scholarly journals Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246) of the bovine CAST gene

2008 ◽  
Vol 43 (5) ◽  
pp. 657-659 ◽  
Author(s):  
Rogério Abdallah Curi ◽  
Luis Artur Loyola Chardulo ◽  
Antônio Carlos Silveira ◽  
Henrique Nunes de Oliveira
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Direct Sequencing ◽  
Bos Indicus ◽  
Basic Structure ◽  
Meat Tenderness ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Cast Gene

The objective of this work was to genotype the single nucleotide polymorphism (SNP) A2959G (AF159246) of bovine CAST gene by PCR-RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A) in Bos indicus was confirmed. The use of PCR-RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.

scholarly journals Genetic Variation of Calpastation Gene of Indigenous Bali Cattle (Bos javanicus) in Indonesia

2019 ◽  
Vol 26 (1) ◽  
pp. 44
Author(s):  
Endang Tri Margawati ◽  
Slamet Diah Volkandari ◽  
Indriawati Indriawati ◽  
Emma M. Svensson
Keyword(s):  
Genetic Variation ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Meat Tenderness ◽  
Gene Markers ◽  
Bos Javanicus ◽  
Restriction Fragment Polymorphism ◽  
Pcr Rflp ◽  
Bali Cattle ◽  
Cast Gene

Calpastatin is one of gene markers affecting meat tenderness. The study aimed to evaluate genetic variation of calpastatin (CAST) gene of Bali cattle (Bos javanicus) in lndonesia. A total of 61 samples consisting of 21 Bali cattle, 22 Ongole cattle (Bos indicus), and 18 Friesian Holstein (FH) cattle (Bos taurus) were applied. The Ongole and FH cattle were involved for breed comparison. DNA was extracted from fresh blood using a High Salt method and measured their quality by a Spectrophotometer. A 523 bp of Calpastatin gene fragment was amplified by Polymerase Chain Reaction and Restriction Fragment Polymorphism (PCR-RFLP) technique with RsaI restriction enzyme for genotyping. Result showed that two variants alleles (C and G) and three genotypes (CC, GC, GG) were found in those Bali, Ongole and FH samples. Allele G was dominant allele with the highest G allele was in Bali cattle population (0.88). The higher percentage of allele C was found in Ongole and Friesian Holstein compared to that in Bali cattle. The Ongole breed tends to have a potential source of lean meat quality. This finding identified that genetic variation of CAST gene was exist in Bali cattle and adapted cattle of Ongole and FH in Indonesian.

scholarly journals Frecuencias alélicas para variantes SNP en el gen Nramp1 en bovinos infectados con Brucella abortus o clasificados por resistencia al patógeno

2009 ◽  
Vol 10 (1) ◽  
pp. 43
Author(s):  
Fernando Cerquera M. ◽  
Rodrigo Martínez S. ◽  
Rubén Toro O. ◽  
Jaime Tobón C. ◽  
Jaime Gallego G. ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Brucella Abortus ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Natural Resistance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Allelic Frequencies ◽  
Bos Taurus Indicus

<p>La resistencia natural a la brucelosis en bovinos ha sido asociada a factores genéticos, principalmente a algunos polimorfismos de nucleótido simple ubicados dentro del gen Nramp1. La presente investigación evalúa el efecto de variantes tipo polimorfismos de nucleótido simple presentes en regiones codificantes y en la región 3’UTR del gen Nramp1, en la clasificación de los animales como resistentes o susceptibles; además se determinan los genotipos predominantes en animales naturalmente infectados y comprobados como positivos por la presencia de anticuerpos anti <em>Brucella abortus</em>. Se establecieron las frecuencias genotípicas y alélicas para cinco polimorfismos de nucleótido simple identificados dentro del gen Nramp1 en animales de las razas blanco orejinegro (<em>Bos taurus taurus</em>) y cebú (<em>Bos taurus indicus</em>) y en muestras serológicamente positivas provenientes de animales cruzados (<em>Bos taurus </em>x <em>Bos indicus</em>). La determinación de genotipos se realizó mediante la metodología polimorfismo conformacional de cadena sencilla. Se realizó un ensayo de desafío infeccioso in vitro, para estimar la capacidad de los macrófagos bovinos para controlar la sobrevivencia bacterial, lo que permitió definir los individuos como resistentes o susceptibles. Los resultados sugieren una asociación significativa del SNP4 (<em>p </em>= 0,0506) con la variación para el fenotipo de susceptibilidad, pues se encontró el genotipo homocigoto (BB) en alta frecuencia en animales catalogados como resistentes y el genotipo heterocigoto (AB) en alta frecuencia en animales catalogados como susceptibles y en animales con títulos de anticuerpos anti <em>Brucella abortus</em>.  </p><p> </p><p><strong>Allelic frequencies for SNP variants in the gene Nramp1 in bovine infected with </strong><strong><em>Brucella abortus </em></strong><strong>or classified by resistance to the pathogen</strong>  </p><p>The natural resistance to brucellosis in cattle has been associated to genetic factors mainly to some single nucleotide polymorphism (SNP), located within Nramp1 gen. The current research has studied the effect of nucleotide variants to be found in coding regions and other one located in 3 non translated region of Nramp1 gene, on the animal classification as resistant or susceptible, moreover was identified the main genotypes to be found on the infected animals, confirmed as positives by antibody antibrucella titles. Was established the genotypic and allelic frequencies for five single nucleotide polymorphism in animals from blanco orejinegro (<em>Bos taurus taurus</em>) and zebu breeds (<em>Bos taurus indicus</em>) and serum samples belonging to positive crossbred animals (<em>Bos taurus x Bos indicus</em>). The genotype was defined by the methodology known as “single strand conformational polymorphism”. To estimate the macrophage capacity to control the bacterial survival, an in vitro assay was performed, which allowed define the phenotype as resistant or susceptible. The results suggest a significant association for SNP4 (p = 0.0506) with the phenotypic variation for resistant or susceptibility, because was found the genotype (BB) at higher frequency in susceptible animals and naturally infected animals, than those resistant animals. </p>

Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle

2020 ◽  
Vol 60 (15) ◽  
pp. 1769
Author(s):  
J. B. S. Ferraz ◽  
X. -L. Wu ◽  
H. Li ◽  
J. Xu ◽  
R. Ferretti ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genomic Selection ◽  
Bos Taurus ◽  
Imputation Accuracy ◽  
Bos Indicus ◽  
Zebu Cattle ◽  
Low Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Chip

Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

scholarly journals Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

2018 ◽  
Vol 135 (6) ◽  
pp. 432-441 ◽  
Author(s):  
Nilesh Nayee ◽  
Goutam Sahana ◽  
Swapnil Gajjar ◽  
Ananthasayanam Sudhakar ◽  
Kamlesh Trivedi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Genomic Studies

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

Sign in / Sign up

Export Citation Format

Share Document