Sire Families Research Articles

Genome-wide association studies for osteochondrosis in French Trotter horses1

A genome-wide association study for osteochondrosis (OC) in French Trotter horses was carried out to detect QTL using genotype data from the Illumina EquineSNP50 BeadChip assay. Analysis data came from 161 sire families of French Trotter horses with 525 progeny and family sizes ranging from 1 to 20. Genotypes were available for progeny (n = 525) and sires with at least 2 progeny (n = 98). Radiographic data were obtained from progeny using at least 10 views to reveal OC. All radiographic findings were described by at least 2 veterinary experts in equine orthopedics, and severity indices (scores) were assigned based on the size and location of the lesion. Traits used were a global score, the sum of all severity scores lesions (GM, quantitative measurement), and the presence or absence of OC on the fetlock (FM), hock (HM), and other sites (other). Data were analyzed using 2 mixed models including fixed effects, polygenic effects, and SNP or haplotype cluster effects. By combining results with both methods at moderate evidence of association threshold P < 5 × 10(-5), this genome-wide association study displayed 1 region for GM on the Equus caballus chromosome (ECA) 13, 2 for HM on ECA 3 and 14, and 1 for other on ECA 15. One region on ECA 3 for HM represented the most significant hit (P = 3 × 10(-6)). By comparing QTL between traits at a decreased threshold (P < 5 × 10(-4)), the 4 QTL detected for GM were associated to a QTL detected for FM or HM but never both. Another interesting result was that no QTL were found in common between HM and FM.

A genome scan for quantitative trait loci affecting body conformation traits in Spanish Churra dairy sheep

A genome scan for chromosomal regions influencing body conformation traits was conducted for a population of Spanish Churra dairy sheep following a daughter design. A total of 739 ewes from 11 half-sib sire families were included in the study. The ewes were scored for the 5 linear traits used in the breeding scheme of the Churra breed to assess body conformation: stature, rear legs-rear view, foot angle, rump width, and general appearance. All the animals, including the 11 sires, were genotyped for 181 microsatellite markers evenly distributed across the 26 sheep autosomes. Using the yield deviations of the raw scores adjusted for fixed factors as phenotypic measurements, a quantitative trait loci (QTL) analysis was performed on the basis of a multi-marker regression method. Seven suggestive QTL were identified on chromosomes Ovis aries (OAR)2, OAR5, OAR16, OAR23, and OAR26, but none reached a genome-wise significance level. Putative QTL were identified for all of the traits analyzed, except for general appearance score. The suggestive QTL showing the highest test statistic influenced rear legs-rear view and was localized on OAR16, close to the growth hormone receptor coding gene, GHR. Some of the putative linkage associations reported here are consistent with previously reported QTL in cattle for similar traits. To the best of our knowledge, this study provides the first report of QTL for body conformation traits in dairy sheep; further studies will be needed to confirm and redefine the linkage associations reported herein. It is expected that future genome-wide association analyses of larger families will help identify genes underlying these putative genetic effects and provide useful markers for marker-assisted selection of such functional traits.

Associations of marker panel scores with feed intake and efficiency traits in beef cattle using preselected single nucleotide polymorphisms1

Because of the moderate heritability and the expense associated with collecting feed intake data, effective selection for residual feed intake would be enhanced if marker-assisted evaluation were used for accurate estimation of genetic merit. In this study, a suite of genetic markers predictive of residual feed intake, DMI, and ADG were preselected using single-marker regression analysis, and the top 100 SNP were analyzed further to provide prediction equations for the traits. The data used consisted of 728 spring-born beef steers, offspring of a cross between a composite dam line and Angus, Charolais, or University of Alberta hybrid bulls. Feed intake data were collected over a 5-yr period, with 2 groups (fall-winter and winter-spring) tested every year. Training and validation data sets were obtained by splitting the data into 2 distinct sets, by randomly splitting the data into training and testing sets based on sire family (split 1) in 5 replicates or by retaining all animals with no known pedigree relationships as the validation set (split 2). A total of 37,959 SNP were analyzed by single-marker regression, of which only the top 100 that corresponded to a P-value <0.002 were retained. The 100 SNP were then analyzed using random regression BLUP, and only SNP that were jointly significant (P < 0.05) were included in the final marker panels. The marker effects from the selected panels were used to derive the molecular breeding values, which were calculated as a weighted sum of the number of copies of the more frequent allele at each SNP locus, with the weights being the allele substitution effects. The correlation between molecular breeding value and phenotype represented the accuracy of prediction. For all traits evaluated, accuracy across breeds was low, ranging between 0.007 and 0.414. Accuracy was least in data split 2, where the validation individuals had no pedigree relationship with animals in the training data. Given the low predictive ability observed, a large number of individuals may be needed for prediction when using such an admixed population. Further, these results suggest that breed composition of the target population in which the marker panels are likely to be used should be an important consideration when developing prediction equations across breeds, especially where an admixed population is used as the training data set.

