Implementation of Bayesian methods to identify SNP and haplotype regions with transmission ratio distortion across the whole genome: TRDscan v.1.0

Realized deviations from the expected Mendelian inheritance of alleles from heterozygous parents have been previously reported in a broad range of organisms (i.e., transmission ratio distortion; TRD). Various biological mechanisms affecting gametes, embryos, fetuses, or even postnatal offspring can produce patterns of TRD. However, knowledge about its prevalence and potential causes in livestock species is still scarce. Specific Bayesian models have been recently developed for the analyses of TRD for biallelic loci, which accommodated a wide range of population structures, enabling TRD investigation in livestock populations. The parameterization of these models is flexible and allows the study of overall (parent-unspecific) TRD and sire- and dam-specific TRD. This research aimed at deriving Bayesian models for fitting TRD on the basis of haplotypes, testing the models for both haplotype- and SNP-based methods in simulated data and actual Holstein genotypes, and developing a specific software for TRD analyses. Results obtained on simulated data sets showed that the statistical power of the analysis increased with sample size of trios (n), proportion of heterozygous parents, and the magnitude of the TRD. On the other hand, the statistical power to detect TRD decreased with the number of alleles at each loci. Bayesian analyses showed a strong Pearson correlation coefficient (≥0.97) between simulated and estimated TRD that reached the significance level of Bayes factor ≥10 for both single-marker and haplotype analyses when n ≥ 25. Moreover, the accuracy in terms of the mean absolute error decreased with the increase of the sample size and increased with the number of alleles at each loci. Using real data (55,732 genotypes of Holstein trios), SNP- and haplotype-based distortions were detected with overall TRD, sire-TRD, or dam-TRD, showing different magnitudes of TRD and statistical relevance. Additionally, the haplotype-based method showed more ability to capture TRD compared with individual SNP. To discard possible random TRD in real data, an approximate empirical null distribution of TRD was developed. The program TRDscan v.1.0 was written in Fortran 2008 language and provides a powerful statistical tool to scan for TRD regions across the whole genome. This developed program is freely available at http://www.casellas.info/files/TRDscan.zip.     

Genetic and nongenetic factors contributing to differences in αS-casein phosphorylation isoforms and other major milk proteins

Relative concentrations of α_S-casein (α_S-CN) phosphorylation isoforms vary considerably among milk of individual cows. We aimed to explore to what extent genetic and other factors contribute to the variation in relative concentrations of α_S-CN phosphorylation isoforms and the phosphorylation degree of α_S-CN defined as the proportion of isoforms with higher degrees of phosphorylation. We also investigated the associations of genetic variants of milk proteins and casein haplotypes with relative concentrations of α_S-CN phosphorylation isoforms and with the phosphorylation degree of α_S-CN in French Montbéliarde cattle from the cheese production area of Franche-Comté. Detailed milk protein composition was determined by liquid chromatography coupled with electrospray ionization mass spectrometry from 531 test-day morning milk samples. Parity, lactation stage, and genetic variation of cows contributed to the phenotypic variation in relative concentrations of individual α_S-CN phosphorylation isoforms and in the phosphorylation degree of α_S-CN. As lactation progressed, we observed a significant increase for relative concentrations of α_S-CN isoforms with higher degrees of phosphorylation (α_S1-CN-9P, α_S2-CN-13P, and α_S2-CN-14P) as well as for the phosphorylation degree of both α_S1-CN and α_S2-CN. Furthermore, the β-CN I variant was associated with a greater proportion of isoforms with lower degrees of phosphorylation (α_S1-CN-8P, α_S2-CN-10P, and α_S2-CN-11P); the β-CN B variant was associated with a greater proportion of isoforms with higher degrees of phosphorylation (α_S1-CN-9P, α_S2-CN-12P to α_S2-CN-14P). The heritability estimates were low to moderate for relative concentrations of α_S2-CN phosphorylation isoforms (0.07 to 0.32), high for relative concentrations of α_S1-CN-8P (0.84) and α_S1-CN-9P (0.56), and moderate for phosphorylation degrees of α_S1-CN (0.37) and α_S2-CN (0.23). Future studies investigating relations between the phosphorylation degree of α_S-CN and technological properties of milk will be beneficial for the dairy industry.     

Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects

A posteriori and modified granddaughter designs were applied to determine haplotype effects for Holstein bulls and cows with BovineSNP50 [~50,000 single nucleotide polymorphisms (SNP); Illumina Inc., San Diego, CA] genotypes. The a posteriori granddaughter design was applied to 52 sire families, each with ≥100 genotyped sons with genetic evaluations based on progeny tests. For 33 traits (milk, fat, and protein yields; fat and protein percentages; somatic cell score; productive life; daughter pregnancy rate; heifer and cow conception rates; service-sire and daughter calving ease; service-sire and daughter stillbirth; 18 conformation traits; and net merit), the analysis was applied to the autosomal segment with the SNP with the greatest effect in the genomic evaluation of each trait. All traits except 2 had a within-family haplotype effect. The same design was applied with the genetic evaluations of sons corrected for SNP effects associated with chromosomes besides the one under analysis. The number of within-family contrasts was 166 without adjustment and 211 with adjustment. Of the 52 bulls analyzed, 36 had BovineHD (high density; Illumina Inc.) genotypes that were used to test for concordance between sire quantitative trait loci and SNP genotypes; complete concordance was not obtained for any effects. Of the 31 traits with effects from the a posteriori granddaughter design, 21 were analyzed with the modified granddaughter design. Only sires with a contrast for the a posteriori granddaughter design and ≥200 granddaughters with a record usable for genetic evaluation were included. Calving traits could not be analyzed because individual cow evaluations were not computed. Eight traits had within-family haplotype effects. With respect to milk and fat yields and fat percentage, the results on Bos taurus autosome (BTA) 14 corresponded to the hypothesis that a missense mutation in the diacylglycerol O-acyltransferase 1 (DGAT1) gene is the main causative mutation, although other polymorphisms in that gene also modify fat yield and percentage. The positive allele for protein concentration was less frequent, which indicated that selection on that locus could be effective. Although the results can be used to determine causative polymorphisms for most of the analyzed traits, complete DNA sequencing of most of the analyzed sires probably will be required.     

Effects of milk protein variants on the protein composition of bovine milk

The effects of β-lactoglobulin (β-LG), β-casein (β-CN), and κ-CN variants and β-κ-CN haplotypes on the relative concentrations of the major milk proteins α-lactalbumin (α-LA), β-LG, α_S1-CN, α_S2-CN, β-CN, and κ-CN and milk production traits were estimated in the milk of 1,912 Dutch Holstein-Friesian cows. We show that in the Dutch Holstein-Friesian population, the allele frequencies have changed in the past 16 years. In addition, genetic variants and casein haplotypes have a major impact on the protein composition of milk and explain a considerable part of the genetic variation in milk protein composition. The β-LG genotype was associated with the relative concentrations of β-LG (A » B) and of α-LA, α_S1-CN, α_S2-CN, β-CN, and κ-CN (B > A) but not with any milk production trait. The β-CN genotype was associated with the relative concentrations of β-CN and α_S2-CN (A² > A¹) and of α_S1-CN and κ-CN (A¹ > A²) and with protein yield (A² > A¹). The κ-CN genotype was associated with the relative concentrations of κ-CN (B > E > A), α_S2-CN (B > A), α-LA, and α_S1-CN (A > B) and with protein percentage (B > A). Comparing the effects of casein haplotypes with the effects of single casein variants can provide better insight into what really underlies the effect of a variant on protein composition. We conclude that selection for both the β-LG genotype B and the β-κ-CN haplotype A²B will result in cows that produce milk that is more suitable for cheese production.     

Short communication: Polymorphism of casein cluster genes in Czech local goat breeds

The 4 casein loci were evaluated as haplotypes in 2 dairy goat breeds kept in the Czech Republic. Analysis of 41 White Shorthaired (WSH) trio families and 44 Brown Shorthaired (BSH) trio families revealed 14 and 20 haplotypes, respectively. Various genomic techniques were used to type the casein loci. Twenty-two different combinations of these alleles (casein haplotypes, in the order CSN1S1-CSN2-CSN1S2-CSN3) were found. Only 5 haplotypes in the WSH breed and 6 haplotypes in the BSH breed occurred at frequencies >0.05. For the WSH breed, the most common haplotype was FCFB (0.260), whereas for the BSH breed, the most common haplotype was FCFA (0.217). The information on the haplotype variability in both breeds could be used in breeding programs aimed at preserving biodiversity or selecting animals for specific protein production and cheesemaking.     

