Archana Verma | National Dairy Reserach Institute (N.D.R.I. ) Karnal (INDIA) (original) (raw)

Papers by Archana Verma

Animal Biotechnology, 2023

The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as we... more The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population F ST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and F ST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir-and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.

International Journal of Current Microbiology and Applied Sciences

Asian-Australasian Journal of Animal Sciences

Objective: The present study was aimed at (i) reduction in dimensionality using principal compone... more Objective: The present study was aimed at (i) reduction in dimensionality using principal component analysis of 17 linear udder type traits to define those components which best represent udder and teat conformation of Indian Sahiwal cattle and (ii) to identify those components having strongest relationship with milk production traits in Sahiwal cattle. Methods: The Principal Component Analysis (PCA) included 17 linear udder type traits using the correlation matrix between the traits to ensure that all traits are standardized in the analysis. Bartlett's sphericity test was used to determine the degree of interrelations between variables and adequacy for use in factor analysis. The relationship of these principal components with milk production traits was analysed using the general linear model. Results: The means of linear udder type trait measurements varied between-2.21 for udder balance and 136.35 for udder circumference. Out of 17 principal components, six were extracted using Kaiser Rule criterion. The identified six components could explain 75.777% of the cumulative variance between the linear udder type traits. The communality ranged from 0.476 (rear udder width) to 0.967 (fore teat length) for all these 17 different udder type traits. A relation between first principal component and 305-day milk production was significant with a positive and non-significant effect of 305-day milk-fat yield (305 DF) and 305-day milk-protein yield (305 DP). Conclusion: Results of PCA suggest that the use of orthogonal synthetic variables principal component one (PC1), two (PC2) and three (PC3) provided a means of reduction in the number of linear udder type traits to be recorded in Sahiwal cattle which could be used in A c c e p t e d A r t i c l e explaining the whole udder and teat conformation. The PC1 can be used in selection as a means to explain the mammary system of better milk producing animals to be used in breeding programmes.

Indian Journal of Animal Research, 2016

Calcium channel, voltage-dependent, alpha-2/ delta subunit 1 (CACNA2D1) gene plays an important r... more Calcium channel, voltage-dependent, alpha-2/ delta subunit 1 (CACNA2D1) gene plays an important role in excitation-contraction coupling in muscle-cells, glial cells and neurons. The CACNA2D1 gene may be one of the candidate genes related with some phenotypic traits due to its location in QTLs associated with Somatic cell score (SCS ) and mastitis. A total of 120 Sahiwal cattle were selected to characterize exon 19 of CACNA2D1 gene to identify polymorphism and its association with mastitis susceptibility/resistance. A 249 bp PCR fragment of CACNA2D1 gene encompassing the exon 19 and partial intronic region was amplified and digested with Hae III to screen the SNP which was significantly associated with SCS. Genotype analysis using PCR-RFLP revealed a monomorphic banding pattern. Sequencing was also carried out to explore other SNPs which are deposited in dbSNP in the nucleotide sequence of a particular region. This study provides preliminary information that the targeted region of CA...

Indian Journal of Animal Research, 2016

Expression of stress genes under thermal stress partially explain the relatively higher thermal a... more Expression of stress genes under thermal stress partially explain the relatively higher thermal adaptability of indigenous breeds compared to exotic breeds of cattle. ATP1A1 gene is one of such gene that encodes for a1 isomer of Na+, K+- ATPase enzyme for Na+- coupled transport of metabolites, nutrients, ions and represents a plausible candidate for heat tolerance traits. Present study was designed to compare SNP variations in ATP1A1 gene and to evaluate their association with respiration rate, rectal temperature and heat tolerance coefficient in Sahiwal (51) and Karan Fries (50) cows maintained at Livestock Research Centre of National Dairy Research Institute, Karnal. Two SNPs (T27008243C and A27008223G) were identified in both the dairy cattle breeds. Association of each SNP genotype was analyzed using Generalized Linear Model procedure in Statistical Analysis System (SAS). Sahiwal cows with TT (15.91±1.89b) at T27008243C locus had lowest RR compared to TC genotypes (18.25±1.77ab)...

