Association of SNP Marker in IGF-I and MYF5 Candidate Genes with Growth Traits in Korean Cattle

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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Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

International Journal of Molecular Sciences ◽

10.3390/ijms17020243 ◽

2016 ◽

Vol 17 (2) ◽

pp. 243 ◽

Cited By ~ 23

Author(s):

Diego Robledo ◽

Carlos Fernández ◽

Miguel Hermida ◽

Andrés Sciara ◽

José Álvarez-Dios ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Single Nucleotide Polymorphisms ◽

Candidate Genes ◽

Quantitative Trait ◽

Growth Traits ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Trait Loci

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Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population

Genes ◽

10.3390/genes12010117 ◽

2021 ◽

Vol 12 (1) ◽

pp. 117

Author(s):

Donglin Ruan ◽

Zhanwei Zhuang ◽

Rongrong Ding ◽

Yibin Qiu ◽

Shenping Zhou ◽

...

Keyword(s):

Candidate Genes ◽

Bone Growth ◽

Genome Wide Association Study ◽

Growth Traits ◽

Average Daily Gain ◽

Snp Array ◽

Single Step ◽

Economic Traits ◽

Association Analyses ◽

Genealogical Information

Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

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Estimate of the Association of IGF-I and IGFALS Genes with Growth Traits in Hamdani Sheep

Brazilian Archives of Biology and Technology ◽

10.1590/1678-4324-2021210262 ◽

2021 ◽

Vol 64 ◽

Author(s):

Mervan Bayraktar ◽

Omer Shoshin

Keyword(s):

Growth Traits ◽

Igf I

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Insulin-like growth factor-I measured in juvenile pigs is genetically correlated with economically important performance traits

Australian Journal of Experimental Agriculture ◽

10.1071/ea05048 ◽

2005 ◽

Vol 45 (8) ◽

pp. 783 ◽

Cited By ~ 21

Author(s):

K. L. Bunter ◽

S. Hermesch ◽

B. G. Luxford ◽

H-U. Graser ◽

R. E. Crump

Keyword(s):

Growth Factor ◽

Growth Traits ◽

Genetic Correlations ◽

Selection Criterion ◽

Insulin Like Growth Factor ◽

Factor I ◽

Igf I ◽

Performance Traits ◽

Growth Factor I ◽

Daily Gain

Insulin-like growth factor-I (IGF-I) is a naturally occurring polypeptide produced in the liver, muscle and fat tissues. It is known to be associated with growth and development during the postnatal growth period. Evidence for strong genetic correlations between juvenile IGF-I and performance traits would suggest this physiological measure would be useful as an early selection criterion. This paper reports estimates of genetic parameters from 9 trials where IGF-I was measured in juvenile pigs. All trials involved populations undergoing active selection for improved performance (e.g. efficient lean meat growth). Juvenile IGF-I was moderately heritable (average h2: 0.31) and influenced by common litter effects (average c2: 0.15). Genetic correlations (rg) between juvenile IGF-I and backfat (BF), feed intake (FI) or feed conversion ratio (FCR) traits were generally large and positive: rg averaged 0.57, 0.41 and 0.65, respectively. Phenotypic correlations (rp) between juvenile IGF-I and BF, FI or FCR were much lower (rp averaged 0.21, 0.09, and 0.15, respectively) as residual correlations between IGF-I and these performance traits were low, consistent with being measured at very different times. Correlations (genetic or phenotypic) between juvenile IGF-I and growth traits (e.g. lifetime daily gain or test daily gain) were relatively low, with average values within ± 0.09 of zero. Results from the trials reported here, and several physiological studies, indicate that information on juvenile IGF-I concentration can be used as an early physiological indicator of performance traits traditionally measured later in life. There is a clear role for juvenile IGF-I to facilitate pre-selection and more accurate selection of livestock for hard to measure traits, such as FCR, in pig breeding programs.

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