Genetic variances, heritabilities and maternal effects on body weight, breast meat yield, meat quality traits and the shape of the growth curve in turkey birds

<p>Abstract</p> <p>Background</p> <p>Turkey is an important agricultural species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds.</p> <p>Results</p> <p>The average heritability estimate for body weight traits was 0.38, except for early weights that were strongly affected by maternal effects. This study showed that body weight traits, upper asymptote (a growth curve trait), percent breast meat and redness of meat had high heritability whereas heritabilities of breast length, breast width, percent drip loss, ultimate pH, lightness and yellowness of meat were medium to low. We found high positive genetic and phenotypic correlations between body weight, upper asymptote, most breast meat yield traits and percent drip loss but percent drip loss was found strongly negatively correlated with ultimate pH. Percent breast meat, however, showed genetic correlations close to zero with body weight traits and upper asymptote.</p> <p>Conclusion</p> <p>The results of this analysis and the growth curve from the studied population of turkey birds suggest that the turkey birds could be selected for breeding between 60 and 80 days of age in order to improve overall production and the production of desirable cuts of meat. The continuous selection of birds within this age range could promote high growth rates but specific attention to meat quality would be needed to avoid a negative impact on the quality of meat.</p

A nonsense mutation in B3GALNT2 is concordant with hydrocephalus in Friesian horses

Background: Hydrocephalus in Friesian horses is a developmental disorder that often results in stillbirth of affected foals and dystocia in dams. The occurrence is probably related to a founder effect and inbreeding in the population. The aim of our study was to find genomic associations, to investigate the mode of inheritance, to allow a DNA test for hydrocephalus in Friesian horses to be developed. In case of a monogenic inheritance we aimed to identify the causal mutation. Results: A genome-wide association study of hydrocephalus in 13 cases and 69 controls using 29,720 SNPs indicated the involvement of a region on ECA1 (P T corresponding to XP_001491595 p.Gln475* was identical to a B3GALNT2 mutation identified in a human case of muscular dystrophy-dystroglycanopathy with hydrocephalus. All 16 available cases and none of the controls were homozygous for the mutation, and all 17 obligate carriers (= dams of cases) were heterozygous. A random sample of the Friesian horse population (n = 865) was tested for the mutation in a commercial laboratory. One-hundred and forty-seven horses were carrier and 718 horses were homozygous for the normal allele; the estimated allele frequency in the Friesian horse population is 0.085. Conclusions: Hydrocephalus in Friesian horses has an autosomal recessive mode of inheritance. A nonsense mutation XM_001491545 c.1423C>T corresponding to XP_001491595 p.Gln475* in B3GALNT2 (1: 75,859,296-75,909,376) is concordant with hydrocephalus in Friesian horses. Application of a DNA test in the breeding programme will reduce the losses caused by hydrocephalus in the Friesian horse population

Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7

Background: Inbreeding and population bottlenecks in the ancestry of Friesian horses has led to health issues such as dwarfism. The limbs of dwarfs are short and the ribs are protruding inwards at the costochondral junction, while the head and back appear normal. A striking feature of the condition is the flexor tendon laxity that leads to hyperextension of the fetlock joints. The growth plates of dwarfs display disorganized and thickened chondrocyte columns. The aim of this study was to identify the gene defect that causes the recessively inherited trait in Friesian horses to understand the disease process at the molecular level. Results: We have localized the genetic cause of the dwarfism phenotype by a genome wide approach to a 3 Mb region on the p-arm of equine chromosome 14. The DNA of two dwarfs and one control Friesian horse was sequenced completely and we identified the missense mutation ECA14:g.4535550C> T that cosegregated with the phenotype in all Friesians analyzed. The mutation leads to the amino acid substitution p.(Arg17Lys) of xylosylprotein beta 1,4-galactosyltransferase 7 encoded by B4GALT7. The protein is one of the enzymes that synthesize the tetrasaccharide linker between protein and glycosaminoglycan moieties of proteoglycans of the extracellular matrix. The mutation not only affects a conserved arginine codon but also the last nucleotide of the first exon of the gene and we show that it impedes splicing of the primary transcript in cultured fibroblasts from a heterozygous horse. As a result, the level of B4GALT7 mRNA in fibroblasts from a dwarf is only 2 % compared to normal levels. Mutations in B4GALT7 in humans are associated with Ehlers-Danlos syndrome progeroid type 1 and Larsen of Reunion Island syndrome. Growth retardation and ligamentous laxity are common manifestations of these syndromes. Conclusions: We suggest that the identified mutation of equine B4GALT7 leads to the typical dwarfism phenotype in Friesian horses due to deficient splicing of transcripts of the gene. The mutated gene implicates the extracellular matrix in the regular organization of chrondrocyte columns of the growth plate. Conservation of individual amino acids may not be necessary at the protein level but instead may reflect underlying conservation of nucleotide sequence that are required for efficient splicing