Indian Journal of Animal Research, 2015

The objective of this study was to characterize and validate the candidate point mutation in Calc... more The objective of this study was to characterize and validate the candidate point mutation in Calcium channel, voltage-dependent, alpha-2/ delta subunit 1 (CACNA2D1) gene in Karan Fries (Bos taurus x Bos indicus) cattle. The CACNA2D1 gene reported as one of the potential candidate gene influencing Somatic cell Score and Mastitis. A PCR product of 249 bp amplifying the exon 19 and partial 18 and 19 intronic region of CACNA2D1 gene was digested with Hae III restriction enzyme to screen the reported point mutation. A monomorphic banding pattern with genotype AA was found in Karan Fries cattle. Sequencing was also carried out to characterize and explore insilico screened mutation in the nucleotide sequence of a particular region. The result indicates highly conserved sequence in Karan Fries cattle. The Phylogenetic tree revealed that Karan Fries cattle were closer to Bos taurus cattle, Bos mutus (Yak), and Bison bison (American buffalo) compared to other species.

Indian Journal of Animal Research, 2016

Present study was done in thirty Karan Fries bulls to characterize the Exon 3 of PROP1 gene and t... more Present study was done in thirty Karan Fries bulls to characterize the Exon 3 of PROP1 gene and to screen for the H173R polymorphism as well as other variations including reported and novel SNPs in the targeted region. The exon 3 was characterized by sequencing the amplicons obtained after PCR amplification using custom designed primers. The BLAST analysis of the obtained sequence yielded 100% and 99% homology with sequences of Bos taurus and bison respectively. The multiple alignment of the target region sequence with Bos taurus reference sequence revealed that the bulls under the study were free of H173R mutations. No variations were observed thus giving the targeted region a highly conserved one.

Indian Journal of Animal Research, 2016

Present investigation was carried out to study the prevalence of bacterial pathogens in clinical ... more Present investigation was carried out to study the prevalence of bacterial pathogens in clinical and subclinical mastitis in buffaloes during winter season. A total of 118 Murrah buffaloes were screened using California mastitis Test (CMT). Milk samples were collected and analyzed for fat, protein, lactose, SNF, pH, Electrical conductivity (EC) and Somatic Cell Counts (SCC). Out of 118 milk samples, 60 samples (50.84%) were negative for CMT and 58 samples (49.15%) were detected positive for mastitis incidence. Milk pH and EC was significantly higher (p<0.05) in mastitis affected samples than the normal ones, however, protein, fat, SNF and lactose were lower (p<0.05). SCC ranged between 1.28-1.48 x 105 cells/ml (in normal milk samples as compared to 3.85-6.21x 105 cells/ ml (p<0.05) in mastitis milk samples. Out of 58 samples only 51 samples exhibited bacterial growth. The culturally examined and characterized samples revealed S. aureus (35.29%) as the predominant bacteria f...

Animal biotechnology, Jan 20, 2018

The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association ... more The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association with clinical mastitis and production traits. Exon 18 and its flanking regions were screened for the presence of SNPs. Statistical analysis was performed to identify association of period of birth, breed, and genotype with mastitis incidence on randomly selected 103 Sahiwal and 102 Karan Fries cattle. PCR-RFLP analysis revealed that g.38819398G > A mutation in exon 18 (269 bp amplicon) of CACNA2D1 gene resolved into AA, AG, and GG genotypes in Sahiwal and Karan Fries cattle. Wald chi-square analysis revealed that the period of birth, breed, and genotype were significantly associated with mastitis incidence. GG genotyped cattle were found to be less susceptible to mastitis. Least square analysis revealed that GG and AG genotype animals of G38819398A SNP of CACNA2D1 gene in Sahiwal as well as in Karan Fries cattle were associated with higher average milk yields during 1st, 2nd, and 3rd ...

