Effect of Intra-ovarian Injection of Mesenchymal Stem Cells or its Conditioned Media on Repeated OPU-IVEP Outcomes in Jersey Heifers and Its Relationship with Follicular Fluid Inflammatory Markers.

Background: Repeated Ovum Pick Up (OPU) could have a detrimental effect on ovarian function, reducing In Vitro Embryo Production (IVEP). The present study examined the therapeutic effect of adipose-derived Mesenchymal Stem Cells (MSCs) or its Conditioned Medium (ConM) on ovarian trauma following repeated OPU. Resolvin E1 (RvE1) and Interleukin-12 (IL-12) were investigated as biomarkers. Methods: Jersey heifers (n=8) experienced 11 OPU sessions including 5 pre-treatment and 6 treatment sessions. Heifers received intra-ovarian administration of MSCs or ConM (right ovary) and Dulbecco's Modified Phosphate Buffer Saline (DMPBS; left ovary) after OPU in sessions 5 and 8 and 2 weeks after session 11. The concentrations of RvE1 and IL-12 in follicular fluid was evaluated on sessions 1, 5, 6, 9, and 4 weeks after session 11. Following each OPU session, the IVEP parameters were recorded. Results: Intra-ovarian administration of MSCs, ConM, and DMPBS did not affect IVEP parameters (p>0.05). The concentration of IL-12 in follicular fluid increased at the last session of pre-treatment (Session 5; p<0.05) and remained elevated throughout the treatment period. There was no correlation between IL-12 and IVEP parameters (p>0.05). However, RvE1 remained relatively high during the pre-treatment and decreased toward the end of treatment period (p<0.05). This in turn was associated with decline in some IVEP parameters (p<0.05). Conclusion: Intra-ovarian administration of MSCs or ConM during repeated OPU did not enhance IVEP outcomes in Bos taurus heifers. The positive association between RvE1 and some of IVEP parameters could nominate RvE1 as a promising biomarker to predict IVEP parameters following repeated OPU.

Genome-wide association study for body weight and feed consumption traits in Japanese quail using Bayesian approaches.

The aim of this study was to perform a genome-wide association study (GWAS) based on Bayes A and Bayes B statistical methods to identify genomic loci and candidate genes associated with body weight gain, feed intake, and feed conversion ratio in Japanese quail. For this purpose, genomic data obtained from Illumina iSelect 4K quail SNP chip were utilized. After implementing various quality control steps, genotype data from a total of 875 birds for 2,015 SNP markers were used for subsequent analyses. The Bayesian analyses were performed using hibayes package in R (version 4.3.1) and Gibbs sampling algorithm. The results of the analyses showed that Bayes A accounted for 11.43, 11.65, and 11.39% of the phenotypic variance for body weight gain, feed intake, and feed conversion ratio, respectively, while the variance explained by Bayes B was 7.02, 8.61, and 6.48%, respectively. Therefore, in the current study, results obtained from Bayes A were used for further analyses. In order to perform the gene enrichment analysis and to identify the functional pathways and classes of genes that are over-represented in a large set of genes associated with each trait, all markers that accounted for more than 0.1% of the phenotypic variance for each trait were used. The results of this analysis revealed a total of 23, 38, and 14 SNP markers associated with body weight gain, feed intake, and feed conversion ratio in Japanese quail, respectively. The results of the gene enrichment analysis led to the identification of biological pathways (and candidate genes) related to lipid phosphorylation (TTC7A gene) and cell junction (FGFR4 and FLRT2 genes) associated with body weight gain, calcium signaling pathway (ADCY2 and CAMK1D genes) associated with feed intake, and glycerolipid metabolic process (LIPC gene), lipid metabolic process (ADGRF5 and ESR1 genes), and glutathione transferase (GSTK1 gene) associated with feed conversion ratio. Overall, the findings of this study can provide valuable insights into the genetic architecture of growth and feed consumption traits in Japanese quail.

Detecting SNP markers discriminating horse breeds by deep learning.

