Dataset Information

Single tube tetraplex PCR based screening of a SNP at exon 14 region of bovine ITGB6 among different Zebu breeds.

ABSTRACT: The present study was aimed to screen genetic variation within a SNP (rs136500299) located at exon 14 region of bovine ITGB6 gene among different Zebu cattle breeds. The genotyping method describe in the present study is a tetraplex ARMS PCR, which offers extremely fast, economical, and simple detection tool. The distribution of the ITGB6 genotypes among the different breeds studied suggested that the populations were under Hardy-Weinberg equilibrium. Our findings revealed that TT genotypes are widely distributed among different Zebu cattle breeds, which can be associated with the resistance to FMD virus, as the Bos indicus are more resistant to FMD virus in comparison to Bos taurus.

SUBMITTER: Singh R

PROVIDER: S-EPMC4310182 | biostudies-other | 2015 Feb

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Single tube tetraplex PCR based screening of a SNP at exon 14 region of bovine ITGB6 among different Zebu breeds.

Singh Rani R Deb Rajib R Singh Umesh U Raja T V TV Alex Rani R Kumar Sushil S Chakraborti Soumendu S Sengar Gyanendra G Sharma Sheetal S

Meta gene 20150110

The present study was aimed to screen genetic variation within a SNP (rs136500299) located at exon 14 region of bovine ITGB6 gene among different Zebu cattle breeds. The genotyping method describe in the present study is a tetraplex ARMS PCR, which offers extremely fast, economical, and simple detection tool. The distribution of the ITGB6 genotypes among the different breeds studied suggested that the populations were under Hardy-Weinberg equilibrium. Our findings revealed that TT genotypes are ...[more]

PMID: 25685717

Similar Datasets

Project description:BACKGROUND: The muscle fiber number and fiber composition of muscle is largely determined during prenatal development. In order to discover genes that are involved in determining adult muscle phenotypes, we studied the gene expression profile of developing fetal bovine longissimus muscle from animals with two different genetic backgrounds using a bovine cDNA microarray. Fetal longissimus muscle was sampled at 4 stages of myogenesis and muscle maturation: primary myogenesis (d 60), secondary myogenesis (d 135), as well as beginning (d 195) and final stages (birth) of functional differentiation of muscle fibers. All fetuses and newborns (total n = 24) were from Hereford dams and crossed with either Wagyu (high intramuscular fat) or Piedmontese (GDF8 mutant) sires, genotypes that vary markedly in muscle and compositional characteristics later in postnatal life. RESULTS: We obtained expression profiles of three individuals for each time point and genotype to allow comparisons across time and between sire breeds. Quantitative reverse transcription-PCR analysis of RNA from developing longissimus muscle was able to validate the differential expression patterns observed for a selection of differentially expressed genes, with one exception. We detected large-scale changes in temporal gene expression between the four developmental stages in genes coding for extracellular matrix and for muscle fiber structural and metabolic proteins. FSTL1 and IGFBP5 were two genes implicated in growth and differentiation that showed developmentally regulated expression levels in fetal muscle. An abundantly expressed gene with no functional annotation was found to be developmentally regulated in the same manner as muscle structural proteins. We also observed differences in gene expression profiles between the two different sire breeds. Wagyu-sired calves showed higher expression of fatty acid binding protein 5 (FABP5) RNA at birth. The developing longissimus muscle of fetuses carrying the Piedmontese mutation shows an emphasis on glycolytic muscle biochemistry and a large-scale up-regulation of the translational machinery at birth. We also document evidence for timing differences in differentiation events between the two breeds. CONCLUSION: Taken together, these findings provide a detailed description of molecular events accompanying skeletal muscle differentiation in the bovine, as well as gene expression differences that may underpin the phenotype differences between the two breeds. In addition, this study has highlighted a non-coding RNA, which is abundantly expressed and developmentally regulated in bovine fetal muscle.

Project description:The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead chip were used in the current study and principal component analysis (PCA), log-likelihood ratios (LLR) and Neighbor-Joining (NJ) were applied to assess the performance of different assignment methods. The results revealed that the DNN, Garson, and Olden methods are able to assign individuals to true populations with 4270, 4937, and 7999 SNP markers, respectively. The PCA was used to determine how the animals allocated to the groups using all genotyped markers available on 50k Bead chip and the subset of SNP markers identified with different methods. The results indicated that all SNP panels are able to assign individuals into their true breeds. The success percentage of genetic assignment for different methods assessed by different levels of LLR showed that the success rate of 70% in the analysis was obtained by three methods with the number of markers of 110, 208, and 178 tags for DNN, Garson, and Olden methods, respectively. Also the results showed that DNN performed better than other two approaches by achieving 93% accuracy at the most stringent threshold. Finally, the identified SNPs were successfully used in independent out-group breeds consisting 120 individuals from eight breeds and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. Furthermore, the NJ tree of allele-sharing distances on the validation dataset showed that the DNN has a high potential for feature selection. In general, the results of this study indicated that the DNN technique represents an efficient strategy for selecting a reduced pool of highly discriminant markers for assigning individuals to the true population of origin.

Dataset Information

Single tube tetraplex PCR based screening of a SNP at exon 14 region of bovine ITGB6 among different Zebu breeds.

Publications

Single tube tetraplex PCR based screening of a SNP at exon 14 region of bovine ITGB6 among different Zebu breeds.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets