Analysis of candidate genes for milk traits in goats

Resumen

This research has been developed in the framework of a coordinate project Genetic analysis of milk fat content and composition in dairy goats (AGL2007-66161-C02/GAN). We have characterized the polymorphisms of four physiological candidate genes for lipid metabolism traits i.e. stearoyl CoA-desaturase 1 (SCD1), malic enzyme 1 (ME1), hormone sensitive lipase (LIPE), and prolactin receptor (PRLR). Moreover, we have investigated their associations with milk traits in a Murciana-Granadina goat population. Sequencing of 4.7 kb of SCD1 cDNA has allowed us to identify two polymorphisms (c.732C>T, and c.*3504G>A) and an indel at the 3'UTR (c.*1902_1904delTGT). The 3'UTR polymorphisms (marked with an asterisk) were linked and showed suggestive associations (i.e. with uncorrected P-values below 0.05) with several traits such as lactose percentage, trans-10, cis-12 conjugated linoleic acid (CLA) and total CLA. Interestingly, in silico analysis predicted that the TGT deletion promotes a dramatic change in the secondary structure of the SCD1 mRNA, a feature that might affect its stability and half-life. Polymorphism of the goat ME1 gene consisted of 3 synonymous polymorphisms (c.483C>T, c.927C>T, and c.1200G>A) and a missense polymorphism (c.667G>A) involving an aspartate to asparagine substitution at position 223. Suggestive associations were observed between c.483C>T, c.667G>A, and c.1200G>A genotypes and C16:0, C18:1n-9t, and total CLA, respectively. Characterization of the goat LIPE gene revealed the existence of two synonymous SNP (c.327C>A>T and c.558C>T) and a missense c.1162G>T substitution (alanine to serine replacement at position 388). Suggestive associations with milk yield, C12:0, trans-10, cis-12 CLA and C18:3n6g were found. Finally, sequencing of the caprine PRLR gene evidenced the existence of two mRNA isoforms that differ in a 39 bp segment harbouring two premature stop codons. Four polymorphisms were identified (c.177C>T, c.1131A>G, c.1201A>G and c.1355C>T), and two of them produced amino acid substitutions (1201A>G, G401R; c.1355C>T, T452I). Suggestive associations with milk fatty acid traits were also found. As a whole, it is worth to highlight that none of the associations we have detected remained significant after correction for multiple testing. This feature suggests that the 14 polymorphisms we have identified probably do not have causal effects on milk composition (or if they do, the magnitude of these effects must be very small). An additional objective of our research was the identification of polymorphisms mapping to micro RNA (miRNA) target sites at the caprine casein genes. Resequencing the 3'UTR region of the casein genes in 14-25 goats from five breeds allowed us to identify a total of five polymorphisms: c.*175C>T at the CSN1S1 gene; c.*109T>C, c.*139G>C, and c.*160T>C at the CSN1S2 gene; and c.*216C>T at the CSN2 gene. In silico prediction with the Patrocles Finder tool suggested that these polymorphisms might map to putative miRNA sites, but experimental validation is needed to confirm this hypothesis. Performance of an association study between a c.175C>T substitution, disrupting a miR-101 site at CSN1S1, and milk CSN1S1 content did not yield a significant result.