The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead chip were used in the current study and principal component analysis (PCA), log-likelihood ratios (LLR) and Neighbor-Joining (NJ) were applied to assess the performance of different assignment methods. The results revealed that the DNN, Garson, and Olden methods are able to assign individuals to true populations with 4270, 4937, and 7999 SNP markers, respectively. The PCA was used to determine how the animals allocated to the groups using all genotyped markers available on 50k Bead chip and the subset of SNP markers identified with different methods. The results indicated that all SNP panels are able to assign individuals into their true breeds. The success percentage of genetic assignment for different methods assessed by different levels of LLR showed that the success rate of 70% in the analysis was obtained by three methods with the number of markers of 110, 208, and 178 tags for DNN, Garson, and Olden methods, respectively. Also the results showed that DNN performed better than other two approaches by achieving 93% accuracy at the most stringent threshold. Finally, the identified SNPs were successfully used in independent out-group breeds consisting 120 individuals from eight breeds and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. Furthermore, the NJ tree of allele-sharing distances on the validation dataset showed that the DNN has a high potential for feature selection. In general, the results of this study indicated that the DNN technique represents an efficient strategy for selecting a reduced pool of highly discriminant markers for assigning individuals to the true population of origin.

Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep.

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle.

Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds.

Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.

Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection.

The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.

Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep.

The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a 50 K single nucleotide polymorphism (SNP) array. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. The results showed that top ranked genomic windows (1 Mb windows) explained 3.49, 4.04, 5.37, 4.09, 3.80, and 5.24% of the genetic variances for MY, FY, FAT%, PY, PROT%, and total SCS, respectively. Among the candidate genes found, some known associations were confirmed, while several novel candidate genes were also revealed, including PPARGC1A, LYPLA1, LEP, and MYH9 for MY; CACNA1C, PTPN1, ROBO2, CHRM3, and ERCC6 for FY and FAT%; PCSK5 and ANGPT1 for PY and PROT%; and IL26, IFNG, PEX26, NEGR1, LAP3, and MED28 for SCS. These findings increase our understanding of the genetic architecture of six examined traits and provide guidance for subsequent genetic improvement through genome selection.

Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds.

Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.

Genome-wide association study for postweaning weight traits in Lori-Bakhtiari sheep.

Marker-assisted selection is an effective method in novel animal breeding programs. This study was conducted to perform a genome-wide association study to detect candidate genes and quantitative trait loci associated with postweaning weight traits in meat-type sheep. Body weight records were collected during 29 years (1989 to 2017) in Lori-Bakhtiari sheep flock of the Shooli Breeding Station in Iran. A total of 132 animals were selected based on estimates of breeding values (EBVs) for body weight, using two-tailed and random selection strategies. Genomic DNA was extracted from whole blood samples. The samples were genotyped using Illumina OvineSNP50 BeadChip. De-regressed EBVs for postweaning body weight traits were used as pseudo-phenotypes in a genome-wide association study. One SNP on chromosome 10 (rs406324209) and two SNPs on chromosome 13 (rs401963094 and rs418761613) were significantly (Bonferroni-adjusted p-values < 0.05) associated with postweaning body weight traits. The significant variants accounted for 0.20% and 0.48% of the total genetic variances for 6- and 9-month body weights, respectively. Genomic heritabilities estimated for 6-, 9- and 12-month weights and postweaning weight gain were 0.28 ± 0.34, 0.35 ± 0.29, 0.37 ± 0.34, and 0.16 ± 0.33, respectively. Two significant SNPs were located within the ATP8A2 and PLXDC2 genes, on chromosomes 10 and 13, respectively. Based on the known gene ontologies, both ATP8A2 and PLXDC2 could be considered as candidate genes for postweaning body weight traits.

Effects of a Grain Source (Corn Versus Barley) and Starter Protein Content on Performance, Ruminal Fermentation, and Blood Metabolites in Holstein Dairy Calves.

