Genotyping BeadChip Research Articles

Novel pathways linked to the expression of temperament in Merino sheep: a genome-wide association study

Animal temperament refers to the inherent behavioural and emotional characteristics of an animal, influencing how it interacts with its environment. The selection of sheep for temperament can change the temperament traits of the selected line and improve the welfare and production (reproduction, growth, immunity) of those animals. To understand the genetics that underly variation in temperament in sheep, and how selection on temperament can affect other production traits, a genome-wide association study was carried out. Merino sheep from lines selected for traits of calm and nervous temperament, and a commercial population, on which the temperament traits had never been assessed, were used. Blood samples from the three populations were genotyped using an Illumina GGP Ovine 50 K Genotyping BeadChip. The calm and nervous populations in the selected lines presented as distinct genetic populations, and 2 729 of the 45 761 single nucleotide polymorphisms (SNPs) had significantly different proportions between the two lines. Of those 2 729 SNPs, 2 084 were also associated with temperament traits in the commercial population. A genomic annotation identified 81 candidate genes for temperament, nearly half of which are associated with disorders of social behaviour in humans. Five of those 81 candidate genes are related to production traits in sheep. Two genes were associated with personality disorders in humans and with production traits in sheep. We identified significant enrichment in genes involved in nervous system processes such as the regulation of systemic arterial blood pressure, ventricular myocyte action, multicellular organismal signalling, ion transmembrane transport, and calcium ion binding, suggesting that temperament is underpinned by variation in multiple biological systems. Our results contribute to understanding of the genetic basis of animal temperament which could be applied to the genetic evaluation of temperament in sheep and other farm animals.

Genome-wide association study for morphological and hunting-behavior traits in Braque Français Type Pyrénées dogs: A preliminary study

High-throughput genotyping offers great potential to increase our understanding of the genomic basis of canid variation. Braque Français Type Pyrénées (BRA) are smart, agile, and friendly dogs originally developed for tracking, hunting, and retrieving feathered game. On a population of 44 unrelated BRA dogs, single nucleotide polymorphism (SNP) genotype data from the CanineHD Whole-Genome Genotyping BeadChip and evaluation scores for 12 traits related to morphology and hunting performance were available. After quality filtering, 95,859 SNPs on the 38 dog autosomes (CFA) were retained. Phenotypic scores were expressed on a scale from 1 (worst) to 6 (best) and were mostly poorly to moderately correlated except for some morphological traits (e.g. r = 0.81 between the conformation of the head and that of the eye). From GWAS, a total of 378 SNP-phenotype associations with posterior odds of association > 1 have been detected. The strongest associations were found for the eye conformation, for the skull/muzzle ratio, and for connection to the hunter. These included both new and previously identified markers and genes potentially involved with type and behavior traits in BRA. Six of the significant markers mapped within SETDB2, a gene known to be related to pointing behavior in dogs. These results advance our understanding of the genetic basis for morphology and hunting behavior in dogs and identify new variants which are potential targets for further research.

Identification of genes associated with color characteristics of meat and fat tissue of aberdeen-angus cattle

Currently, full genome association studies and identification of candidate genes for economically useful traits in farm animals are topical, scientifically sound and practice-oriented, and fulfill one of the objectives of the Strategy for Scientific and Technical Development of the Russian Federation. This article presents the results of GWAS on color spectral values of meat and fat tissue of Aberdeen-Angus cattle, known for its meat characteristics of high grade. The animals were genotyped on high-density BovineHD Genotyping BeadChip chips containing ≈53,000 SNPs. After quality control, 39,928 remained. By analysis and structural annotation, 25 and 26 candidate genes for meat and fat color were identified, respectively. According to functional annotation, the genes were categorized into 6 groups: nervous system functions, organ development, vascular, joints, metabolic processes and biosynthesis, cellular processes, muscle, tissue and bone, reproduction and embryonic development. The obtained genes were checked through the Animal QTL database, as a result of which 13 genes were confirmed, of which 3 were localized SNPs, in connection with which the LRP2, SCIN and ANTXR1 genes have advantages for their further application in the molecular diagnostics of cattle not only meat, but also dairy productivity.

