Sequence characterization and polymorphism detection in lactoferrin gene of Deoni (Bos indicus) cattle

2015 ◽  
Author(s):  
Arun Pratap Singh ◽  
K. P. Ramesha ◽  
S. Isloor ◽  
P. Divya ◽  
Ashwani Arya ◽  
...  
Keyword(s):  
Bos Indicus ◽  
Point Mutations ◽  
Single Strand Conformation Polymorphism ◽  
Potential Candidate ◽  
Coding Region ◽  
Cattle Breeding ◽  
Sequence Characterization ◽  
Potential Candidate Gene ◽  
Dairy Cattle Breeding ◽  
Lactoferrin Gene

Lactoferrin is an iron binding glycoprotein which plays an essential role in antimicrobial defense and a potential candidate gene in dairy cattle breeding. The present study was undertaken with the objective of sequence characterization and identification of polymorphisms within exons 2, 3 and 14 and their flanking intronic regions in lactoferrin gene of Deoni (Bos indicus) cattle by single strand conformation polymorphism (SSCP). Amplicons of exons 4, 5 and 16 showed monomorphic patterns. PCR-SSCP analysis revealed a total of eight different variants in three investigated regions of the lactoferrin gene. The locus LtfE2 revealed four different variants, viz. LtfE2-A, LtfE2-B, LtfE2-C and LtfE2-D with the frequency of 0.42, 0.26, 0.22 and 0.10, respectively. Analysis of exon 3 and 14 revealed two unique SSCP patterns with the frequencies of 0.54 and 0.46, 0.86 and 0.14 respectively. Comparison of nucleotide sequences of lactoferrin gene of the Deoni cattle with taurine cattle revealed a total of 12 point mutations, 11 of which were found to be in coding region with 10 transitions. Conceptualized translation of nucleotide sequence revealed 5 amino acid changes. The SNPs identified in the coding region of lactoferrin gene may serve as potential genetic marker (s) in cattle for disease resistance.

DGAT1 polymorphism in Bos indicus and Bos taurus cattle breeds

2004 ◽  
Vol 71 (2) ◽  
pp. 182-187 ◽  
Author(s):  
Bernhard Kaupe ◽  
Andreas Winter ◽  
Ruedi Fries ◽  
Georg Erhardt
Keyword(s):  
Milk Fat ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Milk Composition ◽  
Major Effect ◽  
Potential Candidate ◽  
Fat Percentage ◽  
Cattle Breeds ◽  
Potential Candidate Gene ◽  
Trait Locus

As a result of multiple QTL-mapping projects in recent years, a quantitative trait locus for milk fat percentage and milk yield has been described on BTA14. Recent reports name the acyl-CoA[ratio ]diacylglycerol acyltransferase (DGAT1) gene on BTA14 as a potential candidate gene, with a nonconservative substitution of lysine by alanine (K232A) producing a major effect on milk composition and yield. DGAT1K appears to be the ancestral allele and the K232A substitution probably occurred after the divergence of the Bos indicus and Bos taurus lineages. These findings prompted us to genotype 1748 DNA samples of 38 different Bos taurus and Bos indicus cattle breeds from 13 countries on five continents (Europe, Africa, Asia, North America and South America), to examine the occurrence of the DGAT1 polymorphism and characterize the K232A substitution in cattle breeds of different origins and selected for different purposes (e.g., beef, dairy and dual purpose). Calculating pairwise FST values for pooled subpopulations showed least divergence for Bos indicus breeds with high milk fat percentage. Fixation of DGAT1A was found in some Bos taurus breeds and fixation of DGAT1K in one Bos indicus breed. Breeds of no known organized breeding background from the Near East domestication centre of Bos taurus and taurine African N'Dama cattle were found to possess intermediate frequencies of DGAT1K. While beef breeds tended to harbour higher DGAT1A levels, dairy cattle showed everything from very low levels of DGAT1K to unexpectedly high frequencies of this allele.

Genetic characterization and identification of single nucleotide polymorphisms of ATP1A1 gene in Indian humped cattle

2015 ◽  
Author(s):  
A. Barani ◽  
K. P. Ramesha ◽  
M. Basavaraju ◽  
Akhila Rao ◽  
TVL. Narasimha Rao
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Direct Sequencing ◽  
Bos Indicus ◽  
Plasma Potassium ◽  
Single Strand Conformation Polymorphism ◽  
Integral Membrane Protein ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Information Index