Indian Journal of Animal Research

Mastitis is an economically important disease causing great loss to dairy sector owing to its neg... more Mastitis is an economically important disease causing great loss to dairy sector owing to its negative effect on production. Its multi factorial etiology makes it difficult to use prophylactic methods for control. Identification of genetic resistance mechanisms and selection for it is a potential strategy for mastitis control. The present study was done in 101 Murrah buffaloes to find the common causative agents of mastitis in buffaloes, to identify variants in exon 2 and…

Veterinary world, 2017

This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in p... more This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in protein phosphatase 1 regulatory subunit 11 (PPP1R11) gene in Murrah bulls. Genomic DNA was isolated by phenol-chloroform extraction method from the frozen semen samples of 65 Murrah bulls maintained at Artificial Breeding Research Centre, ICAR-National Dairy Research Institute, Karnal. The quality and concentration of DNA was checked by spectrophotometer reading and agarose gel electrophoresis. The target region of PPP1R11 gene was amplified using four sets of primer designed based on Bos taurus reference sequence. The amplified products were sequenced and aligned using Clustal Omega for identification of SNPs. Animals were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using EcoNI restriction enzyme. The sequences in the NCBI accession number NW_005785016.1 for Bubalus bubalis were compared and aligned with the edited sequences of Murrah bulls...

Tropical animal health and production, Jan 31, 2017

Heat shock proteins (HSPs) act as molecular chaperones which are preferentially transcribed in re... more Heat shock proteins (HSPs) act as molecular chaperones which are preferentially transcribed in response to severe perturbations of the cellular homeostasis such as heat stress. The present study was undertaken for molecular characterization and detection of genetic polymorphisms of HSPB6 gene in 100 Karan Fries Cattle. HSPB6 gene was mapped on Bos taurus autosome 18 (BTA 18), comprising three exons and two introns. Four sets of primers for HSPB6 gene were designed using Primer3 software (version 0.4.0). For detecting single nucleotide polymorphisms (SNPs), sequence data was analyzed using BioEdit software (version 7.2). Comparative sequence analysis of HSPB6 gene showed five nucleotide polymorphisms, which included three transitions viz. g.161A > G, g.436G > A and g.2152A > G and two transversions viz. g.1743C > G and g.2417A > T compared to B. taurus (NCBI GenBank: AC_000175.1). HSPB6 gene of Karan Fries cattle exhibited a high percentage of nucleotide identity (47.0...

Indian Journal of Dairy Science, 2008

Tropical animal health and production, Jan 22, 2016

Heat shock proteins (HSPs) act as molecular chaperones those are preferentially transcribed in re... more Heat shock proteins (HSPs) act as molecular chaperones those are preferentially transcribed in respose to heat stress and the polymorphism in HSP genes associated with heat tolerance traits in cows. HSP90AA1 gene has been mapped on Bos taurus autosome 21 (BTA-21) and spans nearly 5368 bp comprising of 11 exons out of which the first exon does not translate. The present study was done on Karan Fries (5/8 HF × 3/8 Tharparkar) cows reared in tropical climate with the objectives of identifying single-nucleotide polymorphisms (SNPs) in targeted regions (exon 3) of HSP90AA1 gene and analyzing their association with heat tolerance traits in Karan Fries cows. Respiration rate (RR) and rectal temperature (RT) were recorded once daily for four consecutive days during probable extreme hours in different seasons or temperature humidity index (THI), viz., winter, spring, and summer. For detecting single-nucleotide polymorphisms, sequence data were analyzed using BioEdit software (version 7.2). C...

Indian Journal of Dairy Science, 2008

Tropical Animal Health and Production, 2015

Heat shock proteins (HSPs) are expressed in response to heat stress, and the polymorphism in HSP ... more Heat shock proteins (HSPs) are expressed in response to heat stress, and the polymorphism in HSP genes at single-nucleotide level has been reported to be associated with heat tolerance and production performance traits in cattle. HSPB8 gene has been mapped on Bos taurus autosome 17 (BTA-17) spanning nearly 13,252 bp and comprising three exons and two introns. The present study was conducted in Sahiwal cows (n = 108) reared in subtropical climate with the objectives to identify SNPs in all three exons and part of intron 1 of HSPB8 gene and to analyze their association with heat tolerance traits in Sahiwal cows. Respiration rate (RR) and rectal temperature (RT) were recorded once during probable extreme hours in different seasons or Temperature-Humidity Index (THI), i.e., winter, spring, and summer. Heat tolerance coefficient (HTC) was also calculated to check the adaptability of the animals during the period of heat stress. The comparative sequence analysis revealed a total two single-nucleotide polymorphisms (SNPs), i.e., g.507G&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;A in exon 1 and g.881T&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;C in intron 1 of HSPB8 gene. Out of these two identified SNPs, only one SNP, i.e.,…