The effects of a grain source (corn grain (CG) vs. barley grain (BG)) and starter protein content (19% vs. 22% CP, dry matter basis) on growth performance, digestibility, ruminal fermentation, and blood metabolites were evaluated in Holstein dairy calves. Forty 3-day-old female calves with a starting body weight of 39.3 kg were subjected to four treatments in a completely randomized design with two by two factorial arrangements. Treatments were: (1) CG + 19% CP (CG-19CP); (2) CG + 22% CP (CG-22CP); (3) BG + 19% CP (BG-19CP); and (4) BG + 22% CP (BG-22CP). All calves were weaned at 59 days of age and remained in the study until 73 days of age. Starter and total DM intake were not affected by grain source and dietary protein content (p > 0.05). The average daily gain and feed efficiency were improved, and ruminal total short-chain fatty acid, propionate, and butyrate concentrations were increased in BG calves compared to CG calves (p < 0.05). The ruminal concentrations of ammonia nitrogen (d 71; p = 0.02) and acetate (d 35; p = 0.02) were increased in CG fed calves compared to BG. The greatest wither height (p = 0.03) and blood insulin concentration (p = 0.03) were seen in BG-22CP treatment. In conclusion, BG has marginal benefit in the height of calves when fed with diet containing 22% CP which may be recommendable in replacement heifer rearing programs.

Synchronous feeding of liquid protein source with different grains on performance, digestibility, ruminal fermentation, blood metabolites, and carcass characters in growing lambs.

The effects of feeding corn steep liquor (CSL; 420 g/kg crude protein, DM basis) along with different cereal grains on performance, digestibility, blood metabolites, ruminal fermentation, and carcass characters of growing lambs were evaluated. The constant amount of CSL was included in basal diet (100 g/kg, DM basis) and grain sources as experimental treatments were as follows: (1) corn grain (CG), (2) barley grain (BG), or (3) wheat grain (WG). The eighteen individually fed Farahani lambs averaging body weight 32 kg were allocated in completely randomized design (6 lambs/each) in a 9-week trial. The results showed that the greatest intake and gain were found in lambs fed CG in contrast to others. Nitrogen intake was constant among diets; however, the greatest nitrogen efficiency was found for corn grain-fed animals. Digestibility of nutrients were reduced in WG-fed animals in comparison with other grains. Ruminal proportions of propionate and butyrate were reduce in WG-fed lambs. The CG-fed animals displayed greater blood glucose and lower BUN concentrations compared with others. The greatest aspartate aminotransferase concentration as well as the greatest liver fat deposition suggested a dysfunction in liver performance in WG-fed animals. Except than that of a tendency for increment in dressing percentage in CG-fed lambs, no carcass character was differed among treatments. In conclusion, results revealed that feeding liquid protein source (CSL) is recommendable when it has been fed along with corn grain in comparison with barley or wheat grains in growing lambs.

Nutritional and physiological responses of broiler chickens to dietary supplementation with de-oiled soyabean lecithin at different metabolisable energy levels and various fat sources.

A 42-d study was conducted to investigate the effects of an emulsifier supplementation (de-oiled soyabean lecithin (DSL)) of diets with different levels of metabolisable energy (ME) and various sources of fat on growth performance, nutrient digestibility, blood profile and jejunal morphology of broiler chickens. Diets were arranged factorially (2 × 2 × 2) and consisted of two concentrations of ME (normal and low), two fat sources (soyabean oil (SO) and poultry fat (PF)) and two levels of DSL supplementation (0 and 1 g/kg). A total of 800 1-d-old male broiler chickens were assigned to eight treatments with five replicates/treatment. The results showed the supplemental DSL caused improvements in the overall feed conversion ratio, fat digestibility and jejunal villus height:crypt depth ratio, but the magnitude of the responses was greater in the PF-containing diets, resulting in significant fat × DSL interactions (P<0·05). Abdominal fat percentage was also reduced by the PF-containing diet, but the response was greater in the normal ME diet, resulting in a significant ME × fat interaction (P = 0·048). Dietary DSL supplementation also increased nitrogen-corrected apparent ME values but decreased blood TAG (P = 0·041) and LDL (P = 0·049) concentrations, regardless of the source of fat used or the ME values in the diet. In conclusion, the present study suggests that the improvements in growth performance, fat digestibility and intestinal morphology that can be achieved with DSL supplementation are highly dependent on the degree of saturation of lipid incorporated into broiler chicken diets.

