Avaliação de painéis de SNP como ferramentas em melhoramento genético de ovinos Corriedale no Uruguai

One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This study´s objective was to compare eggs per gram of feces (FEC) and fiber diameter (FD) estimated breeding values (EBV) and genomic EBV (GEBV) in Corriedale breed. Analysis included 19547 lambs with data, and 454, 711 and 383 genotypes from 170, 507 and 50K SNP chips, respectively. A univariate animal model was used for EBV and GEBV estimation, which included contemporary group, type of birth and dam age as fixed effects, and age at recording as covariate. Differential weights (α) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaike´s Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of α only impacted on low density SNP chips. No differences were observed in mean accuracies for the whole population. However, in the genotyped subgroup accuracies increased by 2% with the 170 SNP chip (α=0.25), and by 5% (α=0.5) and 14% (α=0.75) with the 507 SNP chip. No differences were observed in FD EBV and GEBV mean accuracies. These results show that it is possible to increase GEBV accuracies despite the use of low-density chips.Una alternativa para el control de los nematodos gastrointestinales (NGI) es la selección genética. El objetivo de este trabajo fue comparar las precisiones de los valores de cría (EBV) y los EBV genómicos (GEBV) del recuento de huevos por gramo en heces (HPG) y diámetro de fibra (DF) en la raza Corriedale. El análisis incluyó 19547 corderos con datos fenotípicos y 454, 711 y 383 genotipados con paneles o chips de 170, 507 y 50K SNP, respectivamente. Los EBV y GEBV se estimaron con un modelo animal univariado que incluyó los efectos fijos: grupo contemporáneo, tipo de nacimiento y edad de la madre, y edad al registro como covariable. Se consideraron pesos diferenciales (α) en la matriz de relaciones genómicas, identificándose los modelos con mejor ajuste con el criterio de información de Akaike (AIC), que fueron utilizados para la estimación de los GEBV y sus precisiones. El uso de α solo impactó en el ajuste con paneles de baja densidad. No se encontraron diferencias en las precisiones promedio de la población total. En cambio, en el subgrupo de animales genotipados las precisiones aumentaron 2% con 170 SNP (α=0.25), y con 507 SNP 5% (α=0.5) y 14% (α=0.75). No hubo diferencias en precisiones de los EBV y los GEBV de DF. Los resultados muestran que es posible aumentar las precisiones de los GEBV aun con paneles de baja densidad.Uma alternativa para o controle de nematóides gastrointestinais (NGI) é a seleção genética. O objetivo deste trabalho foi comparar as precisões dos valores genéticos estimados (EBV) e dos EBVs genômicos (GEBV) da contagem de ovos por grama de fezes (OPG) e diâmetro de fibra (DF) na raça Corriedale. A análise incluiu 19547 cordeiros com dados e 454, 711 e 383 genotipados de 170, 507 e 50K SNPs, respectivamente. Foram estimados os EBV e GEBV com um modelo animal univariado que incluiu efeitos fixos de grupo contemporâneo, tipo de nascimento e idade da mãe e idade no registro (covariável). Pesos diferenciais (α) foram considerados na matriz de relações genômicas, identificando os modelos com melhor ajuste via critério de informação de Akaike (AIC), os quais foram utilizados para estimar o GEBV e suas precisões. O uso de α somente impactou no ajuste com painéis de baixa densidade. Não foram encontradas diferenças na precisão média da população total. Em contraste, no subgrupo de animais genotipados as precisões aumentaram 2% com 170 SNPs (α = 0.25), e com 507 SNPs 5% (α = 0.5) e 14% (α = 0.75). Não houve diferenças na precisão de EBV e GEBV de DF. Os resultados mostram que é possível aumentar a precisão de GEBVs mesmo que se utilizem painéis de baixa densidade

SNP, or not SNP? Is this the question?

Genetic evaluations (GE) of commercial species have led to reached an efficient selection of the main economic relevant traits. Despite the great number of QTLs (quantitative trait loci) found in the last years, these have had limited application in formal breeding programs. However, the recent development of high density marker panel (SNP - single nucleotide polymorphism) has allowed the Genomic Selection (GS) application. The objective of this work is to analyze the GS impact in animal breeding and to list the considerations to take into account when genomic projects are developed. The GS allows a potential improvement of the GE mainly by increasing the breeding value accuracy and reducing the generation interval. This specially occurs in traits that are difficult or costly to record, those expressed in only one sex or late in the animal’s life. Previous to begin GS projects, is important to define: (1) Target traits, which must be economically relevant and strategic for the specie/breed/country; (2) Reference population for the association studies; (3) The multidisciplinary team; (4) The incoming frequency of new genotypes; and (5) The amount for initial investment. In this process, the phenomics plays a role as a support science for genomics, which will valorize the recording systems

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep.