Global warming and climate change have become the major threat to the sustainability of livestock... more Global warming and climate change have become the major threat to the sustainability of livestock production systems worldwide. Heat stress produces oxidative stress and affects the alternation of plasma K+ and Na+. In the plasma membrane the ion gradients formed by Na+-K+-ATPase enzyme is necessary for Na+-coupled transport of metabolites, nutrients and ions and represents a plausible candidate for heat tolerance traits. ATP1A1 gene encodes for α subunit of Na+-K+-ATPase enzyme, has been mapped on BTA 3 and spans about 22.77 kb and includes 23 exons and coding sequence of 3066 nucleotides. The present study was carried out in 35 Jersey crossbred cows with the objectives to identify SNPs in targeted regions (part of exon 16 to intron 18) of ATP1A1 gene and to analyze their association with respiration rate and rectal temperature. A total of five SNPs (A27008223G, T27008097A, C27008016T, G27008015A and C27007790A) were identified in Jersey crossbred cattle. Respiration rate (RR) and rectal temperature (RT) was recorded once during probable extreme hours in winter, spring and summer season. Further, heat tolerance coefficient (HTC) also calculated to see the adaptability of the animals during the period of heat stress. RT in Jersey crossbred cows for AA (38.01±0.16a) and GG (37.86±0.14a) genotype at A27008223G locus did not differ significantly while RR for CA genotype at C27007790A locus was highest (21.76±1.68a) as compared to CC (19.25±1.155b) and AA (16.91±1.57ab) genotypes and HTC for CA genotype at C27007790A locus was highest (1.94±0.07a) as compared to CC (1.83±0.05b) and AA (1.72±0.07ab) genotypes. It is concluded that AA genotype at 27007790 nucleotide position in Jersey crossbred cows were desirable for respiration rate and heat tolerance coefficient respectively.

Animal Biotechnology, 2023

The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as we... more The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population F ST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and F ST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir-and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.

International Journal of Current Microbiology and Applied Sciences

Asian-Australasian Journal of Animal Sciences

Objective: The present study was aimed at (i) reduction in dimensionality using principal compone... more Objective: The present study was aimed at (i) reduction in dimensionality using principal component analysis of 17 linear udder type traits to define those components which best represent udder and teat conformation of Indian Sahiwal cattle and (ii) to identify those components having strongest relationship with milk production traits in Sahiwal cattle. Methods: The Principal Component Analysis (PCA) included 17 linear udder type traits using the correlation matrix between the traits to ensure that all traits are standardized in the analysis. Bartlett's sphericity test was used to determine the degree of interrelations between variables and adequacy for use in factor analysis. The relationship of these principal components with milk production traits was analysed using the general linear model. Results: The means of linear udder type trait measurements varied between-2.21 for udder balance and 136.35 for udder circumference. Out of 17 principal components, six were extracted using Kaiser Rule criterion. The identified six components could explain 75.777% of the cumulative variance between the linear udder type traits. The communality ranged from 0.476 (rear udder width) to 0.967 (fore teat length) for all these 17 different udder type traits. A relation between first principal component and 305-day milk production was significant with a positive and non-significant effect of 305-day milk-fat yield (305 DF) and 305-day milk-protein yield (305 DP). Conclusion: Results of PCA suggest that the use of orthogonal synthetic variables principal component one (PC1), two (PC2) and three (PC3) provided a means of reduction in the number of linear udder type traits to be recorded in Sahiwal cattle which could be used in A c c e p t e d A r t i c l e explaining the whole udder and teat conformation. The PC1 can be used in selection as a means to explain the mammary system of better milk producing animals to be used in breeding programmes.

