GWA Analysis for Milk Production Traits in Dairy Sheep and Genetic Support for a QTN Influencing Milk Protein Percentage in the LALBA Gene

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.

Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

“…For example, there were no CCR near the LALBA (alpha-lactalbumin) gene (OAR3∶137 Mb), where a particular variant has been recently been proposed to explain a QTL for milk protein percentage identified in Churra sheep [39]. The lack of signal near this QTL in the F ST analysis of Churra vs Ojalada is consistent with the fact that the causative mutation is still segregating in Churra, which allowed its identification as QTL.…”

Major Histocompatibility Complex class IIB polymorphism in an ancient Spanish breed

“…These rams belonged to the Selection Nucleus of ANCHE and sired 1681 ewes from a commercial population previously analyzed in a genotyping project with the Illumina OvineSNP50 BeadChip (Garcia-Gamez et al 2012). As pedigree heads of this population, the 15 rams studied here were selected as an initial set of animals to assess the genetic variability of the MHC class II genomic region through sequencing analysis.…”

DNA-based identification of novel ovine milk protein gene variants

“…Compared to the complete cds of the sheep gene for alpha lactalbumin (GenBank AB052168) determined by Yamamoto (2000), three nucleotide variants are evident but not further described. Recently, García-Gámez et al (2012) re-identified one of those polymorphisms g.242T > C as the most likely causal mutation influencing milk protein percentage (GenBank NM 001009797.1). Comparing our results with this genomic reference variant (NM 001009797.1) three non-synonymous nucleotide exchanges were discovered.…”