Accuracy of genomic breeding values for residual feed intake in crossbred beef cattle1

The benefit of using genomic breeding values (GEBV) in predicting ADG, DMI, and residual feed intake for an admixed population was investigated. Phenotypic data consisting of individual daily feed intake measurements for 721 beef cattle steers tested over 5 yr was available for analysis. The animals used were an admixed population of spring-born steers, progeny of a cross between 3 sire breeds and a composite dam line. Training and validation data sets were defined by randomly splitting the data into training and testing data sets based on sire family so that there was no overlap of sires in the 2 sets. The random split was replicated to obtain 5 separate data sets. Two methods (BayesB and random regression BLUP) were used to estimate marker effects and to define marker panels and ultimately the GEBV. The accuracy of prediction (the correlation between the phenotypes and GEBV) was compared between SNP panels. Accuracy for all traits was low, ranging from 0.223 to 0.479 for marker panels with 200 SNP, and 0.114 to 0.246 for marker panels with 37,959 SNP, depending on the genomic selection method used. This was less than accuracies observed for polygenic EBV accuracies, which ranged from 0.504 to 0.602. The results obtained from this study demonstrate that the utility of genetic markers for genomic prediction of residual feed intake in beef cattle may be suboptimal. Differences in accuracy were observed between sire breeds when the random regression BLUP method was used, which may imply that the correlations obtained by this method were confounded by the ability of the selected SNP to trace breed differences. This may also suggest that prediction equations derived from such an admixed population may be useful only in populations of similar composition. Given the sample size used in this study, there is a need for increased feed intake testing if substantially greater accuracies are to be achieved.

Differential expression of ruminant ZNF496 variants: Association with quantitative trait locus affecting bovine milk concentration and fertility1,2

A single nucleotide polymorphism in the intergenic region upstream of the ZNF496 gene on Bos taurus chromosome 7 displayed significant population-wide linkage disequilibrium with milk protein percentage in the Israeli Holstein population. The frequency of the allele associated with increased protein concentration was 10%. This single nucleotide polymorphism was located in the promoter region from which a 10-exon transcript of the bovine and the ovine ZNF496 genes are transcribed. The gene architecture was similar to the mouse ortholog Zkscan17. A 5-exon murine antisense transcript was complementary to the 5′ untranslated Zkscan17 region that included a sequence domain conserved between mouse and ruminants, suggesting a regulatory function. In the bovine ZNF496 chromosomal region, segregation of a quantitative trait locus (QTL) for milk protein percentage was confirmed in a daughter design sire family. Concordance was not obtained between QTL status of bulls and any of the polymorphisms in the functional elements of ZNF496. This excludes these variations as the causative polymorphism under the assumption of no epigenetic effect for this locus. However, ZNF496 variants were differentially expressed in bovine ovaries, and only the paternal variant was expressed in liver and kidney in a sheep family with polymorphic ZNF496 sequence. Thus, the search for the mutation underlying the minor QTL allele, which is a top economically favorable allele in Israeli Holstein cattle, may be complicated by the presence of an imprinting center in this QTL confidence interval.

Quantitative trait loci affecting milk production traits on bovine chromosome 6 in zebuine Gyr breed

Fourteen Brazilian dairy Gyr sire families with 657 daughters were analyzed for quantitative trait loci (QTL) on chromosome 6 by using a daughter design for 5 economic traits: milk, fat, and protein production, fat and protein percentage. The cows and sires were genotyped for 27 microsatellites with average spacing between markers of 4.9 cM. In the analyses across 14 families, for the largest significant families, and within family, a QTL was located for milk yield and fat yield close to marker BMS2508 at the 5% chromosome-wide significance level across families and 1% chromosome-wide within families. For fat percentage, a QTL near DIK4482 was identified at the 5% chromosome-wide significance level when all families were analyzed together and at the 1% chromosome-wide significance level within the largest significant families. The different analyses yielded results that were generally consistent for milk yield, fat yield, and fat percentage. The order of the markers in the derived map was consistent with that in the consensus map. Some QTL and candidate genes in dairy cattle for milk production traits are probably preserved in Bos taurus and Bos indicus.

