Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs

Genome wide association studies for carcass traits measured by video image analysis in crossbred lambs

This is the first UK genome wide association study investigating potential links between Video Image Analysis (VIA) carcass traits and molecular polymorphisms in crossbred sheep. Phenotypic and genotypic data were collected from two crossbred lamb populations: Texel x Scotch Mule (TxSM, n = 2330) and Texel x Lleyn (TxL, n = 3816). Traits measured included live weights at birth, eight weeks and weaning (∼15 weeks). VIA-predicted traits included total weights and weights of fat, muscle and bone in the whole carcass and primal (hind leg, saddle, shoulder) regions. Within-breed heritabilities estimated for the VIA traits ranged from 0.01 to 0.70, indicating potential for inclusion of some traits in breeding programmes. The two crossbred populations differed in SNPs associated with different traits. Two SNPs on chromosomes two (s74618.1) and eight (s68536.1), respectively, reached genome-wise significance for TxSM, explaining <1% of trait variance, for whole carcass fat and muscle weights, hind leg and saddle fat weights and shoulder bone weights. For TxL, four SNPs reached genome-wise significance, on chromosome two for hind leg muscle weight (OAR2_117,959,202 and OAR2_11804335), on chromosome 10 for whole carcass bone weight (OAR19_8,995,957.1), and on chromosome 19 for weaning weight (s40847.1), each explaining <1% of trait genetic variation. Differences in apparent genetic control of carcass traits may be influenced by the lambs' cross-breed, but also by management decisions affecting environmental variance and trait definitions, which should be understood in order to define protocols for incorporation of carcass traits into (cross)breeding programmes. IMPLICATIONS: Combining VIA-measured carcass traits with conventional production traits in a breeding programme could potentially improve the production and product quality of meat sheep. Phenotypes for VIA traits could be collected relatively easily if VIA machines were present at all abattoir sites. The current study and future Genome Wide Association Studies may help to identify potentially informative molecular markers, that explain large proportions of the genetic variance observed in VIA-measured carcass traits. Including this information in the estimation of breeding values could increase the accuracy of prediction, increasing the potential rate of genetic improvement for product quality. This study confirms the polygenic architecture of the investigated carcass traits, with a small number of molecular markers that each explain a small amount of genetic variation. Further studies across breed types are recommended to further test and validate molecular markers for traits related to lamb carcass quality, as measured by video image analysis.

Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection

The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for the regional economy and have a cultural and traditional importance for the inhabitants. The aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) and PS (N = 2637) based on genome wide SNPs. Estimates of linkage disequilibrium effective population size (Ne) evidenced more genetic variability in PS (Ne = 838) compared to IS (Ne = 197), regardless of historical time (both recent and ancient genetic variability). The discrepancy in the recent genetic variability between these breeds was additionally confirmed by the estimates of genomic inbreeding (FROH), which was estimated to be notably higher in IS (FROH>2 = 0.062) than in PS (FROH>2 = 0.029). The average FROH2-4, FROH4-8, FROH8-16, and FROH>16 were 0.26, 1.65, 2.14, and 3.72 for IS and 0.22, 0.61, 0.75, and 1.58 for PS, thus evidencing a high contribution of recent inbreeding in the overall inbreeding. One ROH island with > 30% of SNP incidence in ROHs was detected in IS (OAR6; 34,253,440-38,238,124 bp) while there was no ROH islands detected in PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, and SPP1) involved in growth, feed intake, milk production, immune responses, and resistance were associated with the found autozygosity. The results of this study represent the first comprehensive insight into genomic variability of these two Croatian local sheep breeds and will serve as a baseline for setting up the most promising strategy of genomic Optimum Contribution Selection.

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR

BACKGROUND

The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program.

RESULTS

In this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers).

CONCLUSIONS

The first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.

Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping

Identifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R.A. Fisher, genome-wide association studies (GWAS) extract information using averages and variances from genotype-phenotype datasets. Averages and variances are legitimated upon creating distribution density functions obtained through the grouping of data into categories. However, as data from within a given category cannot be differentiated, the investigative power of such methodologies is limited. Genomic Informational Field Theory (GIFT) is a method specifically designed to circumvent this issue. The way GIFT proceeds is opposite to that of GWAS. Whilst GWAS determines the extent to which genes are involved in phenotype formation (bottom-up approach), GIFT determines the degree to which the phenotype can select microstates (genes) for its subsistence (top-down approach). Doing so requires dealing with new genetic concepts, a.k.a. genetic paths, upon which significance levels for genotype-phenotype associations can be determined. By using different datasets obtained in ovis aries related to bone growth (Dataset-1) and to a series of linked metabolic and epigenetic pathways (Dataset-2), we demonstrate that removing the informational barrier linked to categories enhances the investigative and discriminative powers of GIFT, namely that GIFT extracts more information than GWAS. We conclude by suggesting that GIFT is an adequate tool to study how phenotypic plasticity and genetic assimilation are linked.

Recent advances in the genomic resources for sheep

Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.

Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information

Alpine Merino Sheep is a novel breed reared from Australian Merino Sheep as the father and Gansu Alpine Fine-Wool Sheep as the mother, living all year in cold and arid alpine areas with exceptional wool quality and meat performance. Body weight is an important economic trait of the Alpine Merino Sheep, but there is limited research on identifying the genes associated with live weight in the 14th month for improving the accuracy of the genomic prediction of this trait. Therefore, this study's sample comprised 1310 Alpine Merino Sheep ewes, and the Fine Wool Sheep 50K Panel was used for genome-wide association study (GWAS) analysis to identify candidate genes. Moreover, the trial population (1310 ewes) in this study was randomly divided into two groups. One group was used as the population for GWAS analysis and screened for the most significant top 5%, top 10%, top 15%, and top 20% SNPs to obtain prior marker information. The other group was used to estimate the genetic parameters based on the weight assigned by heritability combined with different prior marker information. The aim of this study was to compare the accuracy of genomic breeding value estimation when combined with prior marker information from GWAS analysis with the optimal linear unbiased prediction method for genome selection (GBLUP) for the breeding value of target traits. Finally, the accuracy was evaluated using the five-fold cross-validation method. This research provides theoretical and technical support to improve the accuracy of sheep genome selection and better guide breeding. The results demonstrated that eight candidate genes were associated with GWAS analysis, and the gene function query and literature search results suggested that FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, and SYN3 were candidate genes affecting live weight in the 14th month (WT), which regulated the growth of muscle and bone in sheep. In genome selection analysis, the heritability of GBLUP to calculate the WT was 0.335-0.374, the accuracy after five-fold cross-verification was 0.154-0.190, and after assigning different weights to the top 5%, top 10%, top 15%, and top 20% of the GWAS results in accordance with previous information to construct the G matrix, the accuracy of the WT in the GBLUP model was improved by 2.59-7.79%.

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

BACKGROUND

The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type.

RESULTS

We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis.

CONCLUSIONS

Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

NCAPG Regulates Myogenesis in Sheep, and SNPs Located in Its Putative Promoter Region Are Associated with Growth and Development Traits

Previously, NCAPG was identified as a candidate gene associated with sheep growth traits. This study aimed to investigate the direct role of NCAPG in regulating myogenesis in embryonic myoblast cells and to investigate the association between single-nucleotide polymorphisms (SNPs) in its promoter region and sheep growth traits. The function of NCAPG in myoblast proliferation and differentiation was detected after small interfering RNAs (siRNAs) knocked down the expression of NCAPG. Cell proliferation was detected using CCK-8 assay, EdU proliferation assay, and flow cytometry cell cycle analysis. Cell differentiation was detected via cell immunofluorescence and the quantification of myogenic regulatory factors (MRFs). SNPs in the promoter region were detected using Sanger sequencing and genotyped using the improved multiplex ligation detection reaction (iMLDR®) technique. As a result, a notable decrease (p < 0.01) in the percentage of EdU-positive cells in the siRNA-694-treated group was observed. A significant decrease (p < 0.01) in cell viability after treatment with siRNA-694 for 48 h and 72 h was detected using the CCK-8 method. The quantity of S-phase cells in the siRNA-694 treatment group was significantly decreased (p < 0.01). After interfering with NCAPG in myoblasts during induced differentiation, the relative expression levels of MRFs were markedly (p < 0.05 or p < 0.01) reduced compared with the control group on days 5-7. The myoblast differentiation in the siRNA-694 treatment group was obviously suppressed compared with the control group. SNP1, SNP2, SNP3, and SNP4 were significantly (p < 0.05) associated with all traits except body weight measured at birth and one month of age. SNP5 was significantly (p < 0.05) associated with body weight, body height, and body length in six-month-old sheep. In conclusion, interfering with NCAPG can inhibit the proliferation and differentiation of ovine embryonic myoblasts. SNPs in its promoter region can serve as potential useful markers for selecting sheep growth traits.

Genome-Wide Association Analysis of Muscle pH in Texel Sheep × Altay Sheep F2 Resource Population

pH was one of the important meat quality traits, which was an important factor affecting the storage/shelf life and quality of meat in meat production. In order to find a way to extend the storage/shelf life, the pH values (pH_45min, pH_24h, pH_48h and pH_72h) of the longissimus dorsi muscles in F₂ individuals of 462 Texel sheep × Altay sheep were determined, genotyping was performed using Illumina Ovine SNP 600 K BeadChip and whole genome resequencing technology, a genome-wide association analysis (GWAS) was used to screen the candidate genes and molecular markers for pH values related to the quality traits of mutton, and the effects of population stratification were detected by Q-Q plots. The results showed that the pH population stratification analysis did not find significant systemic bias, and there was no obvious population stratification effect. The results of the association analysis showed that 28 SNPs significantly associated with pH reached the level of genomic significance. The candidate gene associated with pH_45min was identified as the CCDC92 gene by gene annotation and a search of the literature. Candidate genes related to pH_24h were KDM4C, TGFB2 and GOT2 genes. The candidate genes related to pH_48h were MMP12 and MMP13 genes. The candidate genes related to pH_72h were HILPDA and FAT1 genes. Further bioinformatics analyses showed 24 gene ontology terms and five signaling pathways that were significantly enriched (p ≤ 0.05). Many terms and pathways were related to cellular components, processes of protein modification, the activity of protein dimerization and hydrolase activity. These identified SNPs and genes could provide useful information about meat and the storage/shelf life of meat, thereby extending the storage/shelf life and quality of meat.

