The Role of the Bovine Growth Hormone Receptor and ... - Genetics

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2160 S. Viitala et al.Figure 4.—Ninety-five percent normalC.I. for SNP genotype effects oncontent traits estimated from the imputedfamily data. The SNPs are presentedby numbers on the x-axis intheir presumed order in the genome.For each SNP the estimates are givenfor genotypes ‘‘11’’ (d) and ‘‘12’’ (n)in relation to genotype ‘‘22,’’ whose effectis set to 0. The GHR snp1 (F279Y)genotypes 11 and 22 stand for FFand YY. Respectively, the PRLR snp5(S18N ) genotype 11 stands for NNand 22 for SS. On the y-axis the effectsare indicated in percentages (of proteinand fat in milk).model. Note that the set of selected SNPs also dependson the model selection statistics considered, so that theLRT ‘‘chooses’’ different models than the BIC.Table 8 summarizes best models, i.e., the most parsimoniousmodels with sufficiently good fit, while resultsof all the comparisons are available upon request. Generally,both of the applied model selection criteriaselect different models, with l preferring models withmore parameters than BIC. Considering l it can be seenthat for most of the trait 3 lactation combinations, thevariation in a single SNP genotype is not sufficientto explain the nonpolygenic part of the observed traitvariation. The effect of interaction between GHR andPRLR is significant for most of the models. With rankingbased on the BIC it is noteworthy that the PRLR SNPsare especially important in describing variation of yieldtraits, so that snp5 is sufficient for PY 1st , while for FY 1stmodels fitting only snp5 and snp6 are ranked, respectively,as the third- and the second-best models. Consideringcontent traits, it is the snp1 model that showspredominant impact, since snp1 is sufficient for P% 1st ,P% later , and F% 1st and for F% later the model is ranked atsecond place.Effect of the GHR and PRLR polymorphisms in anindependent sample—a confirmation: The effects ofthe GHR F279Y and PRLR S18N on milk yield andcomposition were estimated in an independent sample(data set II) of the general dairy cattle population. Themodel comparison of the importance of GHR F279Yand PRLR S18N on different traits provides the sameconclusions as were obtained for the family data. Theeffect of PRLR S18N (snp5) predominates on yield traitsand GHR F279Y on content traits. The best modelsselected by l and BIC are presented in Table 9. The resultsof all the comparisons are available upon request.For most yield traits (MY 1st ,PY 1st ,MY later ,PY later , andFY later ) the best model is the interaction model, whilefor FY 1st both SNPs are important but interaction is notneeded. The BIC criterion prefers snp5 to snp1 in allyield traits. This was seen especially on PY, where thelikelihood for the model with only snp1 is much lowercompared to the model with only snp5 (Figure 5). Thebest model for P% 1st requires only snp1. For P% later bothSNPs are needed; however, the likelihood for the modelwith only snp5 is quite low. The BIC criterion stronglyprefers snp1 to snp5. The best model for F% 1st andF% later is the interaction model but as in P% the snp1effect is very important.DISCUSSIONWe herein report significant association of GHRand PRLR polymorphism for milk production traits inFinnish Ayrshire dairy cattle. The result is partly in goodagreement with the recently reported association of achromosomal region including GHR F279Y substitutionwith milk production traits in Holstein–Friesian cattle(Blott et al. 2003). In the Finnish Ayrshire population,GHR F279Y is associated with milk yield, proteinpercentage, and fat percentage. Moreover, the PRLRsubstitution S18N is clearly associated with milk yield,protein yield, and fat yield whereas no evidence for theassociation of PRLR variation and milk production was
GHR and PRLR Genes in Milk Production 2161TABLE 8Effects in data set I contained by vector b in the best modelas selected by l and BICTrait Criterion First lactationMilk yield l m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s5 11s5 12 s5 22 s6 11 s6 12 s6 22 s13s6Milk yield BIC m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s4 11s4 12 s4 22 s5 11 s5 12 s5 22 s6 11s6 12 s6 22Protein yield l m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s4 11s4 12 s4 22 s5 11 s5 12 s5 22 s6 11 s6 12s6 22 s13s6Protein yield BIC m s5 11 s5 12 s5 22Fat yield l, BIC m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s5 11s5 12 s5 22 s6 11 s6 12 s6 22Protein content l m s1 11 s1 12 s1 22 s4 11 s4 12 s4 22 s5 11s5 12 s5 22 s13s5Protein content BIC m s1 11 s1 12 