scholarly journals INTEGRATION OF QTL DETECTION OF GROWTH TRAITS AND ASSOCIATION STUDY FOR CHICKEN CHROMOSOME 4

2020 ◽  
Vol 40 (1) ◽  
pp. 191-207
Author(s):  
Tarik Rabie
Keyword(s):  
Association Study ◽  
Growth Traits ◽  
Chicken Chromosome ◽  
Chromosome 4 ◽  
Qtl Detection

scholarly journals Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Bingru Zhao ◽  
Hanpeng Luo ◽  
Xixia Huang ◽  
Chen Wei ◽  
Jiang Di ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Improvement ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Fibre Diameter ◽  
Single Step ◽  
Genome Wide Association ◽  
Six Traits ◽  
Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

A radiation hybrid map of chicken Chromosome 4

2004 ◽  
Vol 15 (7) ◽  
pp. 560-569 ◽  
Author(s):  
Tarik S.K.M. Rabie ◽  
Richard P.M.A. Crooijmans ◽  
Mireille Morisson ◽  
Joanna Andryszkiewicz ◽  
Jan J. van der Poel ◽  
...  
Keyword(s):  
Radiation Hybrid ◽  
Chicken Chromosome ◽  
Chromosome 4 ◽  
Radiation Hybrid Map

Genetic Markers: Association Study in Migraine

Cephalalgia ◽  
1995 ◽  
Vol 15 (3) ◽  
pp. 200-204 ◽  
Author(s):  
J Pardo ◽  
A Carracedo ◽  
I Munoz ◽  
J Castillo ◽  
M Lema ◽  
...  
Keyword(s):  
Acid Phosphatase ◽  
Association Study ◽  
Genetic Markers ◽  
Genetic Factor ◽  
Molecular Genetic ◽  
Chromosome 4 ◽  
Healthy Individuals ◽  
Specific Component ◽  
Alpha 1 Antitrypsin ◽  
Group Component

Eleven genetic markers were typed in 112 unrelated patients with migraine (50 with aura, 62 without aura) and compared with a random sample of healthy individuals. No significant differences were found for the ABO and Rh systems, acid phosphatase 1, phosphoglucomutase 1, adenosine deaminase, haptoglobin, transferrin, alpha-1–antitrypsin, and D1S80. Strong associations between the group of patients with migraine and group-specific component GC 1F-1F and esterase-D ESD 2–2 phenotypes were observed. These associations raise the possibility that a molecular genetic factor for migraine may exist in or near the Group Component (chromosome 4) and Esterase D (chromosome 13) loci, and represent a first comprehensive step in the eventual localization and isolation of the migraine genes.

scholarly journals Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Heredity ◽  
2020 ◽  
Author(s):  
Yanhua Zhang ◽  
Yuzhe Wang ◽  
Yiyi Li ◽  
Junfeng Wu ◽  
Xinlei Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Carcass Traits ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Pathway Enrichment Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

Chromosomal localization of 15 large insert BAC clones containing three microsatellites on chicken chromosome 4 (GGA4) which refine its centromere position

2005 ◽  
Vol 36 (2) ◽  
pp. 161-163 ◽  
Author(s):  
A. A. Sazanov ◽  
M. N. Romanov ◽  
B. Wardecka ◽  
A. L. Sazanova ◽  
M. Korczak ◽  
...  
Keyword(s):  
Chromosomal Localization ◽  
Chicken Chromosome ◽  
Chromosome 4 ◽  
Bac Clones ◽  
Centromere Position

scholarly journals Genome-Wide Association Study Identified a Narrow Chromosome 1 Region Associated with Chicken Growth Traits

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e30910 ◽  
Author(s):  
Liang Xie ◽  
Chenglong Luo ◽  
Chengguang Zhang ◽  
Rong Zhang ◽  
Jun Tang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Genome Wide
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