Correlation of Mitochondrial Haplotypes with Cuticular Hydrocarbon Phenotypes of Sympatric Reticulitermes Species from the Southeastern United States

Three sympatric Reticulitermes species have been identified in Georgia, USA, based on morphological characters from alates and soldiers: R. flavipes, R. virginicus, and R. hageni, but species identification at individual collection sites is often difficult because alate production is seasonal and soldiers comprise 1–3% of the colony. We therefore set up an experiment to determine if chemical phenotypes and mtDNA haplotypes can be used together to separate species of subterranean termites. Subterranean termites of the order Reticulitermes (Isoptera: Rhinotermitidae) were collected from 20 inspection ports across four soil provinces in Georgia. Each collection was identified to species using dichotomous keys. Two collections, HH11 and BH25, however, could not be unequivocally keyed to species and were classified as unknown. The mitochondrial cytochrome oxidase II (COII) gene was sequenced from individual members of each collection and the variation in cuticular hydrocarbon phenotypes from these same collections was characterized. The cuticular hydrocarbon and mtDNA phylogenetic analyses show agreement with both unknown collections falling out in a separate clade. Specimens from HH11 nad BH25 are different morphologically, chemically, and genetically from the three known sympatric species in Georgia. Our results suggest that these two collections may represent at least one new taxon in Reticulitermes. Furthermore, the association of cuticular hydrocarbon phenotypes and mtDNA haplotypes demonstrates that, when combined with morphological characters, they are useful in separating known species, determining new species, and understanding termite evolution.     

Marker-assisted breeding value estimation for mastitis resistance in Finnish Ayrshire cattle

Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20% or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.     

Harmful recessive effects on fertility detected by absence of homozygous haplotypes

Five new recessive defects were discovered in Holsteins, Jerseys, and Brown Swiss by examining haplotypes that had a high population frequency but were never homozygous. The method required genotypes only from apparently normal individuals and not from affected embryos. Genotypes from the BovineSNP50 BeadChip (Illumina, San Diego, CA) were examined for 58,453 Holsteins, 5,288 Jerseys, and 1,991 Brown Swiss with genotypes in the North American database. Haplotypes with a length of ≤75 markers were obtained. Eleven candidate haplotypes were identified, with the earliest carrier born before 1980; 7 to 90 homozygous haplotypes were expected, but none were observed in the genomic data. Expected numbers were calculated using either the actual mating pattern or assuming random mating. Probability of observing no homozygotes ranged from 0.0002 for 7 to 10⁻⁴⁵ for 90 expected homozygotes. Phenotypic effects were confirmed for 5 of the 11 candidate haplotypes using 14,911,387 Holstein, 830,391 Jersey, and 68,443 Brown Swiss records for conception rate. Estimated effect for interaction of carrier service sire with carrier maternal grandsire ranged from −3.0 to −3.7 percentage points, which was slightly smaller than the −3.9 to −4.6 percentage points expected for lethal recessives but slightly larger than estimated effects for previously known lethal alleles of −2.5 percentage points for brachyspina and −2.9 percentage points for complex vertebral malformation. Conception rate was coded as a success only if the gestation went to term or the cow was confirmed to be pregnant. Estimated effect of carrier interaction for stillbirth rate based on 10,876,597 Holstein and 25,456 Jersey records was small. Thus, lethal effects may include conception, gestation, and stillbirth losses. Carrier frequency has been >20% for many years for the confirmed defect in Jerseys and is currently 16% for the defect in Brown Swiss. The 3 defects discovered in Holsteins have carrier frequencies of 2.7 to 6.4% in the current population. For previously known defects, map locations and lack of homozygotes were consistent with the literature and lethal recessive inheritance, but numbers of expected homozygotes for some were small because of low frequency. Very large genotypic and phenotypic data sets allow efficient detection of smaller and less frequent effects. Haplotype tests can help breeders avoid carrier matings for such defects and reduce future frequencies.