Climate change in India is likely to aggravate the heat stress in dairy animals due to rise in temperature coupled with increased precipitation. In animals heat stress affects the alteration of plasma Potassium (K (+)) and Sodium Na (+) ions. ATP1A1 gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na+ and K+ ions across the plasma membrane. The present study is aimed to investigate the polymorphisms in the entire coding region of ATP1A1 gene in Bos indicus (Deoni) cattle by PCR- Single-Strand Conformation Polymorphism (PCR- SSCP) and direct sequencing of variants. Sequence analysis showed 16 SNPs, of which 5 SNPs were in the coding region and the remaining 11 SNPs were detected in the non-coding region of ATP1A1 gene. All the observed variations in the coding regions of ATP1A1 gene were silent mutations. The genotypic, allelic frequencies, c<sup>2</sup> test for Hardy-Weinberg equilibrium and Shannon’s information index were calculated using POPGENE-32. The study revealed a high degree of genetic variability in ATP1A1 gene in the Deoni cattle population which indicated the utility of this gene for further studies for identification of markers associated with heat tolerance in Indian humped cattle for using in marker assisted selection for heat tolerance.

Sequence characterization and polymorphism detectionin AQP7 gene of Murrah buffalo

2016 ◽  
Author(s):  
Ragini Kumari ◽  
K.P. Ramesha ◽  
Rakesh Kumar ◽  
Divya Divya ◽  
Anjali Kumari ◽  
...  
Keyword(s):  
Semen Quality ◽  
Single Strand Conformation Polymorphism ◽  
Sscp Analysis ◽  
Reference Sequence ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Sequence Characterization ◽  
Murrah Buffalo ◽  
Aquaporin 7

Aquaporin 7 (AQP7) gene is a member of aqua-glyceroporins which transports glycerol and water to spermatids. The present study aimed to investigate the polymorphisms within exons 2, 3, 4, 5 and their flanking intronic regions in AQP7 gene of Murrah bulls. Genomic DNA was extracted from 69 Murrah bulls blood samples and was subjected to polymerase chain reaction- single strand conformation polymorphism (PCR-SSCP) analysis. PCR-SSCP analysis revealed a total of eight different variants for amplicons of exons 4 and 5. Amplicon of exon 4 revealed three different patterns viz. E4P1, E4P2 and E4P3 with the frequency of 0.30, 0.22 and 0.48, respectively. Analysis of exon 5 revealed five unique SSCP patterns viz. E5P1, E5P2, E5P3, E5P4 and E5P5, with the frequency of 0.10, 0.37, 0.20, 0.20 and 0.13, respectively. Sequence analysis showed 16 single nucleotide polymorphisms, 7 of which were observed in coding region. Amplicons of exons 2 and 3 showed monomorphic patterns. However, compared to the reference sequence of taurine cattle one transition (C6878T) in exon 3 and 4 transitions (G2099A, C2116T, A2117G, G6848C) in intron 2 were observed for all the bulls under study. The genetic variability identified in the AQP7 gene may serve as potential genetic marker(s) for semen quality traits in buffalo.

Characterization and validation of point mutation in exon 19 of CACNA2D1 gene in Karan Fries (Bos taurus x Bos indicus) cattle

2015 ◽  
Author(s):  
Ankit Magotra ◽  
I. D. Gupta ◽  
Archana Verma ◽  
M. V. Chaudhari ◽  
Ashwani Arya ◽  
...  
Keyword(s):  
Point Mutation ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Potential Candidate ◽  
Conserved Sequence ◽  
Potential Candidate Gene ◽  
Pcr Product ◽  
Voltage Dependent ◽  
Karan Fries ◽  
Exon 19

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.

Sequence characterization and SNP identification of TNP1 gene in Indian cattle breeds

2017 ◽  
Author(s):  
Ashish Ranjan ◽  
K. Raja ◽  
Ranjana Sinha ◽  
I. Ganguly ◽  
I. Gupta ◽  
...  
Keyword(s):  
Promoter Region ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Coding Region ◽  
Sequence Characterization ◽  
Holstein Breed ◽  
Cattle Breeds ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Indian Cattle

Present study was conducted on 50 bulls and 40 male calves of Sahiwal, Tharparkar and Karan Fries cattle maintained at ABRC and LRC, NDRI Karnal (Haryana) to characterize and identify genetic polymorphisms in TNP1 gene. A total of 1568 bp region of TNP-1 gene includes 490 bp of promoter region and two exon and one intron was sequenced and characterized in Bos indicus cattle breeds which are widely distributed in Indian sub-continent. Four sets of primers for TNP1 gene on the basis of Bos Taurus sequence (Acc. No- BK_006511) were designed using Primer3 software and PCR products of 487, 450, 455 and 250 bp were obtained. Amplicons were custom sequenced and subjected to Clustal W analysis which showed no nucleotide changes in coding region and non coding region in Indian cattle breeds as compared to Bos taurus. The 490 bp of promoter region was subjected to transcription factor binding site. Three TATA boxes and two CAAT boxes were identified in the studied fragment. Analysis of SNP was performed using restriction fragment length polymorphism (PCR-RFLP), to detect nucleotide changes in the sequence as reported (g.528G>A, SS1388116558) in Chinese Holstein breed. No polymorphisms were found for tested SNP. Only one genotype GG indicates the absence of variability in the sampled population.

