Mitochondrial DNA single nucleotide polymorphism associated with weight estimated breeding values in Nelore cattle (Bos indicus)

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 Brucella abortus. 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 (Bos taurus taurus) y cebú (Bos taurus indicus) y en muestras serológicamente positivas provenientes de animales cruzados (Bos taurus x Bos indicus). 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 (p = 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 Brucella abortus. Allelic frequencies for SNP variants in the gene Nramp1 in bovine infected with Brucella abortus or classified by resistance to the pathogen 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 (Bos taurus taurus) and zebu breeds (Bos taurus indicus) and serum samples belonging to positive crossbred animals (Bos taurus x Bos indicus). 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.

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The impact of single nucleotide polymorphism selection on prediction of genomewide breeding values

BMC Proceedings ◽

10.1186/1753-6561-3-s1-s13 ◽

2009 ◽

Vol 3 (Suppl 1) ◽

pp. S13 ◽

Cited By ~ 5

Author(s):

Kacper Żukowski ◽

Tomasz Suchocki ◽

Anna Gontarek ◽

Joanna Szyda

Keyword(s):

Single Nucleotide Polymorphism ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Values ◽

Single Nucleotide Polymorphism Selection ◽

The Impact

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Patterns of single nucleotide polymorphism distribution in hypervariable regions of the D-loop of human mitochondrial DNA

Molecular Biology ◽

10.1134/s0026893310030052 ◽

2010 ◽

Vol 44 (3) ◽

pp. 386-392

Author(s):

I. V. Kornienko ◽

D. I. Vodolazhsky

Keyword(s):

Single Nucleotide Polymorphism ◽

Mitochondrial Dna ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Human Mitochondrial Dna ◽

Hypervariable Regions ◽

D Loop

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

Animal Production Science ◽

10.1071/an19396 ◽

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.

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Genomic prediction for carcass traits in Japanese Black cattle using single nucleotide polymorphism markers of different densities

Animal Production Science ◽

10.1071/an15696 ◽

2017 ◽

Vol 57 (8) ◽

pp. 1631 ◽

Cited By ~ 1

Author(s):

Shinichiro Ogawa ◽

Hirokazu Matsuda ◽

Yukio Taniguchi ◽

Toshio Watanabe ◽

Yuki Kitamura ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Genomic Prediction ◽

Carcass Traits ◽

Snp Markers ◽

Carcass Weight ◽

Nucleotide Polymorphism ◽

Japanese Black Cattle ◽

Marbling Score ◽

Single Nucleotide ◽

Breeding Values

Genomic prediction (GP) of breeding values using single nucleotide polymorphism (SNP) markers can be conducted even when pedigree information is unavailable, providing phenotypes are known and marker data are provided. While use of high-density SNP markers is desirable for accurate GP, lower-density SNPs can perform well in some situations. In the present study, GP was performed for carcass weight and marbling score in Japanese Black cattle using SNP markers of varying densities. The 1791 fattened steers with phenotypic data and 189 having predicted breeding values provided by the official genetic evaluation using pedigree data were treated as the training and validation populations respectively. Genotype data on 565837 autosomal SNPs were available and SNPs were selected to provide different equally spaced SNP subsets of lower densities. Genomic estimated breeding values (GEBVs) were obtained using genomic best linear unbiased prediction incorporating one of two types of genomic relationship matrices (G matrices). The GP accuracy assessed as the correlation between the GEBVs and the corrected records divided by the square root of estimated heritability was around 0.85 for carcass weight and 0.60 for marbling score when using 565837 SNPs. The type of G matrix used gave no substantial difference in the results at a given SNP density for traits examined. Around 80% of the GP accuracy was retained when the SNP density was decreased to 1/1000 of that of all available SNPs. These results indicate that even when a SNP panel of a lower density is used, GP may be beneficial to the pre-selection for the carcass traits in Japanese Black young breeding animals.

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