Limits...
Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population.

Wang K, Liu D, Hernandez-Sanchez J, Chen J, Liu C, Wu Z, Fang M, Li N - PLoS ONE (2015)

Bottom Line: The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1).Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb.Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.

ABSTRACT
In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1). Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

No MeSH data available.


Manhattan plots of genome-wide association studies for three production traits in male Duroc pigs.The inserted quantile–quantile (Q–Q) plots show the observed versus expected log p-values.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4587933&req=5

pone.0139207.g001: Manhattan plots of genome-wide association studies for three production traits in male Duroc pigs.The inserted quantile–quantile (Q–Q) plots show the observed versus expected log p-values.

Mentions: The p-value of (in terms of–log10 p) profiles of all SNPs association tested for the three traits examined are shown in Fig 1. The genome-wide significant SNPs at the permutation based critical level detected by the associated test for the three traits are shown in Table 3. In total, 11 genome-wide significant (significant) and 162 chromosome-wide significant (suggestive) SNPs were defined. The proportion of phenotypic variance explained by each significant SNP is shown in Table 3.


Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population.

Wang K, Liu D, Hernandez-Sanchez J, Chen J, Liu C, Wu Z, Fang M, Li N - PLoS ONE (2015)

Manhattan plots of genome-wide association studies for three production traits in male Duroc pigs.The inserted quantile–quantile (Q–Q) plots show the observed versus expected log p-values.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4587933&req=5

pone.0139207.g001: Manhattan plots of genome-wide association studies for three production traits in male Duroc pigs.The inserted quantile–quantile (Q–Q) plots show the observed versus expected log p-values.
Mentions: The p-value of (in terms of–log10 p) profiles of all SNPs association tested for the three traits examined are shown in Fig 1. The genome-wide significant SNPs at the permutation based critical level detected by the associated test for the three traits are shown in Table 3. In total, 11 genome-wide significant (significant) and 162 chromosome-wide significant (suggestive) SNPs were defined. The proportion of phenotypic variance explained by each significant SNP is shown in Table 3.

Bottom Line: The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1).Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb.Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.

ABSTRACT
In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1). Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

No MeSH data available.