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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.


IBS similarity matrix.
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pone.0139207.g003: IBS similarity matrix.

Mentions: The power of genetic association analysis is often compromised by population stratification, which contributes to false positive results. To investigate the population structure, we constructed a principle component analysis (PCA) analysis and plotted the filtered SNP data with first two principle components (Fig 2). The contribution rate of the first two principle components (Principle component 1 and Principle component 2) were 2.78% and 2.31% respectively and the cumulative contribution rate of top ten principle components were 18.25% (S1 Fig). Our further analysis, based on the IBS status, also gave us a similar population structure (Fig 3). We adjusted our data to prevent false positive signals from stratification, even though the evidence for population stratification was not strong.


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)

IBS similarity matrix.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139207.g003: IBS similarity matrix.
Mentions: The power of genetic association analysis is often compromised by population stratification, which contributes to false positive results. To investigate the population structure, we constructed a principle component analysis (PCA) analysis and plotted the filtered SNP data with first two principle components (Fig 2). The contribution rate of the first two principle components (Principle component 1 and Principle component 2) were 2.78% and 2.31% respectively and the cumulative contribution rate of top ten principle components were 18.25% (S1 Fig). Our further analysis, based on the IBS status, also gave us a similar population structure (Fig 3). We adjusted our data to prevent false positive signals from stratification, even though the evidence for population stratification was not strong.

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.