RESUMEN
Along the last decades, the genetic evaluation methodology has evolved, improving breeding value estimates. Many breeding programmes have historical phenotypic records and large number of generations, but to make use of them could result in more inconveniences than benefits. In this study, the prediction ability of genotyped young animals was assessed by simultaneously evaluating the removal of historical data, two pedigree deepness and two methodologies (traditional BLUP and single-step genomic BLUP or ssGBLUP), using milk yield records of 40 years of three Latxa dairy sheep populations. The linear regression method was used to compare predictions of young rams before and after progeny testing, with six cut-off points, by intervals of 4 years (from 1992 to 2012), and statistics of ratio of accuracies, bias, and dispersion were calculated. The prediction accuracy of selection candidates, when genomic information was included, was the highest in all Latxa populations (between 0.54 and 0.69 with full data set). Nevertheless, the deletion of historical phenotypic data resulted on moderate accuracy gain in the bigger data size populations (mean gain 2.5%), and the smaller population took advantage of a moderate data deletion (2.7% gain by removing data until 2004), reducing accuracy when more records were removed. The bias of validation individuals was lower when the breeding value was predicted based on genomic information (between 2.1 and 13.9), being lower when the biggest amount of data was deleted in the bigger data size populations (5.2% reduction), and the smaller population was benefited from data deletion between 1996 and 2008 (3.8% bias reduction). Meanwhile, the slope of estimated genetic trend was lower when less data were included, and an overestimation of the unknown parent group estimates was observed. The results indicated that ssGBLUP evaluations were outstanding, compared with traditional BLUP evaluations, while the depth of pedigree had a very small influence, and deletion of historical phenotypic data was beneficial. Thus, Latxa routine genetic evaluations would benefit from truncating phenotypic records between 2000 and 2004, the use of two pedigree generations and the implementation of ssGBLUP methodology.
Asunto(s)
Cruzamiento , Genotipo , Linaje , Fenotipo , Animales , Femenino , Masculino , Industria Lechera , Ovinos/genética , Ovinos/fisiología , Leche/química , Selección Genética , Modelos Genéticos , Modelos LinealesRESUMEN
Genomic selection has been implemented over the years in several livestock species, due to the achievable higher genetic progress. The use of genomic information in evaluations provides better prediction accuracy than do pedigree-based evaluations, and the makeup of the genotyped population is a decisive point. The aim of this work is to compare the effect of different genotyping strategies (number and type of animals) on the prediction accuracy for dairy sheep Latxa breeds. A simulation study was designed based on the real data structure of each population, and the phenotypic and genotypic data obtained were used in genetic (BLUP) and genomic (single-step genomic BLUP) evaluations of different genotyping strategies. The genotyping of males was beneficial when they were genetically connected individuals and if they had daughters with phenotypic records. Genotyping females with their own lactation records increased prediction accuracy, and the connection level has less relevance. The differences in genotyping females were independent of their estimated breeding value. The combined genotyping of males and females provided intermediate accuracy results regardless of the female selection strategy. Therefore, assuming that genotyping rams is interesting, the incorporation of genotyped females would be beneficial and worthwhile. The benefits of genotyping individuals from various generations were highlighted, although it was also possible to gain prediction accuracy when historic individuals were not considered. Greater genotyped population sizes resulted in more accuracy, even if the increase seems to reach a plateau.
Asunto(s)
Genoma , Genómica , Animales , Femenino , Genotipo , Masculino , Modelos Genéticos , Linaje , Fenotipo , Ovinos/genética , Oveja DomésticaRESUMEN
The availability of genomic marker panels has made possible more precise estimates of breeding values. Sheep breeding programs are implementing genomic selection. In Latxa dairy sheep breed, a previous study using pre-corrected data and a small number of genotyped animals did not show a clear advantage of genomic selection. The objective of the present study was to ascertain the possible benefits of GS for the Latxa breed based on more data than before and using better tools, in particular single-step genomic BLUP using metafounders to model missing pedigree. Goodness of prediction of pedigree and genomic evaluations was analyzed by cross-validation comparing predictions of young rams using whole and partial (truncated) data sets. The results showed that with the current available data, genetic and genomic evaluations have the same accuracy. Contrary to the previous study, predictions were nearly unbiased, which shows the advantage of using single-step genomic BLUP. However, genomic information did not yield more precise evaluations. This could be explained by the small number of sibs in the young rams.
Asunto(s)
Genómica , Selección Artificial , Oveja Doméstica/genética , Animales , Femenino , Efecto Fundador , Genoma , Genómica/métodos , Genotipo , Masculino , LinajeRESUMEN
Traditionally, breeding programs have estimated and managed inbreeding based on pedigree information. The availability of genomic marker panels has made possible new alternatives to achieve more precise estimates, for example in case of missing pedigree. The objective of the present study was to assess and compare, different estimation methods (pedigree-based methodologies, single SNP-based approach (homozygosity) and runs of homozygosity-based method) to analyze the evolution of genetic diversity measured as inbreeding or as coancestry of 3 selected populations of Latxa dairy sheep (Latxa Cara Rubia and Latxa Cara Negra from Euskadi and Navarre). Genomic data came from 972 artificial insemination rams genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) whose genealogy consisted of 4,484 animals. Inbreeding estimates based on molecular data were more similar between them than compared with those based on pedigree information. However, the SNP-based approach estimations of effective population size differed more, reflecting the sensitivity of effective population size to small changes in the evolution of inbreeding. The 2 Latxa Cara Negra populations showed increases of inbreeding rates with time and effective population sizes between 64 and 103 animals, depending on breed and methodology used. The Latxa Cara Rubia population did not show an increase in inbreeding rate, mainly due to semen importation from the related French population of Manech Tête Rousse. The effective size estimates based on coancestry increase show a higher variability and they are more sensitive to the source of information and the data structure considered. Realized effective population size based on individual increase in inbreeding were in agreement with the previous estimates. Coancestry evolution analysis based on DNA information showed an increase on coancestry during the last 10 yr in all breeds, as a consequence of the selection process. Moreover, the increase on coancestry between Latxa Cara Rubia and Manech Tête Rousse was more noticeable between than within each of those breeds.