RESUMEN
Two novel methods for genome wide selection (GWS) were examined for predicting the genetic merit of animals using SNP information alone. A panel of 1,546 dairy bulls with reliable EBVs was genotyped for 15,380 SNPs that spanned the whole bovine genome. Two complexity reduction methods were used, partial least squares (PLS) and regression using a genetic algorithm (GAR), to find optimal solutions of EBVs against SNP information. Extensive internal cross-validation was used tofind the best predictive models followed by external validation (without direct use of the pedigree or SNP location). Both PLS and GAR provided both accurate fit to the training data set for somatic cell count (SCC) (max r = 0.83) and fertility (max r = 0.88) and showed an accuracy of prediction of r = 0.47 for SCC, and r = 0.72 for fertility. This is the first empirical demonstration that genome wide selection can account for a very high proportion of additive genetic variation in fitness traits whilst exploiting only a small percentage of available SNP information, without use of pedigree or QTL mapping. PLS was computationally more efficient than GAR.
Asunto(s)
Industria Lechera , Fertilidad/genética , Genoma , Mastitis/genética , Polimorfismo de Nucleótido Simple , Animales , BovinosRESUMEN
Past breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome-wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [H(o)] and allelic richness [A]) were observed over the 25-year time period (1975-1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub-sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome-wide level.
Asunto(s)
Bovinos/genética , Variación Genética , Genoma , Selección Genética , Animales , Australia , Bovinos/clasificación , Marcadores Genéticos , Endogamia , Polimorfismo de Nucleótido SimpleAsunto(s)
Proteínas de la Membrana/genética , Chaperonas Moleculares/genética , Proteínas del Tejido Nervioso/genética , Lipofuscinosis Ceroideas Neuronales/genética , Mapeo de Híbrido por Radiación/métodos , Animales , Bovinos , Cromosomas de los Mamíferos , Cartilla de ADN , Ligamiento Genético , Reacción en Cadena de la Polimerasa/métodosRESUMEN
The occurrence of severe fetal dystocia due to hydrops fetalis associated with pulmonary aplasia in two male and pulmonary hypoplasia in one female Australian Dexter fetuses from two herds is described. Obstetrical intervention by caesarean section was required for delivery of the fetuses, with mortalities in one dam and the 3 calves. Clinical, pathological and genetic features are tabulated to assist in distinguishing pulmonary hypoplasia-associated hydrops fetalis from the more prevalent disorder of chondrodysplasia in Dexter cattle. Anasarca and complete absence or presence of only rudimentary lung tissue in a large thoracic cavity clearly distinguishes this entity from the lesions of Dexter chondrodysplasia that include severe micromelia and abundant lung tissue in a small thoracic cavity with shortened spine and rib cage. Pedigree information suggested that Dexter hydrops may be transmitted in an autosomal recessive manner.
Asunto(s)
Enfermedades de los Bovinos/genética , Enfermedades de los Bovinos/patología , Hidropesía Fetal/veterinaria , Linaje , Animales , Bovinos , Cesárea/veterinaria , Resultado Fatal , Femenino , Hidropesía Fetal/genética , Hidropesía Fetal/patología , Hiperplasia/patología , Hiperplasia/veterinaria , Pulmón/anomalías , Pulmón/patología , Masculino , Embarazo , Costillas/anomalías , Costillas/patologíaRESUMEN
The bovine genome sequence project and the discovery of many thousands of bovine single nucleotide polymorphisms has opened the door for large-scale genotyping studies to identify genes that contribute to economically important traits with relevance to the beef and dairy industries. Large amounts of DNA will be required for these research projects. This study reports the use of the whole-genome amplification (WGA) method to create an unlimited supply of DNA for use in genotyping studies and long-term storage for future gene discovery projects. Two commercial WGA kits (GenomiPhi, Amersham Biosciences, Sydney, Australia, and REPLI-g, Qiagen, Doncaster, Australia) were used to amplify DNA from straws of bull semen, resulting in an average of 7.2 and 67 microg of DNA per reaction, respectively. The comparison of 3.5 kb of sequences from the amplified and unamplified DNA indicated no detectable DNA differences. Similarly, gene marker analysis conducted on genomic DNA and DNA after WGA indicated no difference in marker amplification or clarity and accuracy of scoring for approximately 10,000 single nucleotide polymorphism markers when compared with WGA samples genotyped in duplicate. These results illustrate that WGA is a suitable method for the amplification and recovery of DNA from bull semen samples for routine genomic investigations.