The symptomatology of Attention-Deficit/Hyperactivity Disorder and the genetic control of vitamin D levels.

Vitamin D deficiency has been associated with psychiatric disorders and behavioral phenotypes such as Attention-Deficit/Hyperactivity Disorder (ADHD). Considering that vitamin D levels are polygenic, we aim to evaluate the overall effects of its genetic architecture on symptoms of inattention, hyperactivity, and impulsivity and on the serum levels of vitamin D in two independent samples of adults, as well as the specific effects of five relevant polymorphisms in vitamin D-related genes. We evaluated 870 subjects from an ADHD sample (407 cases and 463 controls) and 319 subjects from an academic community (nutrigenetic sample). Vitamin D serum levels were obtained through Elisa test and genetic data by TaqMan™ allelic discrimination and Infinium PsychArray-24 BeadChip genotyping. Polygenic Scores (PGS) were calculated on PRSice2 based on the latest GWAS for Vitamin D and statistical analyses were conducted at Plink and SPSS software. Vitamin D PGSs were associated with inattention in the ADHD sample and with hyperactivity when inattention symptoms were included as covariates. In the nutrigenetic sample, CYP2R1 rs10741657 and DHCR7 rs12785878 were nominally associated with impulsivity and hyperactivity, respectively, and both with vitamin D levels. In the clinical sample, RXRG rs2134095 was associated with impulsivity. Our findings suggest a shared genetic architecture between vitamin D levels and ADHD symptoms, as evidenced by the associations observed with PGS and specific genes related to vitamin D levels. Interestingly, differential effects for vitamin D PGS were found in inattention and hyperactivity, which should be considered in further studies involving ADHD.

Advances in understanding the genetic architecture of antibody response to paratuberculosis in sheep by heritability estimate and LDLA mapping analyses and investigation of candidate regions using sequence-based data

BackgroundParatuberculosis is a contagious and incurable disease that is caused by Mycobacterium avium subsp. paratuberculosis (MAP) with significant negative effects on animal welfare and farm profitability. Based on a large naturally infected flock over 12 years, we analyzed repeated enzyme-linked immunosorbent assay tests (ELISA), OvineSNP50 BeadChip genotypes and whole-genome sequences imputed from 56 influential animals. The main goals were to estimate the genetic parameters of proxy traits for resistance to MAP, identify genomic regions associated with the host’s immune response against MAP and search for candidate genes and causative mutations through association and functional annotation analyses of polymorphisms identified by sequencing.ResultsTwo variables were derived from ELISA tests. The first, a binary variable, assessed the infection status of each animal over the entire productive life, while the second considered the level of antibody recorded over time. Very similar results were obtained for both variables. Heritability estimates of about 0.20 were found and a significant region capturing 18% and 13% of the genetic variance was detected on ovine chromosome 20 by linkage disequilibrium and linkage analysis on OvineSNP50 positions. Functional annotation and association analyses on the imputed sequence polymorphisms that were identified in this region were carried out. No significant variants showed a functional effect on the genes that mapped to this region, most of which belong to the major histocompatibility complex class II (MHC II). However, the conditional analysis led to the identification of two significant polymorphisms that can explain the genetic variance associated with the investigated genomic region.ConclusionsOur results confirm the involvement of the host’s genetics in susceptibility to MAP in sheep and suggest that selective breeding may be an option to limit the infection. The estimated heritability is moderate with a relevant portion being due to a highly significant region on ovine chromosome 20. The results of the combined use of sequence-based data and functional analyses suggest several genes belonging to the MHC II as the most likely candidates, although no mutations in their coding regions showed a significant association. Nevertheless, information from genotypes of two highly significant polymorphisms in the region can enhance the efficiency of selective breeding programs.