Indian Journal of Animal Research, 2016

Calcium channel, voltage-dependent, alpha-2/ delta subunit 1 (CACNA2D1) gene plays an important r... more Calcium channel, voltage-dependent, alpha-2/ delta subunit 1 (CACNA2D1) gene plays an important role in excitation-contraction coupling in muscle-cells, glial cells and neurons. The CACNA2D1 gene may be one of the candidate genes related with some phenotypic traits due to its location in QTLs associated with Somatic cell score (SCS ) and mastitis. A total of 120 Sahiwal cattle were selected to characterize exon 19 of CACNA2D1 gene to identify polymorphism and its association with mastitis susceptibility/resistance. A 249 bp PCR fragment of CACNA2D1 gene encompassing the exon 19 and partial intronic region was amplified and digested with Hae III to screen the SNP which was significantly associated with SCS. Genotype analysis using PCR-RFLP revealed a monomorphic banding pattern. Sequencing was also carried out to explore other SNPs which are deposited in dbSNP in the nucleotide sequence of a particular region. This study provides preliminary information that the targeted region of CA...

Indian Journal of Animal Research, 2016

Expression of stress genes under thermal stress partially explain the relatively higher thermal a... more Expression of stress genes under thermal stress partially explain the relatively higher thermal adaptability of indigenous breeds compared to exotic breeds of cattle. ATP1A1 gene is one of such gene that encodes for a1 isomer of Na+, K+- ATPase enzyme for Na+- coupled transport of metabolites, nutrients, ions and represents a plausible candidate for heat tolerance traits. Present study was designed to compare SNP variations in ATP1A1 gene and to evaluate their association with respiration rate, rectal temperature and heat tolerance coefficient in Sahiwal (51) and Karan Fries (50) cows maintained at Livestock Research Centre of National Dairy Research Institute, Karnal. Two SNPs (T27008243C and A27008223G) were identified in both the dairy cattle breeds. Association of each SNP genotype was analyzed using Generalized Linear Model procedure in Statistical Analysis System (SAS). Sahiwal cows with TT (15.91±1.89b) at T27008243C locus had lowest RR compared to TC genotypes (18.25±1.77ab)...

Indian Journal of Animal Research, 2015

The objective of this study was to characterize and validate the candidate point mutation in Calc... more The objective of this study was to characterize and validate the candidate point mutation in Calcium channel, voltage-dependent, alpha-2/ delta subunit 1 (CACNA2D1) gene in Karan Fries (Bos taurus x Bos indicus) cattle. The CACNA2D1 gene reported as one of the potential candidate gene influencing Somatic cell Score and Mastitis. A PCR product of 249 bp amplifying the exon 19 and partial 18 and 19 intronic region of CACNA2D1 gene was digested with Hae III restriction enzyme to screen the reported point mutation. A monomorphic banding pattern with genotype AA was found in Karan Fries cattle. Sequencing was also carried out to characterize and explore insilico screened mutation in the nucleotide sequence of a particular region. The result indicates highly conserved sequence in Karan Fries cattle. The Phylogenetic tree revealed that Karan Fries cattle were closer to Bos taurus cattle, Bos mutus (Yak), and Bison bison (American buffalo) compared to other species.

Indian Journal of Animal Research, 2016

Present study was done in thirty Karan Fries bulls to characterize the Exon 3 of PROP1 gene and t... more Present study was done in thirty Karan Fries bulls to characterize the Exon 3 of PROP1 gene and to screen for the H173R polymorphism as well as other variations including reported and novel SNPs in the targeted region. The exon 3 was characterized by sequencing the amplicons obtained after PCR amplification using custom designed primers. The BLAST analysis of the obtained sequence yielded 100% and 99% homology with sequences of Bos taurus and bison respectively. The multiple alignment of the target region sequence with Bos taurus reference sequence revealed that the bulls under the study were free of H173R mutations. No variations were observed thus giving the targeted region a highly conserved one.

