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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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Related in: MedlinePlus

Statistical profiles obtained from the LDLA analyses in OAR3 for milk protein and fat percentages.Together with the LRT profiles obtained across the whole chromosome for protein percentage (PP) (A) and fat percentage (FP) (B), the detailed view of the profile around the LALBA gene region (from 1.3 to 1.4 Mb) is also provided for both traits, PP (C) and FP (D).
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pone-0047782-g002: Statistical profiles obtained from the LDLA analyses in OAR3 for milk protein and fat percentages.Together with the LRT profiles obtained across the whole chromosome for protein percentage (PP) (A) and fat percentage (FP) (B), the detailed view of the profile around the LALBA gene region (from 1.3 to 1.4 Mb) is also provided for both traits, PP (C) and FP (D).

Mentions: The results from the LDLA performed in OAR3 for PP and FP are shown in Figure 2. For PP, the most significant result was obtained at 137.3 Mb (LRT = 140.2). According to the significance thresholds set through simulation (LRT = 78.5 for a chromosome-wise P-value of 0.0001), the analysis revealed a highly significant QTL located in the middle of a haplotype of 4 SNPs that includes the LALBA gene. The order and names of the markers included in this haplotype were LALBA_g.242T>C, OAR3_147028849, OAR3_147128672 and OAR3_147275963. Using the LOD drop-off method, the CI covered a 4 Kb-long region from 137.2 Mb to 137.6 Mb in OAR3.


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)

Statistical profiles obtained from the LDLA analyses in OAR3 for milk protein and fat percentages.Together with the LRT profiles obtained across the whole chromosome for protein percentage (PP) (A) and fat percentage (FP) (B), the detailed view of the profile around the LALBA gene region (from 1.3 to 1.4 Mb) is also provided for both traits, PP (C) and FP (D).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047782-g002: Statistical profiles obtained from the LDLA analyses in OAR3 for milk protein and fat percentages.Together with the LRT profiles obtained across the whole chromosome for protein percentage (PP) (A) and fat percentage (FP) (B), the detailed view of the profile around the LALBA gene region (from 1.3 to 1.4 Mb) is also provided for both traits, PP (C) and FP (D).
Mentions: The results from the LDLA performed in OAR3 for PP and FP are shown in Figure 2. For PP, the most significant result was obtained at 137.3 Mb (LRT = 140.2). According to the significance thresholds set through simulation (LRT = 78.5 for a chromosome-wise P-value of 0.0001), the analysis revealed a highly significant QTL located in the middle of a haplotype of 4 SNPs that includes the LALBA gene. The order and names of the markers included in this haplotype were LALBA_g.242T>C, OAR3_147028849, OAR3_147128672 and OAR3_147275963. Using the LOD drop-off method, the CI covered a 4 Kb-long region from 137.2 Mb to 137.6 Mb in OAR3.

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