Hepatic Transcriptome Analysis Reveals Genes, Polymorphisms, and Molecules Related to Lamb Tenderness

Tenderness is a key meat quality trait that determines the public acceptance of lamb consumption, so genetic improvement toward lamb with higher tenderness is pivotal for a sustainable sheep industry. However, unravelling the genomics controlling the tenderness is the first step. Therefore, this study aimed to identify the transcriptome signatures and polymorphisms related to divergent lamb tenderness using RNA deep sequencing. Since the molecules and enzymes that control muscle growth and tenderness are metabolized and synthesized in the liver, hepatic tissues of ten sheep with divergent phenotypes: five high- and five low-lamb tenderness samples were applied for deep sequencing. Sequence analysis identified the number of reads ranged from 21.37 to 25.37 million bases with a mean value of 22.90 million bases. In total, 328 genes are detected as differentially expressed (DEGs) including 110 and 218 genes that were up- and down-regulated, respectively. Pathway analysis showed steroid hormone biosynthesis as the dominant pathway behind the lamb tenderness. Gene expression analysis identified the top high (such as TP53INP1, CYP2E1, HSD17B13, ADH1C, and LPIN1) and low (such as ANGPTL2, IGFBP7, FABP5, OLFML3, and THOC5) expressed candidate genes. Polymorphism and association analysis revealed that mutation in OLFML3, ANGPTL2, and THOC5 genes could be potential candidate markers for tenderness in sheep. The genes and pathways identified in this study cause variation in tenderness, thus could be potential genetic markers to improve meat quality in sheep. However, further validation is needed to confirm the effect of these markers in different sheep populations so that these could be used in a selection program for lamb with high tenderness.

Exploring the growth trait molecular markers in two sheep breeds based on Genome-wide association analysis

Growth traits are quantitative traits controlled by multiple micro-effect genes. we identified molecular markers related to sheep growth traits, which formed the basis of molecular breeding. In this study, we randomly selected 100 Qira Black sheep and 84 German Merino sheep for the blood collection the jugular vein to genotype by using the Illumina Ovine SNP 50K Bead Chip. quality control criteria for statistical analysis were: rejection detection rate < 90% and minimum allele frequency (MAF) < 5%. Then, we performed Genome-wide association studies (GWAS) on sheep body weight, body height, body length, and chest circumference using mixed linear models. After getting 55 SNPs with significant correlation, they were annotated by reference genome of Ovis aries genome (Oar_v4.0) and We obtained a total of 84 candidate genes associated with production traits (BMPR1B, HSD17B3, TMEM63C, etc.). We selected BMPR1B for population validation and found a correlation between the FecB locus and body weight traits. Therefore, this study not only supplements the existing knowledge of molecular markers of sheep growth traits, but also has important theoretical significance and reference value for the mining of functional genes of sheep growth traits.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

BACKGROUND

After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits.

REVIEW

Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation.

CONCLUSIONS

Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.

Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes

BACKGROUND

Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for livestock sustainability, allowing animals to cope with more variable environments. BRD has previously been reported to be heritable in ruminants. In the present work, we conducted genome-wide studies (GWAS) in sheep to determine genetic variants associated with BRD. BR (i.e. levels) and BRD (i.e. changes over time) were obtained through body condition score measurements at eight physiological stages throughout each productive cycle in Romane ewes (n = 1034) and were used as phenotypes for GWAS. After quality controls and imputation, 48,593 single nucleotide polymorphisms (SNP) were included in the GWAS.

RESULTS

Among the 23 QTL regions identified, a major QTL associated with BR during pregnancy and lactation was identified on chromosome 1. In this region, several significant SNPs mapped to the leptin receptor gene (LEPR), among which one SNP mapped to the coding sequence. The point mutation induces the p.P1019S substitution in the cytoplasmic domain, close to tyrosine phosphorylation sites. The frequency of the SNP associated with increased BR levels was 32%, and the LEPR genotype explained up to 5% of the variance of the trait. Higher fatness levels in ewes carrying the LEPR p.P1019S mutation were observed all along the productive cycle.

CONCLUSIONS

These results provide strong evidences for involvement of LEPR in the regulation of BR in sheep and highlight it as a major candidate gene for improving adaptive capacities by genetic selection.

Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle

Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.