Indian Journal of Animal Research, 2016

Present investigation was carried out to study the prevalence of bacterial pathogens in clinical ... more Present investigation was carried out to study the prevalence of bacterial pathogens in clinical and subclinical mastitis in buffaloes during winter season. A total of 118 Murrah buffaloes were screened using California mastitis Test (CMT). Milk samples were collected and analyzed for fat, protein, lactose, SNF, pH, Electrical conductivity (EC) and Somatic Cell Counts (SCC). Out of 118 milk samples, 60 samples (50.84%) were negative for CMT and 58 samples (49.15%) were detected positive for mastitis incidence. Milk pH and EC was significantly higher (p<0.05) in mastitis affected samples than the normal ones, however, protein, fat, SNF and lactose were lower (p<0.05). SCC ranged between 1.28-1.48 x 105 cells/ml (in normal milk samples as compared to 3.85-6.21x 105 cells/ ml (p<0.05) in mastitis milk samples. Out of 58 samples only 51 samples exhibited bacterial growth. The culturally examined and characterized samples revealed S. aureus (35.29%) as the predominant bacteria f...

Animal biotechnology, Jan 20, 2018

The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association ... more The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association with clinical mastitis and production traits. Exon 18 and its flanking regions were screened for the presence of SNPs. Statistical analysis was performed to identify association of period of birth, breed, and genotype with mastitis incidence on randomly selected 103 Sahiwal and 102 Karan Fries cattle. PCR-RFLP analysis revealed that g.38819398G > A mutation in exon 18 (269 bp amplicon) of CACNA2D1 gene resolved into AA, AG, and GG genotypes in Sahiwal and Karan Fries cattle. Wald chi-square analysis revealed that the period of birth, breed, and genotype were significantly associated with mastitis incidence. GG genotyped cattle were found to be less susceptible to mastitis. Least square analysis revealed that GG and AG genotype animals of G38819398A SNP of CACNA2D1 gene in Sahiwal as well as in Karan Fries cattle were associated with higher average milk yields during 1st, 2nd, and 3rd ...

Indian Journal of Animal Research

Mastitis is an economically important disease causing great loss to dairy sector owing to its neg... more Mastitis is an economically important disease causing great loss to dairy sector owing to its negative effect on production. Its multi factorial etiology makes it difficult to use prophylactic methods for control. Identification of genetic resistance mechanisms and selection for it is a potential strategy for mastitis control. The present study was done in 101 Murrah buffaloes to find the common causative agents of mastitis in buffaloes, to identify variants in exon 2 and…

Veterinary world, 2017

This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in p... more This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in protein phosphatase 1 regulatory subunit 11 (PPP1R11) gene in Murrah bulls. Genomic DNA was isolated by phenol-chloroform extraction method from the frozen semen samples of 65 Murrah bulls maintained at Artificial Breeding Research Centre, ICAR-National Dairy Research Institute, Karnal. The quality and concentration of DNA was checked by spectrophotometer reading and agarose gel electrophoresis. The target region of PPP1R11 gene was amplified using four sets of primer designed based on Bos taurus reference sequence. The amplified products were sequenced and aligned using Clustal Omega for identification of SNPs. Animals were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using EcoNI restriction enzyme. The sequences in the NCBI accession number NW_005785016.1 for Bubalus bubalis were compared and aligned with the edited sequences of Murrah bulls...

Tropical animal health and production, Jan 31, 2017

Heat shock proteins (HSPs) act as molecular chaperones which are preferentially transcribed in re... more Heat shock proteins (HSPs) act as molecular chaperones which are preferentially transcribed in response to severe perturbations of the cellular homeostasis such as heat stress. The present study was undertaken for molecular characterization and detection of genetic polymorphisms of HSPB6 gene in 100 Karan Fries Cattle. HSPB6 gene was mapped on Bos taurus autosome 18 (BTA 18), comprising three exons and two introns. Four sets of primers for HSPB6 gene were designed using Primer3 software (version 0.4.0). For detecting single nucleotide polymorphisms (SNPs), sequence data was analyzed using BioEdit software (version 7.2). Comparative sequence analysis of HSPB6 gene showed five nucleotide polymorphisms, which included three transitions viz. g.161A > G, g.436G > A and g.2152A > G and two transversions viz. g.1743C > G and g.2417A > T compared to B. taurus (NCBI GenBank: AC_000175.1). HSPB6 gene of Karan Fries cattle exhibited a high percentage of nucleotide identity (47.0...

