Routine Karyotyping Reveals Frequent Mosaic Reciprocal Chromosome Translocations in Swine: Prevalence, Pedigree, and Litter Size.

In the routine commercial karyotype analysis on 5,481 boars, we identified 32 carriers of mosaic reciprocal translocations, half of which were carrying a specific recurrent translocation, mos t(7;9). An additional 7 mosaic translocations were identified through lymphocyte karyotype analysis from parents and relatives of mosaic carriers (n = 45), a control group of non-carrier boars (n = 73), and a mitogen assessment study (n = 20), bringing the total number of mosaic carriers to 39 cases. Mosaic translocations in all carriers were recognized to be confined to hematopoietic cells as no translocations were identified in fibroblasts cells of the carriers. In addition, negative impact on reproduction was not observed as the fertility of the carriers and their relatives were comparable to breed averages, and cryptic mosaicism was not detected in the family tree. This paper presents the first study of mosaic reciprocal translocations identified in swine through routine screening practices on reproductively unproven breeding boars while presenting evidence that these type of chromosome abnormalities are not associated with any affected phenotype on the carrier animals. In addition, the detection of recurrent mosaic translocations in this study may emphasize the non-random nature of mosaic rearrangements in swine and the potential role of genomic elements in their formation.

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle.

BACKGROUND: Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs. RESULTS: Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits. CONCLUSIONS: Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone.

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs.

BACKGROUND: Knowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers). RESULTS: The overall LD (r 2) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire. CONCLUSIONS: An overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals (Landrace × Yorkshire) should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.

Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats.

BACKGROUND: Basic understanding of linkage disequilibrium (LD) and population structure, as well as the consistency of gametic phase across breeds is crucial for genome-wide association studies and successful implementation of genomic selection. However, it is still limited in goats. Therefore, the objectives of this research were: (i) to estimate genome-wide levels of LD in goat breeds using data generated with the Illumina Goat SNP50 BeadChip; (ii) to study the consistency of gametic phase across breeds in order to evaluate the possible use of a multi-breed training population for genomic selection and (iii) develop insights concerning the population history of goat breeds. RESULTS: Average r(2) between adjacent SNP pairs ranged from 0.28 to 0.11 for Boer and Rangeland populations. At the average distance between adjacent SNPs in the current 50 k SNP panel (~0.06 Mb), the breeds LaMancha, Nubian, Toggenburg and Boer exceeded or approached the level of linkage disequilibrium that is useful (r(2) > 0.2) for genomic predictions. In all breeds LD decayed rapidly with increasing inter-marker distance. The estimated correlations for all the breed pairs, except Canadian and Australian Boer populations, were lower than 0.70 for all marker distances greater than 0.02 Mb. These results are not high enough to encourage the pooling of breeds in a single training population for genomic selection. The admixture analysis shows that some breeds have distinct genotypes based on SNP50 genotypes, such as the Boer, Cashmere and Nubian populations. The other groups share higher genome proportions with each other, indicating higher admixture and a more diverse genetic composition. CONCLUSIONS: This work presents results of a diverse collection of breeds, which are of great interest for the implementation of genomic selection in goats. The LD results indicate that, with a large enough training population, genomic selection could potentially be implemented within breed with the current 50 k panel, but some breeds might benefit from a denser panel. For multi-breed genomic evaluation, a denser SNP panel also seems to be required.

Genome-wide association for growth traits in Canchim beef cattle.

Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.