No abstract

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We report an initial analysis of copy number variations (CNVs) in cattle selected for resistance or susceptibility to intestinal nematodes. We performed three array comparative genomic hybridization (CGH) experiments to compare Angus cattle with extreme phenotypes for fecal egg count and serum pepsinogen level. We identified 20 CNVs in total, of which 12 were within known chromosomes harboring or adjacent to gains or losses. About 85% of the CNV identified (17/20) overlapped with cattle CNV regions that were reported recently. Selected CNVs were further validated by independent methods using quantitative PCR (qPCR) and FISH. Pathway analyses indicated that annotated cattle genes within these variable regions are particularly enriched for immune function affecting receptor activities, signal transduction, and transcription. Analysis of transcription factor binding sites (TFBS) within the promoter regions of differentially expressed genes suggested that common transcription factors are probably involved in parasite resistance. These results provide valuable hypotheses for the future study of cattle CNVs underlying economically important health and production traits.

We have investigated the relationship between phenotypic and genetic correlations among a large number of quantitative traits (36) in three different environments in order to determine their degree of disparity and whether phenotypic correlations could be substituted for their genetic counterparts whatever the environment. We also studied the influence of the environment on genetic and phenotypic correlations. Twenty accessions (full-sib families) ofMedicago luPulina were grown in three environments. In two of these two levels of environmental stress were generated by harvesting plants at flowering and by growing plants in competition with barley, respectively. A third environment, with no treatment, was used as a control with no stress. Average values of pod and shoot weight indicate that competition induces the highest level of stress. The genetic and phenotypic correlations among the 36 traits were compared. Significant phenotypic correlations were obtained easily, while there was no genetic variation for 1 or the 2 characters being correlated. The large positive correlation between the genetic and phenotypic correlation matrices indicated a good proportionality between genetic and phenotypic correlations matrices but not their similarity. In a given environment, when only those traits with a significant genetic variance were taken into account, there were still differences between genetic and phenotypic correlations, even when levels of significance for phenotypic correlations were lowered. Consequently, it is dangerous to substitute phenotypic correlations for genetic correlations. The number of traits that showed genetic variability increased with increasing environmental stress, consequently the number of significant genetic correlations also increased with increasing environmental stress. In contrast, the number of significant phenotypic correlations was not influnced by the environment. The structures of both phenotypic and genetic matrices, however, depended on the environment, and not in the same way for both matrices.