Search for Candidate Genes for Live Weight in Southern Meat Breed Sheep

The paper presents the results of candidate genes search for live weight is southern meat sheep breed. The sample of 48 ewes weighed in the age of 24 months and elder was genotyped on Ovine SNP 50 Genotyping BeadChip array. Using a fixation in dices method (Fst), wedetected 55 polymorphisms associated with live weight. 10 SNP swith the highest Fst value were selected to check the effect on the trait under investigation. All the candidate genes showed the association witht helive weight trait. It’s interesting to not ethatin the NDFIP1 gene there were detected two significant SNPs with a high Fst value.

Genome-wide runs of homozygosity in Indian goat breeds reared under small holder production system

Small holder goat production system is often constrained by high inbreeding due to small herd size and uncontrolled breeding. Runs of homozygosity (ROH), the long stretches of homozygous genomic DNA is the most reliable measure of autozygosity. The objective of present study was to investigate the number and coverage of ROH in the genome and to estimate the genomic inbreeding coefficient (FROH) in two divergent Indian goat breeds viz; Attappady Black and Malabari goats farmed under small holder production system. The genome-wide single nucleotide polymorphism (SNP) marker data obtained by Illumina SNP50 goat BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats) sampled from farmers flock in their respective breeding tract was utilised for ROH detection. The ROH of > 1 Mb was defined as tracts of homozygous genotypes with at least 15 SNPs and less than five missing SNPs. The ROH detection was carried out with PLINK 1.9 version. The proportion of goats lacking ROH (per cent) was 66.67 in Attappady Black and 39.13 in Malabari goats. The mean number and length of ROH of 1 Mb or more was higher in Malabari goats (2.1304 ± 0.6369 and 6.0016 ± 0.5271 Mb) compared to Attappady Black goats (0.4583 ± 0.1343 and 4.0197 ± 0.3755 Mb). Mean ± S.E of sum of ROH coverage of genome per individual (SROH) was 1.8423 ± 0.05976 and 8.8236 ± 1.2785 Mb in Attappady Black and Malabari goats, respectively and differed among the two breeds significantly (p ≤ 0.05). Analysis of the distribution of ROH according to their length showed that majority of the detected ROH were < 8 Mb in length in both breeds with no ROH of > 8 Mb in Attappady Black goats. Mean ± S.E of genomic inbreeding coefficient (FROH≥1 Mb) in per cent was 0.519 ± 0.19 and 0.07480 ± 0.0243 in Malabari goats and Attappady Black goats, respectively. The pattern of ROH estimated in the present analysis indicates the inbreeding history of the goats farmed under small holder production system. Results of present study indicate that both breeds are less consanguineous and showed no evidence of recent inbreeding.

The novel candidate genes related to live weight trait in southern meat sheep breed revealed by genome-wide genotyping

The study of the local sheep breeds’ genetic architecture is an important step on the way to preserve their gene pool. The aim of our work was to identify candidate genes associated with the live weight trait in adult southern meat breed sheep. This breed has high productivity, but is under threat of a critical decrease in genetic diversity due to a small number. The live weight of farm animals is one of the key breeding indicators. This quantitative trait is polygenic and breed specific as it has been shown by a number of authors. Animals were genotyped on the Illumina Ovine SNP50 Genotyping Bead Chip assay using standard procedures. Results in quality control, statistics and visualization were carried out in Rstudio 2023.03.0 and plink1.9. Genotyped animals were divided into two groups according to the case/control principle with differences in live weight between representatives of groups of 25–30 kg. Significant genetic variants were determined by the fixation indices method. Further analysis of significant variants (in intron positions) was performed in Ensembl genomic browser and revealed candidate genes localized in chromosomes 5, 6, 12, 20. The statistical analysis of live mass showed significant differences of the studied trait in different genotypes on four genes. The candidate genes identified can be recommended for using as genetic markers, their study could improve the productivity of southern meat sheep breed and help to preserve its gene pool.

