BackgroundIdentification 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.ResultsTwo 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.ConclusionsIn 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.

BackgroundHanwoo 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).MethodsAccuracies 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).ResultsAccuracies 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0283-0) contains supplementary material, which is available to authorized users.

Background: In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results: We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed f 4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

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.

SummaryThe aim of this study was to detect selection signatures considering cows from the German Holstein (GH) and the local dual‐purpose black and white (DSN) population, as well as from generated sub‐populations. The 4654 GH and 261 DSN cows were genotyped with the BovineSNP50 Genotyping BeadChip. The geographical herd location was used as an environmental descriptor to create the East‐DSN and West‐DSN sub‐populations. In addition, two further sub‐populations of GH cows were generated, using the extreme values for solutions of residual effects of cows for the claw disorder dermatitis digitalis. These groups represented the most susceptible and most resistant cows. We used cross‐population extended haplotype homozygosity methodology (XP‐EHH) to identify the most recent selection signatures. Furthermore, we calculated Wright’s fixation index (FST). Chromosomal segments for the top 0.1 percentile of negative or positive XP‐EHH scores were studied in detail. For gene annotations, we used the Ensembl database and we considered a window of 250 kbp downstream and upstream of each core SNP corresponding to peaks of XP‐EHH. In addition, functional interactions among potential candidate genes were inferred via gene network analyses. The most outstanding XP‐EHH score was on chromosome 12 (at 77.34 Mb) for DSN and on chromosome 20 (at 36.29–38.42 Mb) for GH. Selection signature locations harbored QTL for several economically important milk and meat quality traits, reflecting the different breeding goals for GH and DSN. The average FST value between GH and DSN was quite low (0.068), indicating shared founders. For group stratifications according to cow health, several identified potential candidate genes influence disease resistance, especially to dermatitis digitalis.

SummaryThe objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype–phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP‐EHH (cross‐population extend haplotype homozygosity) and FST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori‐Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.

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.

No abstract