Assessment of FecGE genotypes on reproductive traits in Brazilian Morada Nova and Santa Inês sheep.

The aim of this study was to evaluate the effect of the polymorphic FecGE allele on reproductive traits in Santa Inês and Morada Nova ewes. The traits evaluated were as follows: total progeny weights at birth (PWB) and weaning (PWW) and progeny survival rates at birth (PSRB) and weaning (PSRW). A total of 389 animals, belonging to two Santa Inês herds and one Morada Nova herd, were genotyped. There was a difference between the averages for all the traits studied regarding type of parturition, herd/breed, genotype/herd, and genotype/type of parturition. For each additional progeny, if the female was FecGE/E, the PWB decreased by 1.02 kg and the PWW by 3.16 kg, also with a 0.04% reduction in PSRB and no change in PSRW. If the female was FecGE/+, the reduction in PWB was 0.24 kg, with an increase in PSRW by 0.11%, but no change in PWW and PSRB. In general, these results demonstrate that FecG+/+ females have a better ability to increase their number of progenies without reducing PWB and PWW (also similar to FecGE/+). Thus, it is suggested that further studies on the association between the traits of interest and candidate genes in sheep should be carried out so that the regions which have the greatest effect on the expression of these traits are actually identified. It was not possible to verify the effect of the FecGE allele on the PWB, PWW, PSRB, and PSRW in these Morada Nova and Santa Inês herds.

Molecular detection and assessment of risk factors for Theileria lestoquardi in sheep from Balochistan, Pakistan.

This study aimed to determine the molecular prevalence and associated risk factors of theileriosis in sheep from Balochistan, Pakistan. For this purpose, a total of 408 blood samples were collected from tick-infested sheep in three different zones of Balochistan (i.e., Quetta, Zhob, and Loralai). All the collected samples were analyzed using conventional microscopy techniques, polymerase chain reaction (PCR), 18S small subunit rRNA gene sequencing, and phylogenetic analysis. The results of the microscopy and PCR confirmed the highest prevalence of Theileria species in district Zhob (14.22% and 15.68%) followed by district Loralai (11.52% and 13.97%) and district Quetta (10.29% and 12.00%), respectively. In addition, the prevalence of T. lestoquardi was higher in female sheep (84.12%), followed by adult sheep (74.71%) and the Hernai breed of sheep (28.23%) in the studied area. Similarly, the prevalence of theileriosis was higher in the summer season (40.59%), followed by the spring, autumn, and winter seasons. However, numerous risk factors such as age, sex, area, season, and breeds of the sheep were not significantly correlated (P > 0.05) with the presence of T. lestoquardi, except tick abundance and feeding pattern of animals (P < 0.05). Furthermore, sequencing and phylogenetic analyses of the isolated T. lestoquardi displayed 99% sequence similarity with isolates from Germany, Egypt, Iraq, India, Iran, and Pakistan. Altogether these results showed that T. lestoquardi is the main species causing ovine theileriosis in Balochistan. As a result, large-scale studies are required to design practical control approaches to reduce the risk of theileriosis infection in Balochistan, Pakistan.

Assessment of genetic diversity of the fat-tailed Dumba sheep of India by mitochondrial and microsatellite markers.

India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country.

Risk assessment of three sheep stocking modes via identification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes.

In order to protect the prairie ecological environment, intensive farming has become a prevalent method of sheep stocking. However, the link between captivity stocking mode and ecological risk of sheep feces is still poorly understood. In this study, metagenomics was used to identify the environmental risk of sheep feces among three stocking modes. Our results showed that captivity mode (C) elevated antibiotic resistance in feces, with the abundance of antibiotic resistance genes (ARGs) (5.381 copies/cell) higher than that of half-pen stocking (Fh) (1.093 copies/cell) and grazing mode (Fr) (0.315 copies/cell) (Duncan's test, P < 0.05). Virulence factor genes (VFGs) analysis showed offensive virulence factors had the highest abundance in captivity feces (C: 3.826 copies/cell, Fh: 0.342 copies/cell, Fr: 0.163 copies/cell) (Duncan's test, P < 0.05). 15 metagenome-assembled genomes (MAGs) were identified as potential pathogenic antibiotic resistant bacteria (PARB) and revealed that Escherichia, Klebsiella may be the main host of ARGs and VFGs in sheep feces. Furthermore, the minimal inhibition concentrations (MIC) of tetracycline of E. coli in the captivity feces was 8.6 times and 4.7 times than that of grazing and half-pen stocking samples, respectively. The Non-metric multidimensional scaling (NMDS) revealed that high stocking density leads to feces causing increased harm to the environment. Although feces from sheep raised in captivity and half-pen stocking modes are easier to collect, they are more harmful to the environment and aerobic composting should be done before their application to farmland. This work provides a guideline for better control of the environmental risk of sheep feces from different stocking modes.