Genome-wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep

Sheep are considered as a major contributor of global food security. Moreover, sheep preweaning growth traits as well as in vivo carcass composition traits such as ultrasonic measurements of Longissimus dorsi muscle depth (UMD) and back-fat thickness (UFD) are crucially important indicators of meat yield and hot carcass composition. Despite their relative importance for productivity and profitability of a sheep production system, detected QTL for these traits are quite scarce. Therefore, we implemented GWAS for these traits using animal mixed model-based association approach provided by GenABEL in Esme sheep. Three genome-wide and 14 individual chromosome-wide associated SNPs were discovered. As a result, ESRP1, LOC105613082, ZNF641, DUSP5, TEAD1, SMOX, PTPRT, RALYL, POM121C, PHIP, LOC101106051, ZIM3, PEG3, TRPC7, FBXL4, LOC105610397, LOC105616489 and DNAAF2 were suggested as candidates. Some of the discovered genes and involved pathways were already annotated to contribute growth and development in various species including human, mice and cattle. All in all, the results of this study are expected to strongly contribute to shed a light on the underlying molecular mechanisms behind growth and carcass composition traits, with potential implications on studies aiming faster genetic improvement, targeted low-resolution SNP panel designs and genome-editing studies.

Analysis of selection signatures reveals important insights into the adaptability of high-altitude Indian sheep breed Changthangi

Changthangi is a high-altitude sheep breed of India that is adapted to cold and hypoxic climate of Himalayas. In the present study, we analysed population structure of Changthangi and contrasted it with selected Indian and European commercial sheep breeds to detect genomic regions under positive selection. The Illumina OvineSNP50v1 genotype data on 292 animals from seven different sheep breeds i.e., Changthangi (n = 29), Garole (n = 26), Deccani (n = 24), Tibetan (n = 37), Rambouillet (n = 102) and Australian Merino (n = 50) was used. European Mouflon (n = 24) was used as an out-group for studying the stratification and phylogenetic lineage. While the principal component analysis (PCA) revealed Changthangi to cluster with Tibetan sheep; TREEMIX and ADMIXTURE results also detected the introgression of lowland Indian sheep inheritance in Changthangi. Changthangi sheep were compared with other breed groups as reference i.e., commercial (Australian Merino and Rambouillet), Indian (Deccani, Garole and Tibetan) and breeds inhabiting plains (Australian Merino, Rambouillet, Deccani and Garole). Genomic comparisons of Changthangi using cross population extended haplotype homozygosity (XP-EHH) showed multiple functional regions present on Ovis aries (Oar) chromosomes 2, 3, 6 and 18 to be under selection in Changthangi sheep. These regions were related with adaptation to climatic and hypoxic stressors, fleece characteristics and functioning of immune and reproductive systems. UCP genes, associated with adaptation to cold and hypoxic conditions, were the main loci under positive selection in Changthangi sheep population. The selection signals in Indian and European commercial sheep breeds were mainly associated with body weight and carcass traits. Furthermore, selection signals found in different comparisons were found to be part of different quantitative trait loci (QTLs) associated with important traits in different breed classes. The genes present in these regions are suitable candidates for future studies on the genetic mechanisms underlying high-altitude adaptation.

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

Body size is an important indicator of growth and health in sheep. In the present study, we performed Genome-Wide Association Studies (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) associated with Hu sheep's body size. After genotyping parental (G1) and offspring (G2) generation of the nucleus herd for meat production of Hu sheep and conducting GWAS on the body height, chest circumference, body length, tail length, and tail width of the two groups, 5 SNPs associated with body height and 4 SNPs correlated with chest circumference were identified at the chromosomal significance level. No SNPs were significantly correlated to body length, tail length, and width. Four out of the 9 SNPs were found to be located within the 4 genes. KITLG and CADM2 are considered as candidate functional genes related to body height; MCTP1 and COL4A6 are candidate functional genes related to chest circumference. The 9 SNPs found in GWAS were verified using the G3 generation of the nucleus herd for meat production. Nine products were amplified around the 9 sites, and 29 SNPs were found; 3 mutation sites, G > C mutation at 134 bp downstream of s554331, T > G mutation at 19 bp upstream of s26859.1, and A > G mutation at 81 bp downstream of s26859.1, were significantly correlated to the body height. Dual-luciferase reporter gene experiments showed that the 3 SNPs could significantly impact dual-luciferase and gene transcription activity.

Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping

The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of 6 years (2006–2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities and repeatabilities within and across lactations were estimated, fitting parity, litter size, season of lambing and fortnights in milk, as fixed; and additive genetic, permanent environment within and across lactations, flock by test‐day interaction and residual as random effects. For the RHM analysis, the model included the same fixed and random effects as before, plus an additional regional genomic additive effect (specific for the region being tested) as random. While the whole genomic additive effect was estimated using the genomic relationship matrix (GRM) constructed from all SNPs, the regional genomic additive effect was estimated from a GRM matrix constructed from the SNPs within each region. Heritability estimates ranged between 0.06 and 0.15, with repeatabilities being between 0.14 and 0.24 across lactations and between 0.23 and 0.39 within lactation for all milk production traits. A substantial effect of flock‐test‐day on milk production traits was also estimated. Significant genomic regions at either genome‐wide (p < .05) or suggestive (i.e., one false positive per genome scan) level were identified on chromosome (OAR) 2, 3 and 20 for F% and on OAR3 for P%, with the regions on OAR3 in common between the two traits. Our results confirmed the role of LALBA and AQP genes, on OAR3, as candidate genes for milk production traits in sheep.

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits

Background

Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles.

Results

Whereas a relatively small number of molecular phenotypes were significantly heritable (h² > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles.