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture

震災豫防調査會報告第十八號正誤

<p>Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.</p

Genetic parameters for social effects on survival in cannibalistic layers: Combining survival analysis and a linear animal model

<p>Abstract</p> <p>Background</p> <p>Mortality due to cannibalism in laying hens is a difficult trait to improve genetically, because censoring is high (animals still alive at the end of the testing period) and it may depend on both the individual itself and the behaviour of its group members, so-called associative effects (social interactions). To analyse survival data, survival analysis can be used. However, it is not possible to include associative effects in the current software for survival analysis. A solution could be to combine survival analysis and a linear animal model including associative effects. This paper presents a two-step approach (2STEP), combining survival analysis and a linear animal model including associative effects (LAM).</p> <p>Methods</p> <p>Data of three purebred White Leghorn layer lines from Institut de Sélection Animale B.V., a Hendrix Genetics company, were used in this study. For the statistical analysis, survival data on 16,780 hens kept in four-bird cages with intact beaks were used. Genetic parameters for direct and associative effects on survival time were estimated using 2STEP. Cross validation was used to compare 2STEP with LAM. LAM was applied directly to estimate genetic parameters for social effects on observed survival days.</p> <p>Results</p> <p>Using 2STEP, total heritable variance, including both direct and associative genetic effects, expressed as the proportion of phenotypic variance, ranged from 32% to 64%. These results were substantially larger than when using LAM. However, cross validation showed that 2STEP gave approximately the same survival curves and rank correlations as LAM. Furthermore, cross validation showed that selection based on both direct and associative genetic effects, using either 2STEP or LAM, gave the best prediction of survival time.</p> <p>Conclusion</p> <p>It can be concluded that 2STEP can be used to estimate genetic parameters for direct and associative effects on survival time in laying hens. Using 2STEP increased the heritable variance in survival time. Cross validation showed that social genetic effects contribute to a large difference in survival days between two extreme groups. Genetic selection targeting both direct and associative effects is expected to reduce mortality due to cannibalism in laying hens.</p

Boosted trees to predict pneumonia, growth, and meat percentage of growing-finishing pigs

In pig production, efficiency is benefiting from uniform growth in pens resulting in single deliveries from a pen of possibly all animals in the targeted weight range. Abnormalities, like pneumonia or aberrant growth, reduce production efficiency as it reduces the uniformity and might cause multiple deliveries per batch and pigs delivered with a low meat yield or outside the targeted weight range. Early identification of pigs prone to develop these abnormalities, for example, at the onset of the growing-finishing phase, would help to prevent heterogeneous pens through management interventions. Data about previous production cycles at the farm combined with data from the piglet's own history may help in identifying these abnormalities. The aim of this study, therefore, was to predict at the onset of the growing-finishing phase, that is, at 3 mo in advance, deviant pigs at slaughter with a machine-learning technique called boosted trees. The dataset used was extracted from the farm management system of a research center. It contained over 70,000 records of individual pigs born between 2004 and 2016, including information on, for example, offspring, litter size, transfer dates between production stages, their respective locations within the barns, and individual live-weights at several production stages. Results obtained on an independent test set showed that at a 90% specificity rate, the sensitivity was 16% for low meat percentage, 20% for pneumonia and 36% for low lifetime growth rate. For low lifetime growth rate, this meant an almost three times increase in positive predictive value compared to the current situation. From these results, it was concluded that routine performance information available at the onset of the growing-finishing phase combined with data about previous production cycles formed a moderate base to identify pigs prone to develop pneumonia (AUC > 0.60) and a good base to identify pigs prone to develop growth aberrations (AUC > 0.70) during the growing-finishing phase. The mentioned information, however, was not a sufficient base to identify pigs prone to develop low meat percentage (AUC < 0.60). The shown ability to identify growth aberrations and pneumonia can be considered a good first step towards the development of an early warning system for pigs in the growing-finishing phase