Relative contribution of Imprinting, X chromosome and Litter effects to phenotypic variation in economic traits of sheep.

Data on Zandi sheep were analysed to quantify maternal and paternal imprinting, X chromosome and litter effects' contribution to phenotypic variation in birth weight (BW), weaning weight (WW), growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR). To this end, a two-step approach was adopted. In the first step, each trait was analysed with a series of 16 animal models, which were identical for fixed and autosomal additive genetic effects but differed for combinations of maternal permanent environmental, maternal genetic, X chromosome and litter effects. For each trait, the best model was selected by the Akaike information criterion (AIC) and likelihood ratio tests (LRTs). In the second step, three additional models were fitted by adding maternal imprinting, paternal imprinting or both (models 17, 18 and 19) to the best model selected in the first step. Estimators of bias, dispersion and accuracy of breeding values estimated within 19 models with whole, and partial data were used to evaluate how well were the 19 models in estimating breeding values for the animals when their records were masked. For all traits studied, fitting the litter effect led to a better data fit. Also, it resulted in noticeable decreases in residual variance and other maternal variances. For growth traits, models containing the X-linked effects fitted the data substantially better than corresponding models without the X-linked effects. For BW, WW and GR, estimates of X-linked heritability ( h s 2 ) ranged between 0.09 (GR) and 0.14 (BW). Ignoring X-linked effects from the genetic evaluation model resulted in significant inflated autosomal additive genetic variance. For BW, WW, EF and RGR, models containing the imprinting effects provided a better fit of the data than otherwise identical models. Imprinting effects contributed significantly to the phenotypic variation of these traits in a range between 5% (RGR) and 8% (BW, WW). A sharp decline was observed in autosomal additive genetic variance following including imprinting effects in the model (27% to 40% depending on the trait). The least bias and dispersion, as well as greater accuracies for breeding values of focal animals, were for a model which included imprinting, X-linked and litter effects. It was concluded that imprinting, X-linked and litter effects need to be included in the genetic evaluation models for growth and efficiency-related traits of Zandi lambs.

Insights into the assessment of highly pathogenic Shiga toxin-producing Escherichia coli in raw milk and raw milk cheeses by High Throughput Real-time PCR.

Current methods for screening Enterohemorrhagic Escherichia coli (EHEC) O157 and non-O157 serogroups in raw milk products typically rely on the molecular detection of stx, eae, and serogroup-specific wzx or wzy genes. As these genetic markers can also be carried by non-EHEC strains, a number of 'false positive' results are obtained during the screening step. The suitability of new EHEC markers (espK, espV, ureD, Z2098, and CRISPRO26:H11) were tested as candidates for a more accurate screening of EHEC in dairy products. High-throughput PCR analysis of 1451 DNA extracts from milk and raw milk cheeses positive for both stx and eae demonstrated that addition of these new markers in the detection scheme resulted in a higher selectivity with a systematic reduction of the number of presumptive positive samples that require further O-group testing and confirmation by strain isolation. This reduction is more important (26% to 52%, depending on the animal production species) in the absence of prior IMS treatment of the enriched culture for the Top7 EHEC serotypes. However, even with prior treatment of the enriched cultures by IMS, the reduction rate varied between 5% and >25%. Analysis of eae-subtype, stx-subtypes indicated strong differences in the STEC (Shiga toxin producing E. coli) flora between animal species (goat, sheep, and cow). This study also pointed toward the possible presence of EHEC O80 (a new emerging EHEC serogroup in Europe) in cow's raw milk cheeses, which warrants further investigations.

