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

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.

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Association study between single nucleotide polymorphisms in leptin and growth traits in Cyprinus carpio var. Jian

Genetics and Molecular Research ◽

10.4238/gmr.15037635 ◽

2016 ◽

Vol 15 (3) ◽

Author(s):

Y. Tang ◽

H. Li ◽

J. Li ◽

F. Yu ◽

J. Yu

Keyword(s):

Single Nucleotide Polymorphisms ◽

Association Study ◽

Cyprinus Carpio ◽

Growth Traits ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Overview of Genomic Insights into Chicken Growth Traits Based on Genome- Wide Association Study and microRNA Regulation

Current Genomics ◽

10.2174/1389202911314020006 ◽

2013 ◽

Vol 14 (2) ◽

pp. 137-146 ◽

Cited By ~ 12

Author(s):

Zhenqiang Xu ◽

Qinghua Nie ◽

Xiquan Zhang

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Growth Traits ◽

Genome Wide Association ◽

Microrna Regulation ◽

Genome Wide

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A radiation hybrid map of chicken Chromosome 4

Mammalian Genome ◽

10.1007/s00335-004-2362-8 ◽

2004 ◽

Vol 15 (7) ◽

pp. 560-569 ◽

Cited By ~ 9

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

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Genetic Markers: Association Study in Migraine

Cephalalgia ◽

10.1046/j.1468-2982.1995.015003200.x ◽

1995 ◽

Vol 15 (3) ◽

pp. 200-204 ◽

Cited By ~ 11

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.

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The chicken 9E3/CEF4 CXC chemokine is the avian orthologue of IL8 and maps to chicken Chromosome 4 syntenic with genes flanking the mammalian chemokine cluster

Immunogenetics ◽

10.1007/s002510050664 ◽

1999 ◽

Vol 49 (7-8) ◽

pp. 673-684 ◽

Cited By ~ 67

Author(s):

P. Kaiser ◽

Simon Hughes ◽

Nat Bumstead

Keyword(s):

Chicken Chromosome ◽

Chromosome 4 ◽

Cxc Chemokine

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

Heredity ◽

10.1038/s41437-020-00365-x ◽

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.

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