s1 22Fat content l, BIC m s1 11 s1 12 s1 22Trait Criterion Later lactationsMilk yield l m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s5 11s5 12 s5 22 s6 11 s6 12 s6 22 s13s6Milk yield BIC m s5 11 s5 12 s5 22Protein yield l m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s5 11s5 12 s5 22 s6 11 s6 12 s6 22 s13s5Protein yield BIC m s5 11 s5 12 s5 22Fat yield l m s1 11 s1 12 s1 22 s4 11 s4 12 s4 22 s5 11s5 12 s5 22 s6 11 s6 12 s6 22 s13s5Fat yield BIC m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s4 11s4 12 s4 22 s5 11 s5 12 s5 22 s6 11s6 12 s6 22Protein content l m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s5 11s5 12 s5 22 s13s5Protein content BIC m s1 11 s1 12 s1 22Fat content l, BIC m s1 11 s1 12 s1 22 s2 11 s2 12 s2 22 s4 11s4 12 s4 22sX ij represents effects of the ijth genotype of the Xth SNP,s1 3 s5 and s1 3 s6 represent effects of interaction betweensnp1 and, respectively, snp5 and snp6.found in Holstein–Friesian cattle (Blott et al. 2003). Itis possible that the latter association exists in FinnishAyrshire but not in Holstein–Friesians. The discrepancyof the results might, however, originate either from adifferent type of analysis or from the map position ofPRLR used. In our study two PRLR SNPs causing theamino acid substitutions S18N and L186P were used inassociation analysis, whereas in Blott et al. (2003) aPRLR haplotype built from the PRLR S18N and fewintronic SNPs was used in combined linkage and LDanalysis. In addition, we provide here a new map positionfor PRLR differing from the one used in Blottet al. (2003).In Finnish Ayrshire four amino acid substitutionswere detected in GHR. F279Y stood out as the mostpromising candidate for the effect because accordingto the multiple sequence alignments the phenylalanineTABLE 9Effects in data set II contained by vector b in the best modelas selected by l and BICTrait Criterion First lactationMilk yield l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22 s1 3 s5Protein yield l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22 s1 3 s5Fat yield l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22Protein content l, BIC m s1 11 s1 12 s1 22Fat content l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22 s1 3 s5Trait Criterion Later lactationsMilk yield l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22 s1 3 s5Protein yield l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22 s1 3 s5Fat yield l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22 s1 3 s5Protein content l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s5 22Fat content l, BIC m s1 11 s1 12 s1 22 s5 11 s5 12 s1 3 s5sX ij represents effects of the ijth genotype of the Xth SNP,s1 3 s5 represents effect of interaction between snp1 andsnp5.(F ) residue is highly conserved among mammals. Moreover,3 of 4 sires that are segregating for the QTL areheterozygous for the F279Y substitution. The remaining18 sires are homozygous for the F-allele. The amino acidpositions of other substitutions (N528T, A541S, andS555G) were less conserved among studied species;however, the serine residue at position 541 and theglycine residue at position 555 have been observedonly in B. taurus. In the Finnish Ayrshire population, theGHR amino acid substitutions exist as six differenthaplotypes (F-N-S-S, F-N-A-S, F-T-A-G, F-T-A-S, Y-N-A-S,andY-T-A-G), two of which account for 71% of the chromosomes(F-N-A-S and F-T-A-S).In PRLR two contiguous SNPs generate an amino acidsubstitution S18N in the signal peptide of the proteinand a single SNP in the extracellular domain leads to anamino acid substitution L186P. According to sequencealignment PRLR S18N was not as promising as the GHRF279Y because both serine and asparagine residues arecommonly seen at that position in different species. Thesecond substitution L186P on the other hand seemedpromising because at the position of substitution glycineresidue is highly conserved among studied vertebratesexcept artiodactyls. However, 15 of 21 sires wereheterozygous for the L186P substitution.As a first step, conventional multimarker regressionanalysis with one- and two-QTL models was performed(Viitala et al. 2003). For that purpose a new densermarker map with additional microsatellites, GHR haplotype,and PRLR S18N was built. The GHR haplotypewe use in this study is not exactly the same as in Blottet al. (2003) because we have used only the SNPs causingamino acid substitutions in Finnish Ayrshire. The resultconfirms that, like in Holstein–Friesians, in FinnishAyrshire, there is a QTL with strong effect on protein
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