Conclusions

We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

BACKGROUND

Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available.

RESULTS

The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep).

CONCLUSIONS

We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

Genome-Wide Association Study of Weaning Traits in Lori-Bakhtiari Sheep

Weaning traits, including preweaning daily gain (PWDG) and weaning weight (WW) are important economic traits, especially for meat type mammals, with high impacts on growth performance and survival rate in higher ages. This study was conducted to perform a genome-wide association study (GWAS) on weaning traits in a meat type breed of sheep. Body weight records of 7557 Lori-Bakhtiari sheep with PWDG and WW records were used to estimate breeding values (EBVs) using an animal mixed model. A total of 132 animals were selected by two-tailed selection strategy, based on EBVs for body weight and then were genotyped using Illumina 50k Ovine SNP chip. After quality control, a total of 130 animals and 41323 SNPs were remained for further analyses. De-regressed estimates of breeding values were used as a pseudo-phenotype in GWAS analysis. Based on Bonferroni-adjusted p-values, five SNPs, located on chromosomes 2, 3, 4, 12 and 22 were significantly (p < 0.05) associated with weaning traits and accounted for 5.06% and 0.37% of total genetic variations of PWDG and WW, respectively. Two SNPs on chromosomes 2 and 3 were located near to previously reported QTLs for weaning traits. Three genes, including ANGPTL7, mTOR and WDR11, were found within 50 kbp distances from the significant SNPs and thus could be considered as candidate genes for weaning traits. The detected QTLs and candidate genes could be studied for construction of breeding programs for genetic improvement of growth performance in meat type sheep.

Genome-Wide Association Study of Body Weights in Hu Sheep and Population Verification of Related Single-Nucleotide Polymorphisms

Body weight (BW) is a critical economic trait for meat production in sheep. The current study aimed to perform a genome-wide association study (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) that are associated with BW in Hu sheep. The comparison and analysis of the G1 and G2 generations of a nucleus meat Hu sheep breeding herd revealed four SNPs identified by GWAS. The subsequent verification of the significant SNP loci in the Hu sheep G3 generation nucleus herd also detected nine SNPs in significant SNP regions. Two SNPs were significantly associated with the BW of Hu sheep (p < 0.05). OARX_76354330.1 and s64890.1 could be identified as functional SNPs for the growth traits of Hu sheep. CAPN6, as a candidate gene, was significantly different in the biceps femoris and longissimus dorsi muscles of weaning (60-day) and 6-month sheep, which facilitated the discovery of causal variants for BW and contributed to the marker-assisted selection breeding of Hu sheep.

Single nucleotide polymorphisms in the growth hormone receptor gene and Alu1 polymorphisms in the diacylglycerol acyltransferase 1 gene as related to meat production in sheep

Aim:

This study aimed to investigate the polymorphisms in genes related to meat production, including growth hormone receptor (GHR) and diacylglycerol acyltransferase 1 (DGAT1) genes, in different breeds of sheep, including Barki, Najdi, and Harri.

Materials and Methods:

Blood samples were collected from 75 randomly selected healthy Barki, Najdi, and Harri breeds of sheep, with 25 samples per breed. GHR and DGAT1 genes were identified using a single nucleotide polymorphism assay followed by digestion with the restriction enzyme Alu1.

Results:

The analysis of the GHR gene sequence showed nucleotide substitutions at nt 69 in exon 10 (c.69 G > A); this mutation is considered a transition mutation. The sequences of detected SNPs in the GHR gene in the different sheep breeds were submitted to the GenBank database with accession numbers MG906773 to MG906781. The substitutions at exon 10 (c.69 G > A) results in an alteration to the amino acid (p. Lysine > Arginine). At c.69, the A allele frequency was 0.61, 0.59, and 0.54, while the G allele frequency was 0.39, 0.41, and 0.46, for Barki, Najdi, and Harri breeds, respectively. The genotype AG at nt 69 locus had the highest frequency in the Najdi and Harri sheep. The frequency of AG was 0.62, 0.61, and 0.64, while the frequency of AA was 0.30, 0.28, and 0.22, for Barki, Najdi, and Harri sheep, respectively. After digestion with the restriction enzyme AluI, the DGAT1 locus had two genotypes, CC and CT. The highest frequency, 0.88, was found for allele C, which was detected in Barki breed. The lowest frequency, 0.75, for the same allele was found for Harri.

Conclusions:

The detected CT genotype may explain the moderate intramuscular fat content and muscle marbling in the Barki sheep breed.