THE AIM OF THIS STUDY WAS TO INVESTIGATE THE GENETIC DIVERSITY WITHIN AND AMONG THREE BREEDS OF SHEEP: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip(®). Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (FST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (FST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (FST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds

Genetic progress in sheep evaluation in Uruguay

This study examined the present status and genetic progress achieved in the sheep population of Uruguay between the years 2001 and 2011. Annual genetic gains in the Corriedale, Polwarth, Merilin, Australian Merino, Romney Marsh, and Texel breeds were estimated. The number of breeding flocks evaluated annually increased from 11 to 86, and the number of animals recorded from 3 740 to 25 259. The following traits related to meat and wool production and quality were evaluated: greasy (PVS) and clean (PVL) fleece weight, mean fibre diameter (DPF), staple length (LM), liveweight at weaning (PVD), at shearing (PVE), and at ultrasound scanning (PVAOB); rib eye area (AOB); and backfat thickness (EG). The total number of rams evaluated for breeding value and/or Flock-Testing information would cover 45% of the annual demand for stud service of the national flock. The highest estimated annual gains by breed were: Corriedale, PVD (0.75%), PVE (0.54%), DPF (-0.48%), and PVL (0.41%); Polwarth, PVL (0.80%), PVS (0.72%), and PVE (0.52%); Merilin, PVD and PVE (0.58%); Merino, DPF (-0.64%), PVL (0.54%), and PVE (0.39%); Romney, PVS (1.08%), PVE (0.78%), and PVD (0.72%); and Texel, AOB (1.88%), PVAOB (1.75%), and PVD (1.11%)

Building the GLENCOE Platform -Grasslands LENding eConomic and ecOsystems sErvices

To feed the rising population whilst also preserving ecosystem functions, creative solutions are needed for the ecological intensification of natural grassland-based livestock systems. In Uruguay, natural grasslands are the main nutritional resource for livestock production. In these ecosystems, cattle and sheep graze together all the year round, and grasslands are frequently heavily grazed. Considerable research has been generated concerning grassland management, but there is still no knowledge about the impact of decision rules that supports management actions on long-term ecosystem functioning, at the system level. To meet this deficit, a participatory working group of farmers, researchers, and consultants have developed the GLENCOE platform. This platform is a large-scale facility, supported by INIA-Uruguay, designed to answer the following question: How to intensify the grazing management to improve the sustainability of livestock systems based on natural grasslands? To build the platform three steps were followed: (I) definition of the research problem using a problem tree analysis; (ii) conceptualization of the platform and the design of the grazing systems to be evaluated; and, (iii) spatial allocation of the grazing systems according to the variability of soil, slopes, and seasonal dynamic of vegetation indexes. These criteria were considered across farmlets that were equivalent in the initial stage, allowing causal inferences for the systems trajectories on productive and environmental traits. The platform is composed of three independent farmlets of 50 ha each, where multiparous Hereford cows and Merinos wethers co-graze under three grazing management systems. Each farmlet is managed according to different spatio-temporal decisions of the specific management of vegetation communities, grazing methods, and the stockpile of forage that is allowed by the number of the existing paddocks. Farmlet-1; comprises less decisions (2 paddocks), Farmlet-2; intermediate (8 paddocks), and Farmlet-3; high level of decisions (32 paddocks). This innovative platform will be used as a participatory and interdisciplinary space for research and co-learning of management on processes that can only be observed in long-term evaluations, and at farmlet scale. We expect that this new approach will contribute to the developement and implemention of sustainable grazing management systems in Uruguay

Exclusion of paternity based on a panel of 89 SNP markers in a sample of Corriedale and Merino sheep from Uruguay

The performance of an 89 single nucleotide polymorphism (SNP) marker panel for paternity exclusion was studied in populations of Corriedale and Merino sheep in Uruguay. Minor allele frequency (MAF) values of the markers ranged from 0.05 to 0.5 for Corriedale and from 0.08 to 0.5 for Merino. Using fewer than 50 markers, high probability values (0.9999) were achieved for excluding both parents and also when one of the parents was known. In the most common case of paternity exclusion, when only the genotype of a possible parent is given and the mother is unknown, achieving a probability value of 0.9999 involved almost all the markers for Merino and it was not possible to reach that level for Corriedale (maximum value = 0.9998). These results suggest that the panel could be useful with Corriedale and Merino populations. However, it may be insufficient to establish paternity in highly related populations. For that reason, development of an SNP panel for paternity exclusion under more complex situations is suggested

Molecular characterization of parasite resistant/susceptible Uruguayan Merino lambs