scholarly journals Association of a non-synonymous SNP of IL17RA gene with litter size traits in Large White and Landrace pigs

2021 ◽  
Vol 19 (3) ◽  
pp. 391-405
Author(s):  
Worrarak Norseeda ◽  
◽  
Guisheng Liu ◽  
Tawatchai Teltathum ◽  
Korawan Sringarm ◽  
...  
Keyword(s):  
Immune Responses ◽  
Litter Size ◽  
Interleukin 17 ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Large White ◽  
Single Nucleotide ◽  
Reproductive Process ◽  
Potential Candidate Gene

Interleukin-17 receptor A (IL17RA) is one of the cytokine receptors of the pro-inflammatory interleukin-17 (IL17) cytokine family. The IL17 and IL17RA genes are involved in inflammatory and immune responses as well as reproductive process of mammals. The purposes of this study were to examine polymorphisms in the porcine IL17RA gene and to assess its effects on litter size traits in Large White and Landrace pigs. Three non-synonymous single nucleotide polymorphisms (SNPs) in the porcine IL17RA gene were verified. The porcine IL17RA c.785C>T (p.Ala262Val) was found to be segregating in the Large White and Landrace pigs. No polymorphisms in the coding region of the porcine IL17RA gene at the two non-synonymous SNPs loci of c.997G>A (p.Val333Ile) and c.1962T>G (p.Asp654Glu) were found. The porcine IL17RA c.785C>T polymorphism was significantly associated with the total number born (TNB) and the number born alive (NBA) in Large White pigs (P<0.05). Moreover, the porcine IL17RA c.785C>T was significantly associated with the TNB, NBA, total birth weight (TBW), and total weaning weight of piglets at 21 days (TWW) in Landrace pigs (P<0.05). These results supported the importance of the porcine IL17RA gene in the litter size traits of pigs. Thus, the porcine IL17RA could be used as a potential candidate gene for improving litter size traits in pig breeding.

Variation in lactoferrin gene affects milk lactoferrin content and somatic cell count in murrah buffaloes

2019 ◽  
Author(s):  
Arun Pratap Singh ◽  
K. P. Ramesha ◽  
M. A. Mir ◽  
Ashwani Arya ◽  
S. Isloor
Keyword(s):  
Somatic Cell ◽  
Cell Count ◽  
Somatic Cell Count ◽  
Sscp Analysis ◽  
Reference Sequence ◽  
Potential Candidate ◽  
Coding Region ◽  
Murrah Buffaloes ◽  
Lactoferrin Gene ◽  
Exon 10

Lactoferrin plays an important role in antimicrobial defence and is a potential candidate gene for mastitis resistance. In the present investigation, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) studies were carried out in Murrah (Bubalus bubalis) buffaloes to detect single nucleotide polymorphisms (SNPs) of lactoferrin gene and to analyse the association between the observed polymorphisms with milk lactoferrin content and Somatic cell count (SCC). PCR-SSCP analysis revealed a total of 07 different variants in the partial coding region of the lactoferrin gene. PCR-SSCP analysis of exon 10 of lactoferrin gene revealed three and that of exons 4 and 5 revealed two unique patterns each, while all other exons exhibited monomorphic pattern. Comparison of nucleotide sequences of lactoferrin gene of the Murrah buffaloes with taurine reference sequence revealed a total of 14 point mutations, 09 of which were found to be in coding region. Conceptualized translation of nucleotide sequence revealed 07 amino acid changes. SSCP variants of exon 10 (P less than 0.01) had significant effect on milk SCC. The SSCP variants of exon 4 and exon 5 had significant (P less than 0.05) effect on lactoferrin content. The SCC and lactoferrin content in Murrah buffaloes was highest in 4th and above parity group. Stage of lactation had highly significant (P less than 0.01) effect on both milk SCC and lactoferrin content. There was a high and significant (p less than 0.01) correlation (0.741) between SCC and lactoferrin content in milk. The observed association between SSCP variants in lactoferrin gene with milk SCC and milk lactoferrin content can be used as prognostic markers for selection of animals for high lactoferrin content and low somatic cell count, as well as a marker of susceptibility/resistance to mastitis in Murrah buffaloes

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