Indian Journal of Dairy Science, 2008

Tropical animal health and production, Jan 22, 2016

Heat shock proteins (HSPs) act as molecular chaperones those are preferentially transcribed in re... more Heat shock proteins (HSPs) act as molecular chaperones those are preferentially transcribed in respose to heat stress and the polymorphism in HSP genes associated with heat tolerance traits in cows. HSP90AA1 gene has been mapped on Bos taurus autosome 21 (BTA-21) and spans nearly 5368 bp comprising of 11 exons out of which the first exon does not translate. The present study was done on Karan Fries (5/8 HF × 3/8 Tharparkar) cows reared in tropical climate with the objectives of identifying single-nucleotide polymorphisms (SNPs) in targeted regions (exon 3) of HSP90AA1 gene and analyzing their association with heat tolerance traits in Karan Fries cows. Respiration rate (RR) and rectal temperature (RT) were recorded once daily for four consecutive days during probable extreme hours in different seasons or temperature humidity index (THI), viz., winter, spring, and summer. For detecting single-nucleotide polymorphisms, sequence data were analyzed using BioEdit software (version 7.2). C...

Indian Journal of Dairy Science, 2008

Tropical Animal Health and Production, 2015

Heat shock proteins (HSPs) are expressed in response to heat stress, and the polymorphism in HSP ... more Heat shock proteins (HSPs) are expressed in response to heat stress, and the polymorphism in HSP genes at single-nucleotide level has been reported to be associated with heat tolerance and production performance traits in cattle. HSPB8 gene has been mapped on Bos taurus autosome 17 (BTA-17) spanning nearly 13,252 bp and comprising three exons and two introns. The present study was conducted in Sahiwal cows (n = 108) reared in subtropical climate with the objectives to identify SNPs in all three exons and part of intron 1 of HSPB8 gene and to analyze their association with heat tolerance traits in Sahiwal cows. Respiration rate (RR) and rectal temperature (RT) were recorded once during probable extreme hours in different seasons or Temperature-Humidity Index (THI), i.e., winter, spring, and summer. Heat tolerance coefficient (HTC) was also calculated to check the adaptability of the animals during the period of heat stress. The comparative sequence analysis revealed a total two single-nucleotide polymorphisms (SNPs), i.e., g.507G&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;A in exon 1 and g.881T&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;C in intron 1 of HSPB8 gene. Out of these two identified SNPs, only one SNP, i.e.,…

Global warming and climate change have become the major threat to the sustainability of livestock... more Global warming and climate change have become the major threat to the sustainability of livestock production systems worldwide. Heat stress produces oxidative stress and affects the alternation of plasma K+ and Na+. In the plasma membrane the ion gradients formed by Na+-K+-ATPase enzyme is necessary for Na+-coupled transport of metabolites, nutrients and ions and represents a plausible candidate for heat tolerance traits. ATP1A1 gene encodes for α subunit of Na+-K+-ATPase enzyme, has been mapped on BTA 3 and spans about 22.77 kb and includes 23 exons and coding sequence of 3066 nucleotides. The present study was carried out in 35 Jersey crossbred cows with the objectives to identify SNPs in targeted regions (part of exon 16 to intron 18) of ATP1A1 gene and to analyze their association with respiration rate and rectal temperature. A total of five SNPs (A27008223G, T27008097A, C27008016T, G27008015A and C27007790A) were identified in Jersey crossbred cattle. Respiration rate (RR) and rectal temperature (RT) was recorded once during probable extreme hours in winter, spring and summer season. Further, heat tolerance coefficient (HTC) also calculated to see the adaptability of the animals during the period of heat stress. RT in Jersey crossbred cows for AA (38.01±0.16a) and GG (37.86±0.14a) genotype at A27008223G locus did not differ significantly while RR for CA genotype at C27007790A locus was highest (21.76±1.68a) as compared to CC (19.25±1.155b) and AA (16.91±1.57ab) genotypes and HTC for CA genotype at C27007790A locus was highest (1.94±0.07a) as compared to CC (1.83±0.05b) and AA (1.72±0.07ab) genotypes. It is concluded that AA genotype at 27007790 nucleotide position in Jersey crossbred cows were desirable for respiration rate and heat tolerance coefficient respectively.