Genome-Wide Association Study Using Fix-Length Haplotypes and Network Analysis Revealed New Candidate Genes for Nematode Resistance and Body Weight in Blackface Lambs

The objectives of this study were to identify genomic regions by Bayesian methods (BayesA, BayesB, or BayesN) that fit fixed-length haplotypes or SNPs using GenSel. Covariates for haplo-type alleles of five lengths (125, 250, 500 kb, 1 or 2 Mb) were generated, and rare haplotypes were removed at three thresholds (1, 5, or 10%). Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same across traits. Genotypes at 41,034 SNPs that were common on OvineSNP50 panel were phased for 751 Scottish Blackface (SBF) lambs. This is the first study to quantify the proportion of genetic variance using haplotypes across the whole genome in an SBF population. The genetic variance explained of haplotype-based GWAS was higher than that of SNP-based GWAS in across traits studied. In this population, fitting 500kb haplotypes with a 1% frequency threshold resulted in the highest proportion of genetic variance explained for nematode resistance and fitting 2Mb haplotypes with a 10% frequency threshold improved genetic variance explained for body weight comparable to fitting SNPs by BayesB. Candidate genes, including CXCR4, STAT4, CCL1, CCL2, CCL3, CCL5, CCL8, CCL16, CCL18, CARMIL2, and HSPA14 were identified for nematode resistance and ADH5, PPP3CA, and FABP4 for body weight traits. Network analysis provided annotation results linking to all identified candidate genes. This study supported previous results from GWAS of nematode resistance and body weight and revealed additional regions in the ovine genome associated with these economically important traits. These results suggest that network analysis can provide new information regarding biological mechanisms and genes leading to complex phenotypes, like nematode resistance and body weight of lamb.

Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Body weight is an important economic trait for sheep and it is vital for their successful production and breeding. Therefore, identifying the genomic regions and biological pathways that contribute to understanding variability in body weight traits is significant for selection purposes. In this study, the genome-wide associations of birth, weaning, yearling, and adult weights of 460 fine-wool sheep were determined using resequencing technology. The results showed that 113 single nucleotide polymorphisms (SNPs) reached the genome-wide significance levels for the four body weight traits and 30 genes were annotated effectively, including AADACL3, VGF, NPC1, and SERPINA12. The genes annotated by these SNPs significantly enriched 78 gene ontology terms and 25 signaling pathways, and were found to mainly participate in skeletal muscle development and lipid metabolism. These genes can be used as candidate genes for body weight in sheep, and provide useful information for the production and genomic selection of Chinese fine-wool sheep.

Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens

Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.

Recent advances in understanding genetic variants associated with growth, carcass and meat productivity traits in sheep (Ovis aries): an update

Identification of quantitative trait loci (QTLs) and candidate genes that affect growth intensity is a prerequisite for the marker-assisted selection of economically important traits. The number of QTL studies on sheep is relatively small in comparison to those on cattle and pigs. The current QTL sheep database - Sheep QTLdb - contains information on 1658 QTLs for 225 different traits. A few genes and markers associated with growth, carcass and meat productivity traits have been reported. The information about QTLs from the Sheep QTLdb cannot be directly used in marker-assisted selection due to the lack of essential information such as effective and reference alleles, the effect direction etc., and it requires manual curation and validation. In this study we performed a comprehensive search for QTLs focusing on single nucleotide polymorphisms (SNPs) associated with growth and meat traits in sheep. The database contains information about 156 SNP-trait associations (123 unique SNPs) and a list of 165 associated genes. The updated information is freely available at https://github.com/Defrag1236/Ovines_2018 (last access: 18 September 2019). This information can be useful for further association studies and preliminary estimation of genetic variability for economically important traits in different breeds.

Genome-wide association study reveals candidate genes associated with body measurement traits in Chinese Wagyu beef cattle

We performed a genome-wide association study to identify candidate genes for body measurement traits in 463 Wagyu beef cattle typed with the Illumina Bovine HD 770K SNP array. At the genome-wide level, we detected 18, five and one SNPs associated with hip height, body height and body length respectively. In total, these SNPs are within or near 11 genes, six of which (PENK, XKR4, IMPAD1, PLAG1, CCND2 and SNTG1) have been reported previously and five of which (CSMD3, LAP3, SYN3, FAM19A5 and TIMP3) are novel candidate genes that we found to be associated with body measurement traits. Further exploration of these candidate genes will facilitate genetic improvement in Chinese Wagyu beef cattle.

Identification of genomic regions and candidate genes of functional importance for gastrointestinal parasite resistance traits in Djallonké sheep of Burkina Faso

A total of 184 Djallonké lambs from Burkina Faso with phenotypes for packed-cell volume (PCV), log-transformed fecal egg count (lnFEC), and FAffa MAlan CHArt (FAMACHA©) eye scores were typed with the OvineSNP50 BeadChip of Illumina to contribute to the knowledge of the genetic basis of gastrointestinal (GIN) parasite resistance in sheep. Association analysis identified a total of 22 single-nucleotide polymorphisms (SNPs) related with PCV (6 SNPs), lnFEC (7), and FAMACHA scores (9) distributed among 14 Ovis aries chromosomes (OAR). The identified SNPs accounted for 18.76 % of the phenotypic variance for PCV, 21.24 % for lnFEC, and 34.38 % for FAMACHA scores. Analyses pointed out the importance of OAR2 for PCV, OAR3 for FAMACHA scores, and OAR6 for lnFEC. The 125 kb regions surrounding the identified SNPs overlapped with seven previously reported quantitative trait loci (QTLs) for the traits analyzed in the current work. The only chromosome harboring markers associated with the three traits studied was OAR2. In agreement with the literature, two different chromosomal areas on OAR2 can play a major role in the traits studied. Gene-annotation enrichment analysis allowed us to identify a total of 34 potential candidate genes for PCV (6 genes), lnFEC (4), and FAMACHA scores (24). Annotation analysis allowed us to identify one functional term cluster with a significant enrichment score (1.302). The cluster included five genes (TRIB3, CDK4, CSNK2A1, MARK1, and SPATA5) involved in immunity-related and cell-proliferation processes. Furthermore, this research suggests that the MBL2 gene can underlie a previously reported QTL for immunoglobulin A levels on OAR22 and confirms the importance of genes involved in growth and size (such as the ADAMTS17 gene on OAR18) for GIN resistance traits. Since association studies for the ascertainment of the genetic basis of GIN resistance may be affected by genotype-environment interactions, obtaining information from local sheep populations managed in harsh environments contributes to the identification of novel genomic areas of functional importance for GIN resistance for that trait.

Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris

The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G × E interaction (c2int ) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging) and 0.43 (productivity), and total genomic heritability accounted for large proportions (72% to ≈100%) of trait heritability. At the same probability threshold, three marker-trait associations were detected using GWAS, while RHM detected eight QTL encompassing 145 markers along five chromosomes. The proportion of genomic heritability explained by RHM was considerably higher (35.48 to 58.02) than that explained by GWAS (28.39 to 30.37). In general, RHM accounted for larger fractions of the additive genetic variance being captured by markers effects inside the defined regions. Nevertheless, a considerable proportion of the heritability is still missing (∼42% to ∼64%), probably due to LD between markers and genes and/or rare allele variants not sampled. RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.

A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep

Genomewide association study (GWAS) is an efficient tool for the detection of SNPs and candidate genes in quantitative traits. Growth rate is an important trait for increasing the meat production in sheep. A total of 96 Baluchi sheep were genotyped using Illumina Ovine SNP50 BeadChip to run a GWAS for an average daily gain (ADG) and Kleiber ratio (KR) traits in different periods of age in sheep. Traits included were average daily gain from birth to three months (ADG_0-3), from three months to six months (ADG_3-6), from six months to nine months (ADG_6-9), from nine months to yearling (ADG_9-12), from birth to six months (ADG_0-6), from three months to nine months (ADG_3-9), from three months to yearling (ADG_3-12) and corresponding Kleiber ratios (KR_0-3, KR_3-6, KR_6-9, KR_9-12, KR_0-6, KR_3-9 and KR_3-12, respectively). A total of 42,243 SNPs passed the quality-control filters and were analysed by PLINK software in a linear mixed model. Two SNPs were identified on two chromosomes at the 5% genomewide significance level for KR(3-9) and KR(6-9). Two candidate genes, namely MAGI1 and ZNF770, were identified correspondingly harbouring and close to these QTL. Also, a total of 21 SNPs were found on chromosomes 2, 3, 5, 6, 7, 10, 17, 19, 20 and 25 at the 5% chromosomewide significance level for ADG and KR traits. Thus, we suggest more studies to discover the causative variants for growth traits in sheep.

Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep

Background

One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs.

Results

Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species (“selection hotspots”) including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds.

Conclusions

Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4447-x) contains supplementary material, which is available to authorized users.

Expression analyses of candidate genes related to meat quality traits in squabs from two breeds of meat-type pigeon

In this study, meat quality traits were compared between squabs from two pigeon breeds: one Chinese indigenous breed, the Shiqi (SQ) meat-type pigeon, and an imported breed, the white king (WK) meat-type pigeon. Breed differences were detected in the content of intramuscular fat (IMF) in the breast muscle. SQ squabs had significantly higher IMF content than the WK birds. The shear force value (an objective measure of meat tenderness) of SQ birds was also relatively lower than that of the WK squabs. Further analysis of fatty acids profile revealed that SQ squabs exhibited significant advantage in the synthesis of polyunsaturated fatty acids, while WK squabs were significantly higher in the sum of monounsaturated fatty acids. Breast muscle in the SQ squabs was also significantly higher in the ratio of polyunsaturated fatty acids to saturated fatty acids, as well as the sum of omega 6 fatty acids. Variability of expression levels of functional genes in relation to fat accumulation and meat tenderness was analysed by qRT-PCR. Gene expression analyses showed that the hepatic expression of LPL (lipoprotein lipase), FABP4 (fatty acid-binding protein 4), and CAPN2 (calpain-2) were significantly higher in the SQ squabs. In the breast muscle tissue, the FABP3 (fatty acid-binding protein 3) and CAPN2mRNA abundance was significantly higher in SQ squabs. Our results suggested that these differentially expressed genes might be candidate genes used in the programmes of targeted selection for squabs with higher IMF content, tender meat, and more favourable fatty acids composition.