Gastrointestinal parasites (GIP) are one of the main sanitary and economic limitations for Uruguayan sheep production. Many authors suggest a possible relationship between microsatellites and sheep parasite resistance. Based on extreme fecal worm egg count-expected progeny difference (FECEPD), 50 resistant (R) and 50 susceptible (S) lambs were chosen from a Merino flock. In order to investigate the genetic variability and structure in this flock, four polymorphic microsatellites (McM214, McM130, McM357 and CSRD2138) which are potentially associated with quantitative trait loci (QTL) for parasite resistance were analyzed. The number of alleles varied from 8 to 13 showing different frequencies; polymorphic information content values were >0.5 and the observed heterozygosity ranged from 0.735 to 0.773. A considerable genic and genotypic differentiation between R and S subpopulations was observed. McM214 showed a significant deviation from Hardy-Weinberg equilibrium in whole herd and S population. Fixation Indices (FIS) values also indicated a heterozygote excess in the entire population. McM214 showed linkage disequilibrium with McM357 in the R sample, and with McM130 in the S sample. Population structure analysis proved the origin of two clusters (subpopulations) from two different lines (K = 2, similarity coefficient = 0.979). Polymorphism of these markers could be used in association analysis with GIP resistance / susceptibility

Genome-Wide Association Study of Parasite Resistance to Gastrointestinal Nematodes in Corriedale Sheep

Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sheep by single-step genome-wide association studies (ssGWAS) using 170, 507 and 50K single nucleotide polymorphisms (SNPs). Analysis included 19,547 lambs with faecal egg counts (FEC) records, a pedigree file of 40,056 animals and 454, 711 and 383 genotypes from 170, 507 and 50K SNPs, respectively. Genomic estimated breeding values (GEBV) were obtained with single-step genomic BLUP methodology (ssGBLUP), using a univariate animal model, which included contemporary group, type of birth and age of dam as class fixed effects and age at FEC recording as covariate. The SNP effects as wells as p-values were estimated with POSTGSF90 program. Significance level was defined by a chromosome-wise False Discovery Rate of 5%. Significant genomic regions were identified in chromosomes 1, 3, 12 and 19 with the 170 SNP set, in chromosomes 7, 12 and 24 using the 507 SNP chip and only in chromosome 7 with the 50K SNP chip. Candidate genes located in these regions, using Oar_v4.0 as reference genome, were TIMP3, TLR5, LEPR and TLR9 (170 SNPs), SYNDIG1L and MGRN1 (507 SNP chip) and INO80, TLN2, TSHR and EIF2AK4 (50K SNP chip). These results validate genomic regions associated with FEC previously identified in Corriedale and other breeds and report new candidate regions for further investigation

SNP arrays evaluation as tools in genetic improvement in Corriedale sheep in Uruguay

One control strategy for gastrointestinal nematodes (GIN) is genetic selection. This study´s objective was to compare eggs per gram of feces (FEC) and fiber diameter (FD) estimated breeding values (EBV) and genomic EBV (GEBV) in Corriedale breed. Analysis included 19547 lambs with data, and 454, 711 and 383 genotypes from 170, 507 and 50K SNP chips, respectively. A univariate animal model was used for EBV and GEBV estimation, which included contemporary group, type of birth and dam age as fixed effects, and age at recording as covariate. Differential weights (α) were considered in the genomic relationship matrix (G), and the best fit models were identified using Akaike´s Information Criterion (AIC), which were later used for GEBV and accuracies estimation. The use of α only impacted on low density SNP chips. No differences were observed in mean accuracies for the whole population. However, in the genotyped subgroup accuracies increased by 2% with the 170 SNP chip (α=0.25), and by 5% (α=0.5) and 14% (α=0.75) with the 507 SNP chip. No differences were observed in FD EBV and GEBV mean accuracies. These results show that it is possible to increase GEBV accuracies despite the use of low-density chips

Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep

The aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live weight (LW), body condition score (BCS), pregnancy rate (PR) and lambing potential (LP) of Uruguayan Merino sheep. Phenotypic records of approximately 2000 mixed-age ewes were obtained from a Merino nucleus flock. Genome-wide association studies were performed utilizing single-step Bayesian analysis. For wool traits, a total of 35 genomic windows surpassed the significance threshold (PVE ≥ 0.25%). The proportion of the total additive genetic variance explained by those windows was 4.85 and 9.06% for FD and CFW, respectively. There were 42 windows significantly associated with LWM, which collectively explained 43.2% of the additive genetic variance. For BCS, 22 relevant windows accounted for more than 40% of the additive genetic variance, whereas for the reproduction traits, 53 genomic windows (24 and 29 for PR and LP, respectively) reached the suggestive threshold of 0.25% of the PVE. Within the top 10 windows for each trait, we identified several genes showing potential associations with the wool (e.g., IGF-1, TGFB2R, PRKCA), live weight (e.g., CAST, LAP3, MED28, HERC6), body condition score (e.g., CDH10, TMC2, SIRPA, CPXM1) or reproduction traits (e.g., ADCY1, LEPR, GHR, LPAR2) of the mixed-age ewes