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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

Result from the Genome-wide Association analysis based on the analysis of the Illumina OvineSNP50 BeadChip.For the five traits under study (milk yield, MY; protein percentage, PP; fat percentage, FP; protein yield, PY; and fat yield, FY) the log(1/P-value) are depicted here for all the 43,784 SNPs that passed the quality control.
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pone-0047782-g001: Result from the Genome-wide Association analysis based on the analysis of the Illumina OvineSNP50 BeadChip.For the five traits under study (milk yield, MY; protein percentage, PP; fat percentage, FP; protein yield, PY; and fat yield, FY) the log(1/P-value) are depicted here for all the 43,784 SNPs that passed the quality control.

Mentions: After the QC performed on the raw genotypes, a total of 43,784 SNPs distributed on the 26 ovine autosomes were included in the GWA analysis. Descriptive data for the SNP chip, including the number of SNPs per chromosome, the distance between them, the average MAF and heterozygosity and LD calculations, have been previously reported by [28]. Here, we present the significant associations identified through the GWA analysis for the five milk production traits included in the study (MY, PP, FP, PY and FY). A summary of the discovered experiment- and chromosome-wise significant associations is presented in Table 1. Figure 1 depicts Manhattan plots across the whole genome for the five analyzed traits, with SNP associations represented as log(1/P-value) on the y-axis.


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)

Result from the Genome-wide Association analysis based on the analysis of the Illumina OvineSNP50 BeadChip.For the five traits under study (milk yield, MY; protein percentage, PP; fat percentage, FP; protein yield, PY; and fat yield, FY) the log(1/P-value) are depicted here for all the 43,784 SNPs that passed the quality control.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047782-g001: Result from the Genome-wide Association analysis based on the analysis of the Illumina OvineSNP50 BeadChip.For the five traits under study (milk yield, MY; protein percentage, PP; fat percentage, FP; protein yield, PY; and fat yield, FY) the log(1/P-value) are depicted here for all the 43,784 SNPs that passed the quality control.
Mentions: After the QC performed on the raw genotypes, a total of 43,784 SNPs distributed on the 26 ovine autosomes were included in the GWA analysis. Descriptive data for the SNP chip, including the number of SNPs per chromosome, the distance between them, the average MAF and heterozygosity and LD calculations, have been previously reported by [28]. Here, we present the significant associations identified through the GWA analysis for the five milk production traits included in the study (MY, PP, FP, PY and FY). A summary of the discovered experiment- and chromosome-wise significant associations is presented in Table 1. Figure 1 depicts Manhattan plots across the whole genome for the five analyzed traits, with SNP associations represented as log(1/P-value) on the y-axis.

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