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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.


Distribution of the number of SNPs in each haplotype block along the genome.*denotes mean number of SNPs.
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pone.0139207.g005: Distribution of the number of SNPs in each haplotype block along the genome.*denotes mean number of SNPs.

Mentions: In total, 4,975 haplotype blocks were obtained in our study. The number of SNPs ranged from 2 to 14. The average haplotype block length was 117.1559 Kb and the longest was 199.999 Kb (Fig 4). The distribution of haplotype length and the number of the SNPs are shown in Figs 4 and 5. However, the haplotype blocks were not distributed evenly on all chromosomes. In our study of D100, we found 25 suggestive SNPs located in SSC8 from 67.4 to 144.2 Mb and 2 strong haplotype blocks were detected (129.4–129.6 Mb and 141.7–142.2 Mb) (Fig 6A). Five genes, DDIT4L, H2AFZ, PTPN13, MAPK10, and ARHGAP24, were located in the two blocks (S1 Table). In our study of FCR, 26 suggestive SNPs located in SSC15 ranging from 123.7 to 129.4 Mb were detected and they constituted strong haplotype blocks (125.9–126.3 Mb, 127.7–128.1 Mb, 128.3–128.8 Mb and 128.9–129.4 Mb) (Fig 6B). Genes including ERBB4, IKZF2, SPAG16, VWC2L, ENSSSCG00000029683, and ENSSSCG00000029020 were identified in this region (S1 Table). We also observed 11 suggestive FCR SNPs located in SSC16 from 34.9 to 38.9 Mb, of which 10 SNPs were located at 35 Mb. A particularly strong haplotype block from 34.85 to 35.31 Mb was identified in our data (Fig 6C). Further analysis found that the ARL15, NDUFS4, and ENSSSCG00000024947 genes were located in this haplotype block (S1 Table). As for ADG, however, relatively few suggestive SNPs generated less haplotype blocks. It is important to mention that a haplotype block located in SSC10 from 59.0 to 59.2 Mb contained the genes MLLT10 and SKIDA1 (Fig 6D) (S1 Table).


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)

Distribution of the number of SNPs in each haplotype block along the genome.*denotes mean number of SNPs.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139207.g005: Distribution of the number of SNPs in each haplotype block along the genome.*denotes mean number of SNPs.
Mentions: In total, 4,975 haplotype blocks were obtained in our study. The number of SNPs ranged from 2 to 14. The average haplotype block length was 117.1559 Kb and the longest was 199.999 Kb (Fig 4). The distribution of haplotype length and the number of the SNPs are shown in Figs 4 and 5. However, the haplotype blocks were not distributed evenly on all chromosomes. In our study of D100, we found 25 suggestive SNPs located in SSC8 from 67.4 to 144.2 Mb and 2 strong haplotype blocks were detected (129.4–129.6 Mb and 141.7–142.2 Mb) (Fig 6A). Five genes, DDIT4L, H2AFZ, PTPN13, MAPK10, and ARHGAP24, were located in the two blocks (S1 Table). In our study of FCR, 26 suggestive SNPs located in SSC15 ranging from 123.7 to 129.4 Mb were detected and they constituted strong haplotype blocks (125.9–126.3 Mb, 127.7–128.1 Mb, 128.3–128.8 Mb and 128.9–129.4 Mb) (Fig 6B). Genes including ERBB4, IKZF2, SPAG16, VWC2L, ENSSSCG00000029683, and ENSSSCG00000029020 were identified in this region (S1 Table). We also observed 11 suggestive FCR SNPs located in SSC16 from 34.9 to 38.9 Mb, of which 10 SNPs were located at 35 Mb. A particularly strong haplotype block from 34.85 to 35.31 Mb was identified in our data (Fig 6C). Further analysis found that the ARL15, NDUFS4, and ENSSSCG00000024947 genes were located in this haplotype block (S1 Table). As for ADG, however, relatively few suggestive SNPs generated less haplotype blocks. It is important to mention that a haplotype block located in SSC10 from 59.0 to 59.2 Mb contained the genes MLLT10 and SKIDA1 (Fig 6D) (S1 Table).

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.