Association analysis for udder index and milking speed with imputed whole-genome sequence variants in Nordic Holstein cattle

Genome-wide association testing facilitates the identification of genetic variants associated with complex traits. Mapping genes that promote genetic resistance to mastitis could reduce the cost of antibiotic use and enhance animal welfare and milk production by improving outcomes of breeding for udder health. Using imputed whole-genome sequence variants, we carried out association studies for 2 traits related to udder health, udder index, and milking speed in Nordic Holstein cattle. A total of 4,921 bulls genotyped with the BovineSNP50 BeadChip array were imputed to high-density genotypes (Illumina BovineHD BeadChip, Illumina, San Diego, CA) and, subsequently, to whole-genome sequence variants. An association analysis was carried out using a linear mixed model. Phenotypes used in the association analyses were deregressed breeding values. Multitrait meta-analysis was carried out for these 2 traits. We identified 10 and 8 chromosomes harboring markers that were significantly associated with udder index and milking speed, respectively. Strongest association signals were observed on chromosome 20 for udder index and chromosome 19 for milking speed. Multitrait meta-analysis identified 13 chromosomes harboring associated markers for the combination of udder index and milking speed. The associated region on chromosome 20 overlapped with earlier reported quantitative trait loci for similar traits in other cattle populations. Moreover, this region was located close to the FYB gene, which is involved in platelet activation and controls IL-2 expression; FYB is a strong candidate gene for udder health and worthy of further investigation.

High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds

BACKGROUND

With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.

RESULTS

Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.

CONCLUSIONS

Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry

Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Their lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust production performance even in the presence of drug-resistant gastrointestinal nematodes, a rising concern to the industry. Despite the growing importance of hair sheep in the Americas their genetic origins have remained speculative. Prior to this report no genetic studies were able to identify a unique geographical origin of hair sheep in the New World. Our study clarifies the African and European ancestry of Caribbean hair sheep. Whole-genome structural analysis was conducted on four established breeds of hair sheep from the Caribbean region. Using breeds representing Africa and Europe we establish an objective measure indicating Caribbean hair sheep are derived from Iberian and West African origins. Caribbean hair sheep result from West African introgression into established ecotypes of Iberian descent. Genotypes from 47,750 autosomal single nucleotide polymorphism markers scored in 290 animals were used to characterize the population structure of the St. Croix, Barbados Blackbelly, Morada Nova, and Santa Ines. Principal components, admixture, and phylogenetic analyses results correlate with historical patterns of colonization and trade. These patterns support co-migration of these sheep with humans.

Antagonistic genetic correlations for milking traits within the genome of dairy cattle

Genome-wide association studies can be applied to identify useful SNPs associated with complex traits. Furthermore, regional genomic mapping can be used to estimate regional variance and clarify the genomic relationships within and outside regions but has not previously been applied to milk traits in cattle. We applied both single SNP analysis and regional genomic mapping to investigate SNPs or regions associated with milk yield traits in dairy cattle. The de-regressed breeding values of three traits, total yield (kg) of milk (MLK), fat (FAT), and protein (PRT) in 305 days, from 2,590 Holstein sires in Japan were analyzed. All sires were genotyped with 40,646 single-nucleotide polymorphism (SNP) markers. A genome-wide significant region (P < 0.01) common to all three traits was identified by regional genomic mapping on chromosome (BTA) 14. In contrast, single SNP analysis identified significant SNPs only for MLK and FAT (P < 0.01), but not PRT in the same region. Regional genomic mapping revealed an additional significant region (P < 0.01) for FAT on BTA5 that was not identified by single SNP analysis. The additive whole-genomic effects estimated in the regional genomic mapping analysis for the three traits were positively correlated with one another (0.830–0.924). However, the regional genomic effects obtained by using a window size of 20 SNPs for FAT on BTA14 were negatively correlated (P < 0.01) with the regional genomic effect for MLK (–0.940) and PRT (–0.878). The BTA14 regional effect for FAT also showed significant negative correlations (P < 0.01) with the whole genomic effects for MLK (–0.153), FAT (–0.172), and PRT (–0.181). These negative genomic correlations between loci are consistent with the negative linkage disequilibrium expected for traits under directional selection. Such antagonistic correlations may hamper the fixation of the FAT increasing alleles on BTA14. In summary, regional genomic mapping found more regions associated with milk production traits than did single SNP analysis. In addition, the existence of non-zero covariances between regional and whole genomic effects may influence the detection of regional effects, and antagonistic correlations could hamper the fixation of major genes under intensive selection.

Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed

BACKGROUND

Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene.

RESULTS

Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes.

CONCLUSIONS

Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.

Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle

Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study.

Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus

Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K. Total genomic heritabilities accounted for large proportions (64-89%) of pedigree-based trait heritabilities, providing additional evidence that complex traits in eucalypts are controlled by many sequence variants across the frequency spectrum, each with small contributions to the phenotypic variance. RHM detected 26 quantitative trait loci (QTLs) encompassing 2191 single nucleotide polymorphisms (SNPs), whereas GWAS detected 13 single SNP-trait associations. RHM and GWAS QTLs individually explained 5-15% and 4-6% of the genomic heritability, respectively. RHM was superior to GWAS in capturing larger proportions of genomic heritability. Equated to previously mapped QTLs, our results highlighted genomic regions for further examination towards gene discovery. RHM-QTLs bearing a combination of common and rare variants could be useful enhancements to incorporate prior knowledge of the underlying genetic architecture in genomic prediction models.