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GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene.

García-Gámez E, Gutiérrez-Gil B, Sahana G, Sánchez JP, Bayón Y, Arranz JJ - PLoS ONE (2012)

Bottom Line: The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3).These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP.The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association.

View Article: PubMed Central - PubMed

Affiliation: Departmento Producción Animal, Universidad de León, León, Spain.

ABSTRACT
In this study, we used the Illumina OvineSNP50 BeadChip to conduct a genome-wide association (GWA) analysis for milk production traits in dairy sheep by analyzing a commercial population of Spanish Churra sheep. The studied population consisted of a total of 1,681 Churra ewes belonging to 16 half-sib families with available records for milk yield (MY), milk protein and fat yields (PY and FY) and milk protein and fat contents (PP and FP). The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3). These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP. Further associations were detected at the chromosome-wise significance level on 14 other chromosomal regions. The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association. Sequencing this gene in the 16 Churra rams of the studied resource population identified additional polymorphisms. One out of the 31 polymorphisms identified was located within the coding gene sequence (LALBA_g.242T>C) and was predicted to cause an amino acid change in the protein (Val27Ala). Different approaches, including GWA analysis, a combined linkage and linkage disequilibrium study and a concordance test with the QTL segregating status of the sires, were utilized to assess the role of this mutation as a putative QTN for the genetic effects detected on OAR3. Our results strongly support the polymorphism LALBA_g.242T>C as the most likely causal mutation of the studied OAR3 QTL affecting PP and FP, although we cannot rule out the possibility that this SNP is in perfect linkage disequilibrium with the true causal polymorphism.

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Association analyses for milk protein and fat percentages (PP and FP) including the LALBA_g.242T>C genotypes.Genotypes used in the analysis included SNPs from the Illumina OvineSNP50 BeadChip and the single SNP detected in the exonic sequence of the LALBA gene (LALBA_g.242T>C). The significance thresholds are set at the 5% chromosome-wise level (dashed lines). A and B) Log(1/P-value) profiles for the analysis including the pedigree information as a random polygenic effect and each SNPs’ genotypes as a fixed effect in the mixed model for PP and FP, respectively. C and D) Results for the analysis where the genotypes of the LALBA_g.242T>C mutation were included as a fixed effect in the mixed model equation for PP and FP, respectively. E and F). Results of the analysis when the SNP OAR3_147028849 was included as a fixed effect in the mixed model equation for PP and FP, respectively.
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pone-0047782-g003: Association analyses for milk protein and fat percentages (PP and FP) including the LALBA_g.242T>C genotypes.Genotypes used in the analysis included SNPs from the Illumina OvineSNP50 BeadChip and the single SNP detected in the exonic sequence of the LALBA gene (LALBA_g.242T>C). The significance thresholds are set at the 5% chromosome-wise level (dashed lines). A and B) Log(1/P-value) profiles for the analysis including the pedigree information as a random polygenic effect and each SNPs’ genotypes as a fixed effect in the mixed model for PP and FP, respectively. C and D) Results for the analysis where the genotypes of the LALBA_g.242T>C mutation were included as a fixed effect in the mixed model equation for PP and FP, respectively. E and F). Results of the analysis when the SNP OAR3_147028849 was included as a fixed effect in the mixed model equation for PP and FP, respectively.

Mentions: The association analysis was repeated for OAR3 incorporating the genotyped SNP located in the LALBA exon, LALBA_g.242T>C, and the results for PP and FP are presented in Figure 3A. For both of the traits, the SNP LALBA_g.242T>C showed the most significant association (P-value for PP = 2.34×10−30; P-value for FP = 1.62×10−12). The allele substitution effect was higher for PP (0.46 SD) than for FP (0.30 SD). The second most significantly associated SNP for both PP and FP was also located in the intronic region of the LALBA gene that was identified as the top SNP in the initial GWA analysis, OAR3_147028849.


GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene.