Quantitative trait loci affecting lactose and total solids on chromosome 6 in Brazilian Gir dairy cattle

Fourteen Brazilian Gir sire families with 657 daughters were analyzed for quantitative trait loci (QTL) on chromosome 6 affecting lactose and total solids. Cows and sires were genotyped with 27 microsatellites with a mean spacing between markers of 4.9 cM. We used a 1% chromosome-wide threshold for QTL qualification. A QTL for lactose yield was found close to marker MNB66 in three families. A QTL for total solid yield was identified close to marker BMS2508 in three families. A QTL for lactose percentage, close to marker DIK1182, was identified in two families. A QTL for total solid percentage, close to marker MNB208, was identified in four families. These QTLs could be used for selection of animals in dairy production systems.

Medullated fibres and fleece characteristics in Corriedale hoggets from two flocks in Uruguay

The incidence of medullation in 549 Corriedale hoggets from two experimental flocks, its association with other characteristics of the fleece, and the sire effect were evaluated. The investigation was carried out during 2005–06 in hoggets from the Faculty of Agriculture and Faculty of Veterinary Science experimental flocks. Fleeces were weighed and samples were taken at shearing by picking 104 staples from fleeces to measure medullation. A mid-side wool sample was taken to determine wool characteristics (fleece weight, wool yield, mean fibre diameter, staple strength and length). A Dark Fibre Detector was used to identify total medullated fibres and fibre type: medullated fibres (med) and kemp, which were confirmed by light microscope. Mean total medullated fibres, med and kemp content per 10 g of clean wool were 4.2 ± 11.2; 2.0 ± 8.9 and 2.3 ± 4.9, and median values were 0.9, 0.0 and 0.7, respectively, in 549 fleeces. A high variability between samples and a higher proportion of hoggets with kemp fibres than those with med were observed. There were significant differences between sire families for total medullated fibre content/10 g, med fibre content/10 g and kemp fibre content/10 g, but there were no significant effects between flocks, years or interaction between them. Phenotypic correlations between medullated fibre content and wool characteristics were generally low (less than 0.19). In conclusion, medullated fibre content was highly variable between samples and was not strongly correlated with other fleece characteristics. Medullation varied between sire groups, suggesting genetic variation, which could be exploited to improve wool quality.

QTL Identification Using Combined Linkage and Linkage Disequilibrium Mapping for Milk Production Traits on BTA6 in Chinese Holstein Population

Milk production traits are important economic traits for dairy cattle. The aim of the present study was to refine the position of previously detected quantitative trait loci (QTL) on bovine chromosome 6 affecting milk production traits in Chinese Holstein dairy cattle. A daughter design with 918 daughters from 8 elite sire families and 14 markers spanning the previously identified QTL region were used in the analysis. We employed a combined linkage and linkage disequilibrium analysis (LDLA) approach with two options for calculating the IBD probabilities, one was based on haplotypes of all 14 markers (named Method 1) and the other based on haplotypes with sliding windows of 5 markers (named Method 2). For milk fat yield, the two methods revealed a highly significant QTL located within a 6.5 cM interval (Method 1) and a 4.0 cM interval (Method 2), respectively. For milk protein yield, a highly significant QTL was detected within a 3.0 cM interval (Method 1) or a 2.5 cM interval (Method 2). These results confirmed the findings of our previous study and other studies, and greatly narrowed down the QTL positions.

Genome-wide scan to detect quantitative trait loci for milk urea nitrogen in Dutch Holstein-Friesian cows

Studies have reported genetic variation in milk urea nitrogen (MUN) between cows, suggesting genetic differences in nitrogen efficiency between cows. In this paper, the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in MUN and MUN yield are presented. Two to 3 morning milk samples were taken from 1,926 cows, resulting in 5,502 test-day records. Test-day records were corrected for systematic environmental effects using a repeatability animal model. Averages of corrected phenotypes of 849 cows, belonging to 7 sire families, were used in an across-family multimarker regression approach to detect QTL. Animals were successfully genotyped for 1,341 single nucleotide polymorphisms. The QTL analysis resulted in 4 chromosomal regions with suggestive QTL: Bos taurus autosomes (BTA) 1, 6, 21, and 23. On BTA 1, 2 suggestive QTL affecting MUN were detected at 60 and 140 cM. On BTA 6, 1 suggestive QTL affecting both MUN and MUN yield was detected at 103 cM. On BTA 21, 1 suggestive QTL affecting MUN yield was detected at 83 cM. On BTA 23, 1 suggestive QTL affecting MUN was detected at 54 cM. Quantitative trait loci for MUN and MUN yield were suggestive and each explained between 2 and 3% of the phenotypic variance.

