Information about genetic parameters is essential for selection decisions and genetic evaluation. These estimates are population specific; however, there are few studies with dairy cattle populations reared under tropical and sub-tropical conditions. Thus, the aim was to obtain estimates of heritability and genetic correlations for milk yield and quality traits using pedigree and genomic information from a Holstein population maintained in a tropical environment. Phenotypic records (n = 36 457) of 4203 cows as well as the genotypes for 57 368 single nucleotide polymorphisms from 755 of these cows were used. Covariance components were estimated using the restricted maximum likelihood method under a mixed animal model, considering a pedigree-based relationship matrix or a combined pedigree-genomic matrix. High heritabilities (around 0.30) were estimated for lactose and protein content in milk whereas moderate values (between 0.19 and 0.26) were obtained for percentages of fat, saturated fatty acids and palmitic acid in milk. Genetic correlations ranging from -0.38 to -0.13 were determined between milk yield and composition traits. The smaller estimates compared to other similar studies can be due to poor environmental conditions, which may reduce genetic variability. These results highlight the importance in using genetic parameters estimated in the population under evaluation for selection decisions.
BackgroundDespite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep.ResultsGenomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30.ConclusionsEstimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.
Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F2 chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.
Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify genomic regions associated with traditional milk production traits, including milk yield, somatic cell score, fat, protein and lactose percentages, and fatty acid composition in a Holstein cattle population producing under tropical conditions. For this, 75,228 phenotypic records from 5,981 cows and genotypic data of 56,256 SNP from 1,067 cows were used in a weighted single-step GWAS. A total of 46 windows of 10 SNP explaining more than 1% of the genetic variance across 10 Bos taurus autosomes (BTA) harbored well-known and novel genes. The MGST1 (BTA5), ABCG2 (BTA6), DGAT1 (BTA14), and PAEP (BTA11) genes were confirmed within some of the regions identified in our study. Potential novel genes involved in tissue damage and repair of the mammary gland (COL18A1), immune response (LTTC19), glucose homeostasis (SLC37A1), synthesis of unsaturated fatty acids (LTBP1), and sugar transport (SLC37A1 and MFSD4A) were found for milk yield, somatic cell score, fat percentage, and fatty acid composition. Our findings may assist genomic selection by using these regions to design a customized SNP array to improve milk production traits on farms with similar environmental conditions.
For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r2 and |D′| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r2 for |D′| across all chromosomes. The average r2 between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r2 equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.
Repeated measures from the same individual have been analyzed by using repeatability and finite dimension models under univariate or multivariate analyses. However, in the last decade, the use of random regression models for genetic studies with longitudinal data have become more common. Thus, the aim of this research was to estimate genetic parameters for body weight of four experimental chicken lines by using univariate random regression models. Body weight data from hatching to 84 days of age (n = 34,730) from four experimental free-range chicken lines (7P, Caipirão da ESALQ, Caipirinha da ESALQ and Carijó Barbado) were used. The analysis model included the fixed effects of contemporary group (gender and rearing system), fixed regression coefficients for age at measurement, and random regression coefficients for permanent environmental effects and additive genetic effects. Heterogeneous variances for residual effects were considered, and one residual variance was assigned for each of six subclasses of age at measurement. Random regression curves were modeled by using Legendre polynomials of the second and third orders, with the best model chosen based on the Akaike Information Criterion, Bayesian Information Criterion, and restricted maximum likelihood. Multivariate analyses under the same animal mixed model were also performed for the validation of the random regression models. The Legendre polynomials of second order were better for describing the growth curves of the lines studied. Moderate to high heritabilities (h(2) = 0.15 to 0.98) were estimated for body weight between one and 84 days of age, suggesting that selection for body weight at all ages can be used as a selection criteria. Genetic correlations among body weight records obtained through multivariate analyses ranged from 0.18 to 0.96, 0.12 to 0.89, 0.06 to 0.96, and 0.28 to 0.96 in 7P, Caipirão da ESALQ, Caipirinha da ESALQ, and Carijó Barbado chicken lines, respectively. Results indicate that genetic gain for body weight can be achieved by selection. Also, selection for body weight at 42 days of age can be maintained as a selection criterion.
Measurements of milk yield (MY), somatic cell score (SCS), percentage of fat (FP), protein (PP), lactose (LP), casein (CP) and percentage of palmitic (C16:0), stearic (C18:0), oleic (C18:1), total saturated (SFA), unsaturated (UFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids in milk from 5,224 Holstein cows were evaluated as a function of a temperature and humidity index (THI). Legendre orthogonal polynomials from second to seventh order were tested. The best fit order for MY, PP and C18:0 was the third, whereas the second for all other traits. The heritability estimates decreased for MY (0.31 to 0.14), FP (0.28 to 0.16), LP (0.43 to 0.30), SCS (0.14 to 0.09), SFA (0.33 to 0.22) and C16:0 (0.31 to 0.26), whereas increased for CP (0.32 to 0.42), MUFA (0.08 to 0.13), UFA (0.07 to 0.11) and C18:1 (0.07 to 0.11) as the THI level increased. For PP, heritabilities (0.26 to 0.39) presented larger values in intermediate THI. For PUFA and C18:0, heritabilities were approximately constant (0.13 to 0.14 and 0.15, respectively). However, the greatest variations may have been the result of the limitations of Legendre polynomials at the extreme points of the curve, and the pattern of heritabilities curves was approximately constant for the evaluated traits. Spearman's rank correlations between breeding values in extreme THI levels were greater than 0.80 for all traits considering all animals, only cows and only bulls. When considering the top 1% and the top 50% animals (only cows, only bulls and all), Spearman correlations smaller than 0.70 were found, suggesting reranking of the animals. Although there was little variation in the variance components over THI, it is possible that there is no heat stress in the animals studied, because, on average, there was no great impact of the thermal load on the traits. One possible explanation is the use of herds with little climatic difference among herds, as well as the use of fans and sprinklers into the barns. However, the THI levels may be important factors in the selection process, as reranking of animals was verified.
Limited knowledge about the agronomic potential of Paspalum species from the Americas hinders their use in pastures. The response mechanisms to water deficit and waterlogging were studied in five accessions of Paspalum sp. (P. regnellii cv. BRS Guará and BGP 397, P. conspersum BGP 402 and P. malacophyllum BGP 289 and BGP 293) and Urochloa brizantha cv. Marandu. Morphological and physiological traits at the end of the stress and after the recovery period were measured. All Paspalum accessions, especially BGP 289, BGP 402 and BGP 397, and also cv. Marandu, showed survival mechanisms to water deficit. BRS Guará showed adaptive features to waterlogging, although had with a low survival rate to water deficit. Under waterlogging, BGP 289 and cv. Marandu showed reduced growth, and after the recovery period, they presented low plant survival and root recovery. Although growth of BGP 293 was reduced during waterlogging, it presented high tiller survival rate. BGP 293, BGP 402 and BGP 397 showed adaptive potential strategies for waterlogging and water deficit. There is genetic variability among the evaluated accessions for water deficit and waterlogging stresses, suggesting that they may be used per se or as progenitors in crosses with other genotypes in breeding programmes.
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