García-Gámez E, Gutiérrez-Gil B, Sahana G, Sánchez JP, Bayón Y, Arranz JJ - PLoS ONE (2012)

Association analyses for milk protein and fat percentages (PP and FP) including the LALBA_g.242T>C genotypes.Genotypes used in the analysis included SNPs from the Illumina OvineSNP50 BeadChip and the single SNP detected in the exonic sequence of the LALBA gene (LALBA_g.242T>C). The significance thresholds are set at the 5% chromosome-wise level (dashed lines). A and B) Log(1/P-value) profiles for the analysis including the pedigree information as a random polygenic effect and each SNPs’ genotypes as a fixed effect in the mixed model for PP and FP, respectively. C and D) Results for the analysis where the genotypes of the LALBA_g.242T>C mutation were included as a fixed effect in the mixed model equation for PP and FP, respectively. E and F). Results of the analysis when the SNP OAR3_147028849 was included as a fixed effect in the mixed model equation for PP and FP, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475704&req=5

pone-0047782-g003: Association analyses for milk protein and fat percentages (PP and FP) including the LALBA_g.242T>C genotypes.Genotypes used in the analysis included SNPs from the Illumina OvineSNP50 BeadChip and the single SNP detected in the exonic sequence of the LALBA gene (LALBA_g.242T>C). The significance thresholds are set at the 5% chromosome-wise level (dashed lines). A and B) Log(1/P-value) profiles for the analysis including the pedigree information as a random polygenic effect and each SNPs’ genotypes as a fixed effect in the mixed model for PP and FP, respectively. C and D) Results for the analysis where the genotypes of the LALBA_g.242T>C mutation were included as a fixed effect in the mixed model equation for PP and FP, respectively. E and F). Results of the analysis when the SNP OAR3_147028849 was included as a fixed effect in the mixed model equation for PP and FP, respectively.
Mentions: The association analysis was repeated for OAR3 incorporating the genotyped SNP located in the LALBA exon, LALBA_g.242T>C, and the results for PP and FP are presented in Figure 3A. For both of the traits, the SNP LALBA_g.242T>C showed the most significant association (P-value for PP = 2.34×10−30; P-value for FP = 1.62×10−12). The allele substitution effect was higher for PP (0.46 SD) than for FP (0.30 SD). The second most significantly associated SNP for both PP and FP was also located in the intronic region of the LALBA gene that was identified as the top SNP in the initial GWA analysis, OAR3_147028849.

Bottom Line: The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3).These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP.The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association.

View Article: PubMed Central - PubMed

Affiliation: Departmento Producción Animal, Universidad de León, León, Spain.

ABSTRACT
In this study, we used the Illumina OvineSNP50 BeadChip to conduct a genome-wide association (GWA) analysis for milk production traits in dairy sheep by analyzing a commercial population of Spanish Churra sheep. The studied population consisted of a total of 1,681 Churra ewes belonging to 16 half-sib families with available records for milk yield (MY), milk protein and fat yields (PY and FY) and milk protein and fat contents (PP and FP). The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3). These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP. Further associations were detected at the chromosome-wise significance level on 14 other chromosomal regions. The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association. Sequencing this gene in the 16 Churra rams of the studied resource population identified additional polymorphisms. One out of the 31 polymorphisms identified was located within the coding gene sequence (LALBA_g.242T>C) and was predicted to cause an amino acid change in the protein (Val27Ala). Different approaches, including GWA analysis, a combined linkage and linkage disequilibrium study and a concordance test with the QTL segregating status of the sires, were utilized to assess the role of this mutation as a putative QTN for the genetic effects detected on OAR3. Our results strongly support the polymorphism LALBA_g.242T>C as the most likely causal mutation of the studied OAR3 QTL affecting PP and FP, although we cannot rule out the possibility that this SNP is in perfect linkage disequilibrium with the true causal polymorphism.

Show MeSH
Related in: MedlinePlus