Boosted trees to predict pneumonia, growth, and meat percentage of growing-finishing pigs

In pig production, efficiency is benefiting from uniform growth in pens resulting in single deliveries from a pen of possibly all animals in the targeted weight range. Abnormalities, like pneumonia or aberrant growth, reduce production efficiency as it reduces the uniformity and might cause multiple deliveries per batch and pigs delivered with a low meat yield or outside the targeted weight range. Early identification of pigs prone to develop these abnormalities, for example, at the onset of the growing-finishing phase, would help to prevent heterogeneous pens through management interventions. Data about previous production cycles at the farm combined with data from the piglet's own history may help in identifying these abnormalities. The aim of this study, therefore, was to predict at the onset of the growing-finishing phase, that is, at 3 mo in advance, deviant pigs at slaughter with a machine-learning technique called boosted trees. The dataset used was extracted from the farm management system of a research center. It contained over 70,000 records of individual pigs born between 2004 and 2016, including information on, for example, offspring, litter size, transfer dates between production stages, their respective locations within the barns, and individual live-weights at several production stages. Results obtained on an independent test set showed that at a 90% specificity rate, the sensitivity was 16% for low meat percentage, 20% for pneumonia and 36% for low lifetime growth rate. For low lifetime growth rate, this meant an almost three times increase in positive predictive value compared to the current situation. From these results, it was concluded that routine performance information available at the onset of the growing-finishing phase combined with data about previous production cycles formed a moderate base to identify pigs prone to develop pneumonia (AUC > 0.60) and a good base to identify pigs prone to develop growth aberrations (AUC > 0.70) during the growing-finishing phase. The mentioned information, however, was not a sufficient base to identify pigs prone to develop low meat percentage (AUC < 0.60). The shown ability to identify growth aberrations and pneumonia can be considered a good first step towards the development of an early warning system for pigs in the growing-finishing phase.</p

Genetic parameters of cryptorchidism and testis size in Friesian colts

In males with cryptorchidism, one or both testes do not descend into the scrotum thereby affecting among other things fertility. Testis size has been suggested to contribute to cryptorchidism. Therefore, the aim of our study was to estimate genetic parameters of cryptorchidism and testis size in Friesian colts. Data on cryptorchidism (0/1, n=1327) and testis size (cm, n=868 with size of both testes estimated) in Friesian colts of 1–7 months-of-age were gathered by a veterinarian during inspections from 2009 to 2012. Heritabilities, phenotypic and genetic correlations were estimated using ASReml4 including age of the colt (in months), location, year and month of inspection as fixed effects. Prevalence of cryptorchidism was 14.2%. Most affected colts (88.3%) were unilateral, while 11.7% were bilateral cases. Of the unilateral cases, significantly fewer colts had a left retained testis (35.5%) compared to a right retained testis (64.5%). Heritability of cryptorchidism was 0.13 (SE=0.06) and increased slightly when only cases of 4 months and older were considered. Based on literature and our findings we advise not to inspect colts at a very young age. Mean testis size significantly differed between left (3.47 cm) and right testis (3.19 cm). Heritability of left testis size (0.12±0.07) was lower compared to heritability of right testis size (0.31±0.10), where genetic correlation between left and right testis size was 0.87 (SE=0.12). The genetic correlation between left testis size and cryptorchidism was −0.94 (SE=0.15) and between right testis size and cryptorchidism was −0.64 (SE=0.23). At the age of the investigated Friesian colts, cryptorchidism genetically coincides with smaller testis size. The development of the left and right testis might differ, which could be hereditary in nature. More precise phenotyping, like recording position and size (and side) of the retained testis and age of the stallion, might contribute additionally to disentangling the genetic background of equine cryptorchidism and identifying the gene(s) affecting this disorder. For now, the continuation of the data recording as described in our study will enable the studbook to estimate breeding values and thereby select against cryptorchidism.</p