scholarly journals Investigation of Genetic Markers for Intramuscular Fat in the Hybrid Wagyu Cattle With Bulked Segregant Analysis

2021 ◽  
Author(s):  
Yun Zhu ◽  
Liyun Han ◽  
Peng Li ◽  
Xiaolong Kang ◽  
Xingang Dan ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Beef Cattle ◽  
Genetic Markers ◽  
Bulked Segregant Analysis ◽  
Low Cost ◽  
Intramuscular Fat ◽  
Mixed Population ◽  
High Density ◽  
Genome Wide ◽  
Qtls Mapping

Abstract Bulked Segregant Analysis（BSA）is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8M~29.6M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.

scholarly journals Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yun Zhu ◽  
Liyun Han ◽  
Peng Li ◽  
Xiaolong Kang ◽  
Xingang Dan ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Beef Cattle ◽  
Genetic Markers ◽  
Bulked Segregant Analysis ◽  
Low Cost ◽  
Intramuscular Fat ◽  
Mixed Population ◽  
High Density ◽  
Genome Wide ◽  
Qtls Mapping

Abstractulked Segregant Analysis (BSA) is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8 M ~ 29.6 M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.

scholarly journals Advanced Strategies in Bulked Segregant Analysis and its Applications

2021 ◽  
Author(s):  
Harshavardan J. Hilli
Keyword(s):  
Genetic Markers ◽  
Mapping Population ◽  
Bulked Segregant Analysis ◽  
High Density ◽  
Mutant Phenotype ◽  
Linkage Maps ◽  
Quick Method ◽  
Reduced Time

Bulked segregant analysis (BSA) is a technique used to identify genetic markers associated with a mutant phenotype and is a quick method for identifying markers in particular genome regions. The paper focussed on Advanced methods which escape the requirement of genotyping all the individuals of the mapping population and generation of high-density linkage maps for mapping of the gene for the trait of interest. With the emergence of re-sequencing techniques, quick mapping of genes has become possible with reduced time and cost by using advanced methodologies like MutMap, MutMap+, MutMap-Gap, QTL-Seq, RNAseq BSA, NGS BSA and QTG seq. The procedure for various advanced BSA strategies has been described.

scholarly journals Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Priscila Arrigucci Bernardes ◽  
Guilherme Batista do Nascimento ◽  
Rodrigo Pelicioni Savegnago ◽  
Marcos Eli Buzanskas ◽  
Rafael Nakamura Watanabe ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Beef Cattle ◽  
Haplotype Block ◽  
Imputation Accuracy ◽  
High Density ◽  
Low Density ◽  
Common Snps ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Trait Locus

AbstractThis study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.

scholarly journals Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 845 ◽  
Author(s):  
María Muñoz ◽  
M Carmen Rodríguez ◽  
Estefânia Alves ◽  
Josep María Folch ◽  
Noelia Ibañez-Escriche ◽  
...  
Keyword(s):  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Intramuscular Fat ◽  
High Density ◽  
Expression Data ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-wide Identification of Molecular Markers Based on Genomic Re-sequencing of Foxtail Millet Elite Cultivar Jingu 21

2018 ◽  
Vol 44 (5) ◽  
pp. 686 ◽  
Author(s):  
Qing-Ying ZHAO ◽  
Rui-Juan ZHANG ◽  
Rui-Liang WANG ◽  
Jian-Hua GAO ◽  
Yuan-Huai HAN ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Foxtail Millet ◽  
Genome Wide ◽  
Elite Cultivar

P6017 A high density genome-wide scan for genetic risk factors of insect bite hypersensitivity (IBH): A Horsegene Project Initiative

2016 ◽  
Vol 94 (suppl_4) ◽  
pp. 156-157
Author(s):  
B. D. Velie ◽  
M. Shrestha ◽  
L. Francois ◽  
A. Schurink ◽  
A. Stinckens ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Risk ◽  
Genetic Risk Factors ◽  
High Density ◽  
Genome Wide ◽  
Insect Bite Hypersensitivity ◽  
Genome Wide Scan

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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