Low-density lipoprotein receptor-related protein 8 gene association with egg traits in dwarf chickens

Low-density lipoprotein receptor-related protein 8 (LRP8), a member of the low-density lipoprotein receptor gene family with a role in clusterin processing, was investigated as a candidate gene for egg quality-related traits. One SNP from C to T at position 1623 of the open reading frame of LRP8 was identified and genotyped by a high-throughput genotyping method, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry in 747 egg-type dwarf layers from 44 sire families. There were no significant differences among genotypes for any interior egg traits measured, except for yolk color, in which color was deeper for the TT genotype than CC or CT (P < 0.05). For shell traits, strength and thickness were greater for TT than CC (P < 0.05), with CT intermediate and not different from either. Shape index was lower for CT than either TT or CC, which did not differ, whereas for shell color, CT was intermediate to the homozygotes, which differed (CC > TT). The present results indicated that LRP8, as a new member of eggshell matrix protein, may be a candidate gene associated with eggshell traits.

Inbreeding and effective population size in the Malaysian nucleus of the GIFT strain of Nile tilapia ( Oreochromis niloticus)

A fully pedigreed population of the GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia ( Oreochromis niloticus) was established in Malaysia during 2001 and 2002. The selection program was focused on the improvement of growth rate to harvest weight and the mate allocation strategy was aimed at avoiding inbreeding and ensuring that most sire families were represented as parents of the next generation. We examined the build up of inbreeding and we estimated the effective population size by different methods (namely, from: the number of selected parents, the variance in family size, the inbreeding coefficient, and the co-ancestry among selected individuals). The rate of inbreeding was 0.0037 per generation and the effective population size calculated from the rate of increase in the co-ancestry was 88. We conclude that the mate allocation strategy has been successful in containing inbreeding and that the effective population size is satisfactory for the sustainability of the selection program. By contrast, the effective population size is below the minimum (e.g. 500) necessary for the retention of evolutionary potential, hence the population would be unlikely to adapt and cope with severe environmental challenges. The results are discussed in relation to the development and maintenance of selection lines in farmed aquatic animals.

Detecting QTL for feed intake traits and other performance traits in growing pigs in a Piétrain–Large White backcross

Knowing the large difference in daily feed intake (DFI) between Large White (LW) and Piétrain (PI) growing pigs, a backcross (BC) population has been set up to map QTL that could be used in marker assisted selection strategies. LW × PI boars were mated with sows from two LW lines to produce 16 sire families. A total of 717 BC progeny were fed ad libitum from 30 to 108 kg BW using single-place electronic feeders. A genome scan was conducted using genotypes for the halothane gene and 118 microsatellite markers spread on the 18 porcine autosomes. Interval mapping analyses were carried out, assuming different QTL alleles between sire families to account for within breed variability using the QTLMap software. The effects of the halothane genotype and of the dam line on the QTL effect estimates were tested. One QTL for DFI (P < 0.05 at the chromosome-wide (CW) level) and one QTL for feed conversion ratio (P < 0.01 at the CW level) were mapped to chromosomes SSC6 – probably due to the halothane alleles – and SSC7, respectively. Three putative QTL for feed intake traits were detected (P < 0.06 at the CW level) on SSC2, SSC7 and SSC9. QTL on feeding traits had effects in the range of 0.20 phenotypic s.d. The relatively low number of QTL detected for these traits suggests a large QTL allele variability within breeds and/or low effects of individual loci. Significant QTL were detected for traits related to carcass composition on chromosomes SSC6, SSC15 and SSC17, and to meat quality on chromosome SSC6 (P < 0.01 at the genome-wide level). QTL effects for body composition on SSC13 and SSC17 differed according to the LW dam line, which confirmed that QTL alleles were segregating in the LW breed. An epistatic effect involving the halothane locus and a QTL for loin weight on SSC7 was identified, the estimated substitution effects for the QTL differing by 200 g between Nn and NN individuals. The interactions between QTL alleles and genetic background or particular genes suggest further work to validate QTL segregations in the populations where marker assisted selection for the QTL would be applied.