Linkage disequilibrium and effective population size in Indian goat breeds

Genomic linkage disequilibrium (LD) is an important population diversity measure and an indicator determining the efficacy of genomic applications. The present population genomic study was carried out to comprehensively characterise the extent and pattern of LD in the two divergent Indian goat breeds namely, Attappady Black and Malabari goats reared under small holder production system. The LD was estimated using genome-wide single nucleotide polymorphism (SNP) marker data obtained by Illumina SNP50 goat BeadChip genotyping. The LD between adjacent SNPs across all autosomes measured as correlation coefficient (r2) in the studied population was low and mean ± standard deviation of LD were 0.0657 ± 0.0921 and 0.0661 ± 0.0911 for Attappady Black and Malabari goats, respectively. The LD varied significantly (p < 0.0001) among chromosomes, interaction between chromosome and breed and among marker intervals. The LD (r2) of 0.2 and 0.3 were extended up to 20 kb and 10 kb marker intervals, respectively. Based on the genomic data, Ne was estimated as 512.8198 in Malabari and 371.2220 in Attappady Black goats at 17 generations back. The weak LD observed in Indian goat breeds indicates increased diversity of these Indian goat breeds and also implies that denser SNP panel might be more beneficial for genomic applications.

Characterization of Danube Swabian population samples on a high-resolution genome-wide basis

BackgroundGerman-derived ethnicities are one of the largest ethnic groups in Hungary, dating back to the formation of the Kingdom of Hungary, which took place at the beginning of the 11th century. Germans arrived in Hungary in many waves. The most significant immigration wave took place following the collapse of the Ottoman Empire in East-Central Europe which closed the 150 year long Ottoman occupation. To date, there are no comprehensive genome-wide studies investigating the genetic makeup of the Danube Swabians. Here we analyzed 47 Danube Swabian samples collected from elderly Swabian individuals living in the Dunaszekcső-Bár area, in Danube side villages of Southwest Hungary. These Swabians, according to self-declaration, did not admix with other ethnic groups for 3–6 succeeding generations. Using Illumina Infinium 720 K Beadchip genotype data, we applied allele frequency-based and haplotype-based genome-wide marker data analyses to investigate the ancestry and genetic composition of the collected Danube Swabian samples.ResultsHaplotype-based analyses like identity by descent segment analysis show that the investigated Danube Swabians possess significant German and other West European ancestry, but their Hungarian ancestry is also prominent. Our results suggest that their main source of ancestry can be traced back to Western Europe, presumably to the region of Germany.ConclusionThis is the first analysis of Danube Swabian population samples based on genome-wide autosomal data. Our results establish the basis for conducting further comprehensive research on Danube Swabians and on other German ethnicities of the Carpathian basin, which can help reconstruct their origin, and identify their major archaic genomic patterns.

An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs.

Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16-26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.

Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert

The southern margin of the Taklimakan Desert is characterized by low rainfall, heavy sandstorms, sparse vegetation and harsh ecological environment. The indigenous sheep in this area are rich in resources, with the advantages of perennial estrus and good resistance to stress in most sheep. Exploring the molecular markers of livestock adaptability in this environment will provide the molecular basis for breeding research to cope with extreme future changes in the desert environment. In this study, we analyzed the population genetic structure and linkage imbalance of five sheep breeds with three different agricultural geographic characteristics using four complementary genomic selection signals: fixation index (FST), cross-population extended haplotype homozygosity (xp-EHH), Rsb (extended haplotype homozygosity between-populations) and iHS (integrated haplotype homozygosity score). We used Illumina Ovine SNP 50K Genotyping BeadChip Array, and gene annotation and enrichment analysis were performed on selected regions of the obtained genome. The ovary of Qira Black sheep (Follicular phase, Luteal phase, 30th day of pregnancy, 45th day of pregnancy) was collected, and the differentially expressed genes were screened by transcriptomic sequencing. Genome-wide selective sweep results and transcriptome data were combined for association analysis to obtain candidate genes associated with perennial estrus and stable reproduction. In order to verify the significance of the results, 15 resulting genes were randomly selected for fluorescence quantitative analysis. The results showed that Dolang sheep and Qira Black sheep evolved from Kazak sheep. Linkage disequilibrium analysis showed that the decay rate of sheep breeds in the Taklimakan Desert was higher than that in Yili grassland. The signals of FST, xp-EHH, Rsb and iHS detected 526, 332, 308 and 408 genes, respectively, under the threshold of 1% and 17 overlapping genes under the threshold of 5%. A total of 29 genes were detected in association analysis of whole-genome and transcriptome data. This study reveals the genetic mechanism of perennial estrus and environmental adaptability of indigenous sheep breeds in the Taklimakan Desert. It provides a theoretical basis for the conservation and exploitation of genetic resources of indigenous sheep breeds in extreme desert environment. This provides a new perspective for the quick adaptation of sheep and other mammals to extreme environments and future climate changes.