Comparison of conventional BLUP and single-step genomic BLUP evaluations for yearling weight and carcass traits in Hanwoo beef cattle using single trait and multi-trait models.

Hanwoo, an important indigenous and popular breed of beef cattle in Korea, shows rapid growth and has high meat quality. Its yearling weight (YW) and carcass traits (backfat thickness, carcass weight- CW, eye muscle area, and marbling score) are economically important for selection of young and proven bulls. However, measuring carcass traits is difficult and expensive, and can only be performed postmortem. Genomic selection has become an appealing procedure for genetic evaluation of these traits (by inclusion of the genomic data) along with the possibility of multi-trait analysis. The aim of this study was to compare conventional best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP) methods, using both single-trait (ST-BLUP, ST-ssGBLUP) and multi-trait (MT-BLUP, MT-ssGBLUP) models to investigate the improvement of breeding-value accuracy for carcass traits and YW. The data comprised of 15,279 phenotypic records for YW and 5,824 records for carcass traits, and 1,541 genotyped animals for 34,479 single-nucleotide polymorphisms. Accuracy for each trait and model was estimated only for genotyped animals by five-fold cross-validation. ssGBLUP models (ST-ssGBLUP and MT-ssGBLUP) showed ~19% and ~36% greater accuracy than conventional BLUP models (ST-BLUP and MT-BLUP) for YW and carcass traits, respectively. Within ssGBLUP models, the accuracy of the genomically estimated breeding value for CW increased (19%) when ST-ssGBLUP was replaced with the MT-ssGBLUP model, as the inclusion of YW in the analysis led to a strong genetic correlation with CW (0.76). For backfat thickness, eye muscle area, and marbling score, ST- and MT-ssGBLUP models yielded similar accuracy. Thus, combining pedigree and genomic data via the ssGBLUP model may be a promising way to ensure acceptable accuracy of predictions, especially among young animals, for ongoing Hanwoo cattle breeding programs. MT-ssGBLUP is highly recommended when phenotypic records are limited for one of the two highly correlated genetic traits.

Predictive performance of genomic selection methods for carcass traits in Hanwoo beef cattle: impacts of the genetic architecture.

BACKGROUND: Hanwoo beef is known for its marbled fat, tenderness, juiciness and characteristic flavor, as well as for its low cholesterol and high omega 3 fatty acid contents. As yet, there has been no comprehensive investigation to estimate genomic selection accuracy for carcass traits in Hanwoo cattle using dense markers. This study aimed at evaluating the accuracy of alternative statistical methods that differed in assumptions about the underlying genetic model for various carcass traits: backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS). METHODS: Accuracies of direct genomic breeding values (DGV) for carcass traits were estimated by applying fivefold cross-validation to a dataset including 1183 animals and approximately 34,000 single nucleotide polymorphisms (SNPs). RESULTS: Accuracies of BayesC, Bayesian LASSO (BayesL) and genomic best linear unbiased prediction (GBLUP) methods were similar for BT, EMA and MS. However, for CW, DGV accuracy was 7% higher with BayesC than with BayesL and GBLUP. The increased accuracy of BayesC, compared to GBLUP and BayesL, was maintained for CW, regardless of the training sample size, but not for BT, EMA, and MS. Genome-wide association studies detected consistent large effects for SNPs on chromosomes 6 and 14 for CW. CONCLUSIONS: The predictive performance of the models depended on the trait analyzed. For CW, the results showed a clear superiority of BayesC compared to GBLUP and BayesL. These findings indicate the importance of using a proper variable selection method for genomic selection of traits and also suggest that the genetic architecture that underlies CW differs from that of the other carcass traits analyzed. Thus, our study provides significant new insights into the carcass traits of Hanwoo cattle.

Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition.

BACKGROUND: Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds. RESULTS: Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. CONCLUSIONS: In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.