Estimation of the associations between GH and DGAT1 genes and growth traits by using decision tree in Awassi sheep.

GH and DGAT1 are candidate genes associated with growth traits in sheep breeds. This study aims to determine the association between growth traits and GH and DGAT1 gene polymorphism using three statistical methods in Awassi sheep. The polymorphism was detected by the PCR-RFLP method. Three genotypes (AA, AB and BB) were observed for GH gene locus with allele and genotype frequency 0.70(A) and 0.30(B); 0.60(AA), 0.20(AB) and 0.20(BB). Three genotypes (CC, CT and TT) were found for DGAT1 gene locus with allele and genotype frequency 0.58(C) and 0.42(T); 0.47(CC), 0.23(CT) and 0.30(TT). The genes were in agreement with Hardy-Weinberg equilibrium (p > 0.05). CHAID, CRT and GLM were used to identify the association between growth traits and gene polymorphism. The results showed an association between GH locus and body weight and tail length. Also, found an association between DGAT1 locus and tail length. The three methods showed similar results in determining the association between genes and growth traits. Thus, the CHAID and CRT methods can evaluate the association between genes and growth traits.

Genetic and economic benefits of foreign sire contributions to a domestic sheep industry; including an Ireland-New Zealand case study.

BACKGROUND: Importation of foreign genetics is a widely used genetic improvement strategy. However, even if the foreign genetic merit is currently greater than the domestic genetic merit, differences in foreign and domestic trends mean that the long-term competitiveness of an importation strategy cannot be guaranteed. Gene flow models are used to quantify the impact that a specific subpopulation, such as foreign genetics, can have over time on the genetic or economic benefit of a domestic industry. METHODS: We used a deterministic recursive gene flow model to predict the commercial performance of lambs born across various subpopulations. Numerous breeding strategies were evaluated by varying market share, proportions of rams selected for mating, genetic trend, superiority of foreign genetics over domestic genetics and frequency of importation. Specifically, an Ireland-New Zealand case study was simulated to quantify the potential gain that could be made by using foreign sire contributions (New Zealand) in a domestic sheep industry (Ireland). RESULTS: Genetic and economic gains were generated from alternative breeding strategies. The 'base scenario' (i.e. representing the current industry) predicted an average genetic merit value of €2.51 for lambs born and an annualised cumulative benefit of €45 million (m) after 20 years. Maximum genetic (€9.45 for lambs born) and economic (annualised cumulative benefit of €180 m after 20 years) benefits were achieved by implementing the 'PRO-intense-market scenario' which involved shifting market share away from conservative domestic breeders and reducing the proportion of rams that were selected for mating by progressive domestic breeders from the top 40% to the top 20%, without the use of any foreign genetics. The 'PROFOR scenario', which considered the use of foreign and progressive domestic genetics, predicted an average genetic merit value of €7.37 for lambs born and an annualised cumulative benefit of €144 m, after 20 years. CONCLUSIONS: Our results demonstrate that there is opportunity for a domestic industry to increase industry benefits without the use of foreign genetics but through an attempt to shift the market share away from conservative domestic breeders towards progressive domestic breeders. However, the importation and use of progressive foreign genetics may be an effective method to trigger a change in behaviour of conservative domestic breeders towards the use of progressive genetics.

Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits.

Russian sheep breeds represent an important economic asset by providing meat and wool, whilst being adapted to extreme climates. By resequencing two Russian breeds from Siberia: Tuva (n = 20) and Baikal (n = 20); and comparing them with a European (UK) sheep outgroup (n = 14), 41 million variants were called, and signatures of selection were identified. High-frequency missense mutations on top of selection peaks were found in genes related to immunity (LOC101109746) in the Baikal breed and wool traits (IDUA), cell differentiation (GLIS1) and fat deposition (AADACL3) in the Tuva breed. In addition, genes found under selection owing to haplotype frequency changes were related to wool traits (DSC2), parasite resistance (CLCA1), insulin receptor pathway (SOCS6) and DNA repair (DDB2) in the Baikal breed, and vision (GPR179) in the Tuva breed. Our results present candidate genes and SNPs for future selection programmes, which are necessary to maintain and increase socioeconomic gain from Siberian breeds.