Genome-Wide Association Study for Lactation Performance in the Early and Peak Stages of Lactation in Holstein Dairy Cows.

Simple SummaryAlthough genome-wide association studies (GWAS) have been carried out within a variety of cattle breeds, they are mainly based on the accumulated 305-day lactation yield traits estimated by summing the test-day recorded every day during the lactation period, or combining the weekly or monthly test-day records by linear interpolation. Since the additive genetic variance for milk yield and composition changes during lactation, the genetic effects of QTL related to these traits are not constant during the lactation period. Therefore, a better understanding of the genetic architecture of milk production traits in different lactation stages (e.g., beginning, peak, and end stages of lactation) is needed. The aim of this study was to detect genomic loci associated with lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. Based on the results of this study, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.This study aimed to detect genomic loci associated with the lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Daily milk yield (MY), fat yield (FY), and protein yield (PY) during 9 to 50 DIM were recorded on 134 multiparous Holstein dairy cows distributed in four research herds. Fat- and protein-corrected milk (FPCM), fat-corrected milk (FCM), and energy-corrected milk (ECM) were predicted. The records collected during 9 to 25 DIM were put into the early stage of lactation (EARLY) and those collected during 26 to 50 DIM were put into the peak stage of lactation (PEAK). Then, the mean of traits in each cow included in each lactation stage (EARLY and PEAK) were estimated and used as phenotypic observations for the genome-wide association study. The included animals were genotyped with the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA, USA) for a total of 777,962 single nucleotide polymorphisms (SNPs). After quality control, 585,109 variants were analyzed using GEMMA software in a mixed linear model. Although there was no SNP associated with traits included at the 5% genome-wide significance threshold, 18 SNPs were identified to be associated with milk yield and composition at the suggestive genome-wide significance threshold. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. This suggests that differential sets of candidate genes underlie the phenotypic expression of the considered traits in the EARLY and PEAK stages of lactation. Although further functional studies are needed to validate our findings in independent populations, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.

Genomic analysis of 10 years of artificial selection in community-based breeding programs in two Ethiopian indigenous sheep breeds.

In recent times, community-based breeding programs (CBBPs) have been advocated as the best strategy for genetic improvement of local breeds in smallholder farms in developing countries. Since 2009, CBBPs have been implemented for Ethiopian Bonga and Menz sheep to improve growth rates resulting in significant genetic gains in 6-month weights. With the hypothesis that selection could be impacting their genomes, we systematically screened for possible genome changes in the two breeds by analyzing 600K BeadChip genotype data of 151 individuals (with the highest breeding values for 6-month weights) from CBBP flocks against 98 individuals from non-CBBP flocks. We observed no differences in genetic diversity and demographic dynamics between CBBP and non-CBBP flocks. Selection signature analysis employing ROH, logistic regression genome-wide association study , FST , XP-EHH and iHS revealed 5 (Bonga) and 11 (Menz) overlapping regions under selection, that co-localized with QTLs for production (body size/weight, growth, milk yield), meat/milk quality, and health/parasite resistance, suggesting that the decade-long selection has likely started to impact their genomes. However, genome-wide genetic differentiation between the CBBP and non-CBBP flocks is not yet clearly evident.

An inherited night blindness in Wiltshire sheep.

