performances of animals with homozygote AA genotype exhibited significantly higher milk production (P≤0.01) and growth performance (P≤0.05) than heterozygote genotype. Heterozygous genotype exhibited superior performance for the SNP C72068620A which was found to be significantly associated (P≤0.05) with 18M wt, WFS, WFC, FCI and FL305DMY.
Present study includes the effect of inbreeding on expected genetic gain and estimation of regression with respect to first lactation production, reproduction and lifetime traits in Karan Fries crossbred cattle maintained at ICAR-NDRI, Karnal. Out of total, only 36.97% were found to be inbred with an average inbreeding coefficient 3.68%. Overall least squares mean for reproduction traits (days) AFC, SP, DP and CI were 1020.41 ± 5.49, 141.42± 3.86, 74.54 ± 2.04 and 421.20 ± 3.81 respectively. For production traits (kg) were 305MY, LL, LTMY, FY and SNFY were 3169.15 ± 37.87, 353.25 ± 4.18, 3686.10 ± 55.10, 266.19 ± 4.66 and 127.81 ± 2.26 respectively and lifetime traits like LTMY and stayability were 14588.47 ± 486.09 (kg) and 2444.69 ± 41.26 (days) respectively. Among reproduction traits (days), AFC increased by +3.70, DP +3.66 and CI +68.44 however SP decreased by -0.85 d and production traits (kg), 305MY decreased by -10.2 TMY -16.09, LL -1.23 d, 305FY -1.75, 305SNFY - 0.26, LTMY 202.02 and stayability -17.37 days per unit increase in the inbreeding coefficient. Although there was no inbreeding depression in any of the traits except AFC. The expected genetic gain of AFC increased two folds in IBL2 (Fx >5%) as compared to IBL1 (Fx<5) group that is not desirable, so in future, to maintain the optimum genetic gain we should keep inbreeding at optimum level and so more precise pedigree recording and planned mating strategies should be adopted to avoid inbreeding depression in next generation.
Background: The present study pertained to records on milk production and milk constituents of 100 Sahiwal cattle and 115 Karan Fries cattle, the data collected over a period of 2004 to 2016 from Animal Genetics and Breeding division from ICAR-National Dairy Research Institute, Karnal Haryana. Methods: Good quality genomic DNA was used for amplification of exon 3 of AAT gene (474bp) by polymerase chain reaction under optimized conditions and Sequenced data analysis for SNPs detection. The analysis was carried out with appropriate Statistical method using software’s in the computer centre of the institute under the Restricted Maximum Likelihood Method (REML), Estimation of breeding value, Association Estimation, Effect of genotypes on Breeding Value. Result: In Sahiwal SNP at position G6997C was highly associated for FL305DMY, FLTMY, and FL305DSNFY. The mean ± SE of GG genotype for FL305DMY, FLTMY, FL305DFY, FL305DSNFY and FL305DPYwere found to be 1748.45±6.47, 1962.30±8.47, 100.33±0.44, 154.41±0.09 and 43.99±0.10 respectively and for GC genotype 1860.17±5.86, 2050.44±7.66, 100.35±0.39, 155.28±0.08 and 43.82±0.10 respectively. GG genotype was superior for FL305DPYand Heterozygous GC genotype was superior for rest of other traits. In Karan Fries cattle SNP at position G6997C was highly associated for FL305DMY, FLTMY, FL305DSNFY and FL305DPY. The mean ± SE of GG genotype for FL305DMY, FLTMY, FL305DFY, FL305DSNFY, FL305DPY were found to be 3564.74±6.0, 4584.50±6.00, 135.05±4.76, 278.53±0.06 and 113.80±0.06 respectively and for GC genotypeswere 3459.23±7.48, 4478.76±7.48, 136.19±5.96, 277.50±0.07, 112.75±0.08 respectively. Heterozygous (GC) genotype was superior for FL305DFY and GG genotype was superior for FL305DMY, FLTDMY, FL305DSNFY and FL305DPY.
The present study pertained to records on milk production and milk constituents of 100 Sahiwal cattle and 115 Karan Fries cattle, the data collected over a period of 2004 to 2016 from Animal Genetics and Breeding division from ICAR-National Dairy Research Institute, Karnal, Haryana. In Sahiwal SNP at position G649C was found to be highly associated with FLTMY and FL305DFY and however the association was non-significant for FL305DMY, FL305DSNFY and FL305DPY. GC genotype was superior with respect to FL305DPY and FL305DFY traits, whereas, homozygous (GG) genotype was superior for rest of other traits. In Karan Fries SNP at position G649C was found to be highly associated with FL305DFY and however, the association was non-significant for FL305DMY, FLTMY, FL305DSNFY and FL305DPY. Heterozygote GC genotype was superior for all traits; however the superiority is significantly higher for FL305DFY traits in present study.
Leptin is a 16-kDa protein secreted predominantly from white adipose tissue and performs important roles in controlling the body weight, feed intake, immune function, production and reproduction. In present study, buffalo leptin gene was analyzed using DNA markers for polymorphism and its association with production traits. The PCR-RFLP analysis of leptin gene using BsaAI, Sau3AI and Kpn2I restriction enzymes revealed monomorphism. The PCR-SSCP followed by DNA sequencing of Murrah buffalo leptin gene spanning exon III revealed two SNPs viz., c.25 T>C and c.316A>G, which were used to genotype the Murrah, Surti and Bhadawari populations. The c.25 T>C allele frequencies was found 0.81 and 0.19 for C and T in Murrah; 0.65 and 0.35 for C and T in Surti and 0.65 and 0.35 for C and T in Bhadawari buffaloes respectively. The c.25T>C genotypes were not in Hardy-Weinberg proportions, however c.316A>G genotypes maintained equilibrium at this locus in the populations studied. The c.316A>G SNP allele frequencies were observed in Murrah 0.31 and 0.69 for A and G; Surti 0.3 and 0.7 for A and G and Bhadawari 0.3 and 0.7 for A and G respectively. The Murrah buffalo leptin allelic variant sequences revealed 99 % similarity with cattle sequence. The statistical analysis using general linear model procedure indicated that Murrah buffalo leptin c.25 T>C and c.316A>G SNP genotypes were not related significantly (P>0.01) with Murrah buffalo milk production traits viz; milk yield, fat percentage and SNF percentage.
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