Assessment of between-founder heterogeneity in inbreeding depression for reproductive traits in Baluchi sheep.

Magnitude of inbreeding depression could be different among descendants of various founder animals, when recessive genetic composition of a population is unevenly distributed among founder animal genomes. Reproductive records of Baluchi sheep for the litter variables size at birth (LSB), size at weaning (LSW), mean weight/lamb born (LMWLB), mean weight/lamb weaned (LMWLW), total weight at birth/ewe lambing (TLWB) and total weight at weaning/ewe lambing (TLWW) were used to examine heterogeneity in inbreeding depression between founder animals. Pedigree-based inbreeding coefficients were proportioned into components coming from founder animals and Mendellian contribution from non-founder animals. Two approaches were used to assess effects of inbreeding: overall inbreeding coefficients or partial inbreeding of the four main founder animals as possible covariates included in statistical models. Among the traits evaluated, there were effects on LMWLB, LMWLW and TLWW of inbreeding with there being a -8, -48, and -95 g decrease per 1% increase in inbreeding, respectively. Linear regressions of traits on partial inbreeding coefficients due to founder animals were of different magnitudes and ranged between -0.12 and +0.128. Heterogeneous contribution of founder animals to inbreeding depression occurred for LSB, LMWLB, and TLWW. These results indicate there was uneven distribution of recessive genetic composition among genomes of founder animals or differences in selection pressures on unfavorable alleles between different founder lines. The observed variation in founder-specific inbreeding depression indicates a small number of alleles with major effects are contributing to inbreeding depression.

Genetic parameter estimates for gastrointestinal nematode parasite resistance and maternal efficiency indicator traits in Santa Inês breed.

Infection with Haemonchus contortus is the most economically important gastrointestinal nematode parasitosis and the most important cause of mortality in sheep production. The aim of this study was to estimate variance components of gastrointestinal parasite resistance traits, maternal efficiency (ME) and ewe adult weight (AW) in Santa Inês breed in tropical conditions. The phenotypic records were collected from 700 animals, belonging to four flocks located south-east and north-east in Brazil. The evaluated traits were as follows: degree of anaemia assessed using the FAMACHA chart (FMC), haematocrit (HCT), white blood cell (WBC), red blood cell (RBC), haemoglobin (HGB), platelets (PLT), faecal egg count (EPGlog ), ME, metabolic maternal efficiency (MME), AW and metabolic ewe adult weight (MAW). From the 700 animals, 576 (82% of the evaluated population) were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.). Markers with unknown genomic position, located on sex chromosomes, monomorphic, with minor allele frequency <0.05, call rate <90% and with excess heterozygosity were excluded. The variance components were estimated using a single-trait animal model with ssGBLUP procedure. The correlation between the parasite's resistance indicators and the ME suggested that selecting animals with both higher adult weight and ME will also favour the selection of animals with better resistance to gastrointestinal nematodes parasites, specially H. contortus. Therefore, since there are few or no studies with Santa Inês breed in this area, it is important to study those traits to better manage selection programs.

The quality of the algorithm for proven and young with various sets of core animals in a multibreed sheep population1.