Twelve cases of adult-onset blindness were identified in a flock of 130 polled Wiltshire sheep in New Zealand over a 3-year period. Affected sheep developed night blindness between 2 and 3 years of age, which progressed to complete blindness by 4 to 5 years of age. Fundic examination findings included progressive tapetal hyperreflectivity and attenuation of retinal blood vessels. Histologically, the retinas had a selective loss of rod photoreceptors with initial preservation of cone photoreceptors. Retinal degeneration was not accompanied by any other ocular or central nervous system abnormalities, and pedigree analysis suggested an inherited basis for the disease. Mating an affected Wiltshire ram to 2 affected Wiltshire ewes resulted in 6 progeny that all developed retinal degeneration by 2 years of age, while mating of the same affected ram to 6 unaffected ewes resulted in 8 unaffected progeny, consistent with autosomal recessive inheritance. Homozygosity mapping of 5 affected Wiltshire sheep and 1 unaffected Wiltshire sheep using an OvineSNP50 Genotyping BeadChip revealed an identical-by-descent region on chromosome 5, but none of the genes within this region were considered plausible candidate genes. Whole-genome sequencing of 2 affected sheep did not reveal any significant mutations in any of the genes associated with retinitis pigmentosa in humans or progressive retinal atrophy in dogs. Inherited progressive retinal degeneration affecting rod photoreceptors has not been previously reported in sheep, but this disease has several similarities to inherited retinal dystrophies in other species.

Association of low-frequency and rare coding variants with information processing speed

Measures of information processing speed vary between individuals and decline with age. Studies of aging twins suggest heritability may be as high as 67%. The Illumina HumanExome Bead Chip genotyping array was used to examine the association of rare coding variants with performance on the Digit-Symbol Substitution Test (DSST) in community-dwelling adults participating in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. DSST scores were available for 30,576 individuals of European ancestry from nine cohorts and for 5758 individuals of African ancestry from four cohorts who were older than 45 years and free of dementia and clinical stroke. Linear regression models adjusted for age and gender were used for analysis of single genetic variants, and the T5, T1, and T01 burden tests that aggregate the number of rare alleles by gene were also applied. Secondary analyses included further adjustment for education. Meta-analyses to combine cohort-specific results were carried out separately for each ancestry group. Variants in RNF19A reached the threshold for statistical significance (p = 2.01 × 10−6) using the T01 test in individuals of European descent. RNF19A belongs to the class of E3 ubiquitin ligases that confer substrate specificity when proteins are ubiquitinated and targeted for degradation through the 26S proteasome. Variants in SLC22A7 and OR51A7 were suggestively associated with DSST scores after adjustment for education for African-American participants and in the European cohorts, respectively. Further functional characterization of its substrates will be required to confirm the role of RNF19A in cognitive function.

Validation of the Prediction Accuracy for 13 Traits in Chinese Simmental Beef Cattle Using a Preselected Low-Density SNP Panel.

Simple SummaryTo reduce the breeding costs and promote the application of genomic selection (GS) in Chinese Simmental beef cattle, we developed a customized low-density single-nucleotide polymorphism (SNP) panel consisting of 30,684 SNPs. When comparing the predictive performance of the low-density SNP panel to that of the BovineHD Beadchip for 13 traits, we found that this ~30 K panel achieved moderate to high prediction accuracies for most traits, while reducing the prediction accuracies of six traits by 0.04–0.09 and decreasing the prediction accuracy of one trait by 0.2. For the remaining six traits, the usage of the low-density SNP panel was associated with a slight increase in prediction accuracy. Our studies suggested that the low-density SNP panel (~30 K) is a feasible and promising tool for cost-effective genomic prediction in Chinese Simmental beef cattle, which may provide breeding organizations with a cheaper option and greater returns on investment.Chinese Simmental beef cattle play a key role in the Chinese beef industry due to their great adaptability and marketability. To achieve efficient genetic gain at a low breeding cost, it is crucial to develop a customized cost-effective low-density SNP panel for this cattle population. Thirteen growth, carcass, and meat quality traits and a BovineHD Beadchip genotyping of 1346 individuals were used to select trait-associated variants and variants contributing to great genetic variance. In addition, highly informative SNPs with high MAF in each 500 kb sliding window and in each genic region were also included separately. A low-density SNP panel consisting of 30,684 SNPs was developed, with an imputation accuracy of 97.4% when imputed to the 770 K level. Among 13 traits, the average prediction accuracy levels evaluated by genomic best linear unbiased prediction (GBLUP) and BayesA/B/Cπ were 0.22–0.47 and 0.18–0.60 for the ~30 K array and BovineHD Beadchip, respectively. Generally, the predictive performance of the ~30 K array was trait-dependent, with reduced prediction accuracies for seven traits. While differences in terms of prediction accuracy were observed among the 13 traits, the low-density SNP panel achieved moderate to high accuracies for most of the traits and even improved the accuracies for some traits.