Polymorphisms in the HSP90AA1 5′ flanking region are associated with scrapie incubation period in sheep

Susceptibility to scrapie is mainly controlled by point mutations at the PRNP locus. However, additional quantitative trait loci (QTL) have been identified across the genome including a region in OAR18. The gene which encodes the inducible form of the cytoplasmic Hsp90 chaperone (HSP90AA1) maps within this region and seems to be associated with the resistance/susceptibility to scrapie in sheep. Here, we have analyzed several polymorphisms which were previously described in the ovine HSP90AA1 5' flanking region and in intron 10 in two naturally scrapie infected Romanov sheep populations. First, we have studied 58 ARQ/VRQ animals pertaining to the sire family where the QTL influencing scrapie incubation period in OAR18 was detected. We have found a significant association between polymorphisms localized at -660 and -528 in the HSP90AA1 5' flanking region and the scrapie incubation period. These two polymorphisms have also been studied in a second sample constituted by 62 VRQ/VRQ sheep showing an extreme incubation period. Results are concordant with the first dataset. Finally, we have studied the HSP90AA1 expression in scrapie and control animals (N = 41) with different HSP90AA1 genotypes by real time PCR on blood samples. The HSP90AA1 expression rate was equivalent in CC(-600)AA(-528) and CG(-600)AG(-528) scrapie resistant animals (ARR/ARR) and was higher in their CC(-600)AA(-528) than in their CG(-600)AG(-528) scrapie susceptible counterparts (VRQ/VRQ). Our results support the hypothesis that the ovine HSP90AA1 gene acts as a modulator of scrapie susceptibility, contributing to the observed differences in the incubation period of scrapie infected animals with the same PRNP genotype.

Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. II. Genetic parameters and trends1

Design of breeding programs requires knowledge of variance components that exist for traits included in specific breeding goals and the genetic relationships that exist among traits of economic importance. A study was conducted to evaluate direct and correlated genetic responses to selection for intramuscular fat (IMF) and to estimate genetic parameters for economically important traits in Duroc swine. Forty gilts were purchased from US breeders and randomly mated for 2 generations to boars available in regional boar studs to develop a base population of 56 litters. Littermate pairs of gilts from this population were randomly assigned to a select line (SL) or control line (CL) and mated to the same boar to establish genetic ties between lines. In the SL, the top 10 boars and 75 gilts were selected based on IMF EBV obtained from a bivariate animal model that included IMF evaluated on the carcass and IMF predicted via ultrasound. One boar from each sire family and 50 to 60 gilts representing all sire families were randomly selected to maintain the CL. Carcass and ultrasound IMF were both moderately heritable (0.31 and 0.38, respectively). Moderate to high genetic relationships were estimated among carcass backfat and meat quality measures of IMF, Instron tenderness, and objective loin muscle color. Based on estimates obtained in this study, more desirable genetic merit for pH is associated with greater genetic value for loin color, tenderness, and sensory characteristics. Intramuscular fat measures obtained on the carcass and predicted using ultrasound technology were highly correlated (r(g) = 0.86 from a 12-trait analysis; r(g) = 0.90 from a 5-trait analysis). Estimated genetic relationships among IMF measures and other traits evaluated were generally consistent. Intramuscular fat measures were also genetically associated with Instron tenderness and flavor score in a desirable direction. Direct genetic response in IMF measures observed in the SL corresponded to a significant decrease in EBV for carcass loin muscle area (-0.90 cm(2) per generation) and an increase in carcass backfat EBV (0.98 mm per generation). Selection for IMF has led to more desirable EBV for objective tenderness and has had an adverse effect on additive genetic merit for objective loin color.

Selection for Increased Nitric Oxide Production Does Not Increase Resistance to Marek's Disease in a Primary Broiler Breeder Line

Two primary broiler breeder lines, A and B, were examined for their potential to produce nitric oxide (NO) after stimulating splenocytes from 20-day-old embryos with lipopolysaccharide and interferon-gamma. Significant differences were found between lines A and B. Overall, line A had a higher response than line B, but line A also had a large degree of variation between individual sire families. Selection for high and low responders within line A resulted in the segregation of high- and low-responder sire families. Offspring from sire families selected for high and low NO responses and from a nonselected control group from line A were challenged with RB-1B Marek's disease (MD) virus to determine whether these differences could be used to select for improved resistance to MD. Virus isolation rates at 6 and 10 days postinfection were not significantly different, but unexpectedly, the MD incidence in the high-responder group was significantly higher than in the other two groups.

Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. I. Direct and correlated phenotypic responses to selection1

A study was conducted to evaluate the efficacy of selection for intramuscular fat (IMF) in a population of purebred Duroc swine using real-time ultrasound. Forty gilts were purchased from US breeders and randomly mated for 2 generations to boars available in regional boar studs, resulting in a base population of 56 litters. Littermate pairs of gilts from this population were randomly assigned to a select line (SL) or control line (CL) and mated to the same sire to establish genetic ties between lines. At an average BW of 114 kg, a minimum of 4 longitudinal ultrasound images were collected 7 cm off-midline across the 10th to 13th ribs of all pigs for the prediction of IMF (UIMF). At least 1 barrow or gilt was slaughtered from each litter, and carcass data were collected. A sample of the LM from the 10th to 11th rib interface was analyzed for carcass IMF (CIMF). Breeding values for IMF were estimated by fitting a 2-trait (UIMF and CIMF) animal model in MATVEC. In the SL, selection in each subsequent generation was based on EBV for IMF with the top 10 boars and top 75 gilts used to produce the next generation. One boar from each sire family and 50 to 60 gilts representing all sire families were randomly selected to maintain the CL. Through 6 generations of selection, an 88% improvement in IMF has been realized (4.53% in SL vs. 2.41% in CL). Results of this study revealed no significant correlated responses in measures of growth performance. However, 6 generations of selection for IMF have yielded correlated effects of decreased loin muscle area and increased backfat. Additionally, the SL obtained more desirable objective measures of tenderness and sensory evaluations of flavor and off-flavor. Meat quality characteristics of pH, water holding capacity, and percent cooking loss were not significantly affected by selection for IMF. Selection for IMF using real-time ultrasound is effective but may be associated with genetic ramifications for carcass composition traits. Intramuscular fat may be used in purebred Duroc swine breeding programs as an indicator trait for sensory traits that influence consumer acceptance; however, rapid improvement should not be expected when simultaneous improvement in other trait categories is also pursued.

Genetic variability in residual variation of body weight and conformation scores in broiler chickens

The aim of the study was to estimate genetic variance in residual variation of BW and body conformation scores of 34-d-old male and female broiler chickens. The data set included performance records of 52,349 female and 49,001 male birds. Two models were used: an iterative mean-variance restricted maximum likelihood sire plus dam model and a Bayesian sire plus dam model, in each case with heterogeneity in residual variances across sire families. They gave similar results. Estimates of heritability for BW in females and males were, respectively, 0.25 and 0.21, and for conformation score were 0.24 and 0.15, and genetic correlations for the same trait between sexes were high. Estimates of genetic correlations between means and variances were positive for both sexes and both traits. Estimates of the heritability of residual variation were low, between 0.023 and 0.038 for both traits, but genetic CV were substantial (between 0.25 and 0.40), indicating the possibility of improving uniformity of BW and conformation by means of selection.

Mixed Inheritance of Equine Recurrent Airway Obstruction

Mode of inheritance of equine recurrent airway obstruction (RAO) is unknown. Major genes are responsible for RAO. Direct offspring of 2 RAO-affected Warmblood stallions (n = 197; n = 163) and a representative sample of Swiss Warmbloods (n = 401). One environmental and 4 genetic models (general, mixed inheritance, major gene, and polygene) were tested for Horse Owner Assessed Respiratory Signs Index (1-4, unaffected to severely affected) by segregation analyses of the 2 half-sib sire families, both combined and separately, using prevalences estimated in a representative sample. In all data sets the mixed inheritance model was most likely to explain the pattern of inheritance. In all 3 datasets the mixed inheritance model did not differ significantly from the general model (P= .62, P= 1.00, and P= .27) but was always better than the major gene model (P < .01) and the polygene model (P < .01). The frequency of the deleterious allele differed considerably between the 2 sire families (P= .23 and P= .06). In both sire families the displacement was large (t= 17.52 and t= 12.24) and the heritability extremely large (h(2)= 1). Segregation analyses clearly reveal the presence of a major gene playing a role in RAO. In 1 family, the mode of inheritance was autosomal dominant, whereas in the other family it was autosomal recessive. Although the expression of RAO is influenced by exposure to hay, these findings suggest a strong, complex genetic background for RAO.

Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4

To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r2 values of 0.10 and 0.46, respectively; outside the blocks, r2 values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.