The inverses of the pedigree and genomic relationship matrices (A, G) are required for single-step GBLUP (ssGBLUP). While, inverting A is possible for millions of animals at a linear cost, inverting G has a cubic cost and feasible for at most 150,000 animals, using the current conventional algorithms. The algorithm for proven and young (APY) provides approximations of the regular ssGBLUP by splitting genotyped animals into core and noncore groups, with computational costs being cubic for core and linear for noncore animals. The data consisted of 9,406,096 animals in the pedigree, 6,243,753 weaning weight phenotypes, and 46,949 genotyped animals from 5 breeds, composites, and animals with missing breed information from New Zealand. Aiming to find a core sample for a multibreed sheep population that can provide evaluations similar to those from the regular ssGBLUP, different core types, and core sizes were studied. Core types random, composite, oldest, youngest, the most inbred animals in G (GINB), and in A (AINB) were studied in 5K, 10K, and 20K core sizes (K = 1,000). Romney core was studied in 5K and 10K, and Coopworth-Perendale core was studied in 5K. Correlation and regression coefficient (slope) between GEBV from the non-APY and the APY analyses, as indicators for consistency with non-APY and bias from non-APY, showed a large impact of APY on noncore and a small impact on nongenotyped animals. Breed-based 5K cores resulted in large bias from non-APY even for nongenotyped animals. Random and GINB at 20K core size resulted in the highest consistency with non-APY and the lowest bias from non-APY. However, GINB did not perform as well as Random at lower core sizes. The number of animals from a breed in the core sample was very important for the evaluation of that breed. We observed that cores without Texel or Highlander animals resulted in poor evaluations for those breeds. Solving the mixed model equations, within core type, the smallest core size, and within core size, Random core converged in the least number of iterations. However, APY per se did not necessarily reduce the solving time. Random cores performed the best, as they could give a good coverage on the generations and breeds, representative for the genotyped population. Core size 20K performed better than 5K and 10K, and the optimum core size was found to be 18.8K, according to the eigenvalue decomposition of G.

Genetic analysis identifies the missing parchment of New Zealand's founding document, the Treaty of Waitangi.

Genetic analyses provide a powerful tool with which to identify the biological components of historical objects. Te Tiriti o Waitangi | The Treaty of Waitangi is New Zealand's founding document, intended to be a partnership between the indigenous Maori and the British Crown. Here we focus on an archived piece of blank parchment that has been proposed to be the missing portion of the lower parchment of the Waitangi Sheet of the Treaty. However, its physical dimensions and characteristics are not consistent with this hypothesis. We perform genetic analyses on the parchment membranes of the Treaty, plus the blank piece of parchment. We find that all three parchments were made from ewes and that the blank parchment is highly likely to be a portion cut from the lower membrane of the Waitangi Sheet because they share identical whole mitochondrial genomes, including an unusual heteroplasmic site. We suggest that the differences in size and characteristics between the two pieces of parchment may have resulted from the Treaty's exposure to water in the early 20th century and the subsequent repair work, light exposure during exhibition or the later conservation treatments in the 1970s and 80s. The blank piece of parchment will be valuable for comparison tests to study the effects of earlier treatments and to monitor the effects of long-term display on the Treaty.

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia.

BACKGROUND: Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. RESULTS: Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. CONCLUSIONS: Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments.

Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan.

The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan's high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies.

Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin.

Domestic animals play a key role in human survival and the development of civilization. However, the genetic resources of domestic animals are facing an alarming rate of erosion due to socioeconomic changes, economic globalization and financial constraints. In this study, through genome-wide SNP analysis, we estimated the heterozygosity, inbreeding coefficient, effective population size, and runs of homozygosity to identify the breeds facing the risk of extinction for sheep and cattle across the world. In particular, we quantified the contribution of 97 sheep breeds and 53 cattle breeds to genomic diversity (within-breed, between-breed and total) and prioritized the breeds for conservation. Additionally, we compared the average values of genomic diversity between breeds from regions (or countries) in different economic categories (underdeveloped, developing and developed), and found that breeds in developed regions exhibit significantly higher levels of total genomic diversity than those in underdeveloped and developing regions. Altogether, our results suggested that conservation priority should be given to breeds in developed regions to secure the future genomic diversity hotspots of domestic animal resources.

Assessment of the genetic and economic impact of performance recording and genotyping in Australian commercial sheep operations.

With the new opportunities from DNA technology, multitier breeding schemes have the potential to become more effective and more integrated. Integrated breeding schemes can also be better adapted to account for potential genotype by environment interactions (G × E) between tiers. In this case, phenotypic and genotype information from lower tiers becomes more valuable as it involves measurement of traits that directly represent the breeding objective. The objective of this study was to compare scenarios that represented different selection strategies and their economic effectiveness in fine-wool commercial sheep operations that exploit multitier breeding structures. Genomic selection (GS) applied in the multiplier and the commercial tier presented the largest additional revenue among all scenarios, as it resulted in the largest amount of genetic progress. The largest benefits from GS were outweighed by the genotyping costs, which made DNA parentage the most feasible strategy for the multiplier tier, resulting in the highest cumulative net present value (CNPV). The benefits of phenotypes and genotype information from the commercial environment were larger in the presence of G × E between the nucleus and the commercial tier. The CNPV was larger with a 50% reduction in genotyping costs, which increased the returns of GS scenarios by 2.7-fold on average. Higher selection intensity when selecting multiplier rams also resulted in larger benefits. In this case, returns for the breeding scheme were 3.5-fold higher when 33% of multiplier males were selected based on commercial information, compared to scenarios selecting 50% of the available multiplier rams. The benefits of collecting commercial phenotypes and genotypes were long term, which means that return on investment often took more than 10 years to be achieved, and were largely dependent on two-stage selection to reduce cost while maintaining selection efficiency and on the cost of a genotype test.