The Nero Lucano Pig Breed: Recovery and Variability.

Simple SummaryThe reduction of biodiversity determines the loss of species and breeds, with the consequent disappearance of production systems, knowledge, cultures and local traditions. The Nero Lucano pig is a native breed of Southern Italy (Basilicata region) recovered, starting from 2001, because of the high quality of its cured meat products. This study gives a picture of the low genetic variability of this breed. Knowledge of individual inbreeding levels allows for planning of interventions to reduce the negative effects of the low effective population size and, then, improve the efficiency of the actual recovery project.The Nero Lucano (NL) pig is a black coat colored breed characterized by a remarkable ability to adapt to the difficult territory and climatic conditions of Basilicata region in Southern Italy. In the second half of the twentieth century, technological innovation, agricultural evolution, new breeding methods and the demand for increasingly lean meat brought the breed almost to extinction. Only in 2001, thanks to local institutions such as: the Basilicata Region, the University of Basilicata, the Regional Breeders Association and the Medio Basento mountain community, the NL pig returned to populate the area with the consequent possibility to appreciate again its specific cured meat products. We analyzed the pedigrees recorded by the breeders and the Illumina Porcine SNP60 BeadChip genotypes in order to obtain the genetic structure of the NL pig. Results evidenced that this population is characterized by long mean generation intervals (up to 3.5 yr), low effective population size (down to 7.2) and high mean inbreeding coefficients (FMOL = 0.53, FROH = 0.39). This picture highlights the low level of genetic variability and the critical issues to be faced for the complete recovery of this population.

Functional characterization of Copy Number Variations regions in Djallonké sheep.

A total of 184 Djallonké (West African Dwarf) sheep of Burkina Faso were analysed for Copy Number Variations (CNV) using Ovine 50K SNP BeadChip genotyping data and two different CNV calling platforms: PennCNV and QuantiSNP. Analyses allowed to identify a total of 63 candidate Copy Number Variations Regions (CNVR) on 11 different ovine chromosomes covering about 82.5Mb of the sheep genome. Gene-annotation enrichment analysis allowed to identify a total of 751 potential candidate ovine genes located in the candidate CNVR bounds. Functional annotation allowed to identify five statistically significant Functional Clusters (FC; enrichment factor >1.3) involving 61 candidate genes. All genes forming significantly enriched FC were located on ovine chromosome (OAR) 21. FC1 (22 genes including PAG4 and PAG6) and FC5 (three genes: CTSC, CTSW and CTSF), coding proteases (peptidases and cathepsins, respectively), were involved in reproductive performance and modulation of gestation. Both FC3 and FC4 were involved in inflammatory and immunologic response through coding serum amyloid A and B-box-type zinc finger proteins, respectively. Finally, FC2 consisted of 27 genes (including OR10G6 and OR8B8) involved in olfactory receptor activity, key for animals adapting to new food resources. CNVR identified on at least 15% of individuals were considered CNVR hotspots and further overlapped with previously reported quantitative trait loci (QTL). CNVR hotspots spanning genes putatively involved with lipid metabolism (SKP1, TCF7, JADE2, UBE2B and SAR1B) and differential expression in mammary gland (SEC24A and CDKN2AIPNL) on OAR5 and dairy traits (CCDC198 and SLC35F4) on OAR7 overlapped with QTL associated with lipid metabolism, milk protein yield and milk fat percentage. Information obtained from local sheep populations naturally adapted to harsh environments contributes to increase our understanding of the genomic importance of CNV.

Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia

The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.