Genomic Regions in Local Endangered Sheep Encode Potentially Favorable Genes.

The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively. The genes in proximity of these markers were mapped to known pathways of the Gene Ontology to determine which ones were most represented. Our results indicated that the differences of the Alpago breed from the more productive sheep rely upon genes involved in cellular defense and repair mechanisms. A higher number of different markers and genes were detected in the comparison with the specialized dairy sheep. These genes play a role in complex biological processes: metabolic, homeostatic, neurological system, and macromolecular organization; such processes may possibly explain the evolution of gene function as a result of selection to improve milk yield.

Analysis of single nucleotide polymorphisms variation associated with important economic and computed tomography measured traits in Texel sheep.

Sheep are an important part of the global agricultural economy. Growth and meat production traits are significant economic traits in sheep. The Texel breed is the most popular terminal sire breed in the UK, mainly selected for muscle growth and lean carcasses. This is a study based on a genome-wide association approach that investigates the links between some economically important traits, including computed tomography (CT) measurements, and molecular polymorphisms in UK Texel sheep. Our main aim was to identify single nucleotide polymorphisms (SNP) associated with growth, carcass, health and welfare traits of the Texel sheep breed. This study used data from 384 Texel rams. Data comprised ten traits, including two CT measured traits. The phenotypic data were placed in four categories: growth traits, carcass traits, health traits and welfare traits. De-regressed estimated breeding values (EBV) for these traits together with sire genotypes derived with the Ovine 50 K SNP array of Illumina were jointly analysed in a genome wide association analysis. Eight novel chromosome-wise significant associations were found for carcass, growth, health and welfare traits. Three significant markers were intronic variants and the remainder intergenic variants. This study is a first step to search for genomic regions controlling CT-based productivity traits related to body and carcass composition in a terminal sire sheep breed using a 50 K SNP genome-wide array. Results are important for the further development of strategies to identify causal variants associated with CT measures and other commercial traits in sheep. Independent studies are needed to confirm these results and identify candidate genes for the studied traits.

A fast, low-cost and efficient method for the diagnosis of sperm DNA fragmentation in several species.

Sperm DNA fragmentation is a condition that interferes directly in the reproductive efficiency. Currently, there are several methods for assessing the sperm DNA integrity, such as Alkaline Comet, TUNEL and Sperm Chromatin Structure Assay. However, many of these techniques are laborious and require high-precision equipment. Thus, the development of new techniques can optimize the evaluation of sperm DNA damage. Therefore, the aim of this study was to standardize the toluidine blue (TB) stain technique for the analysis of DNA fragmentation of dog, cat, bull, stallion and ram spermatozoa. For this purpose, we used six animals of each specie (n = 30), in reproductive age. Sperm was collected by different methods according to the particularities of each species, and such samples were divided into two aliquots: a sperm sample was kept at 5°C (considered as intact sperm DNA), and the remaining samples were submitted to the induction of DNA fragmentation by exposure to ultraviolet light for 4 hr. Samples were then mixed with the intact sample to obtain known and progressive proportions of sperm with fragmented DNA (0%, 25%, 50%, 75% and 100%). Semen smears were performed and subjected to staining with TB. Blue-stained spermatozoa were considered to have DNA fragmentation. We observed high linear regression coefficients between the expected proportion of damaged DNA and the results of TB for dog, cat, ram, bull and stallion samples. In conclusion, TB stain was considered a fast and effective technique for the study of spermatozoa DNA in several species.