Predicting site index from climate and soil variables for cork oak (Quercus suber L.) stands in Portugal

Site productivity, assessed through site index, was modelled using partial least squares regression as a function of soil and climatic variables. Two alternative models were developed: a full model, considering all available explanatory variables, and a reduced model, considering only variables that can be obtained without digging a soil pit. The reduced model was used for mapping the site index distribution in Portugal, on the basis of existing digital cartography available for the whole country. The developed models indicate the importance of water availability and soil water holding capacity for site index value distribution. Site index was related to climate, namely evaporation and frost, and soil characteristics such as lithology, soil texture, soil depth, thickness of the A horizon and soil classification. The variability of the estimated values within the map (9.5–16.8 m with an average value of 13.4 m) reflects the impact of soil characteristics on the site productivity estimation. These variables should be taken into consideration during the establishment of new plantations of cork oak, and management of existing plantations. Results confirm the potential distribution of cork oak in coastal regions. They also suggest the existence of a considerable area, located both North and South of the Tagus river, where site indices values of medium (]13;15]) to high (]15;17]) productivity classes may be expected. The species is then expected to be able to have good productivity along the northern coastal areas of Portugal, where presently it is not a common species but where, according to historical records, it occurred until the middle of the sixteenth century. The present research focused on tree growth. Cork growth and cork quality distribution needs to be further researched through the establishment of long term experimental sites along the distribution area of cork oak, namely in the central and northern coastal areas of the countryinfo:eu-repo/semantics/publishedVersio

Evaluating alternate models to estimate genetic parameters of calving traits in United Kingdom Holstein-Friesian dairy cattle

<p>Abstract</p> <p>Background</p> <p>The focus in dairy cattle breeding is gradually shifting from production to functional traits and genetic parameters of calving traits are estimated more frequently. However, across countries, various statistical models are used to estimate these parameters. This study evaluates different models for calving ease and stillbirth in United Kingdom Holstein-Friesian cattle.</p> <p>Methods</p> <p>Data from first and later parity records were used. Genetic parameters for calving ease, stillbirth and gestation length were estimated using the restricted maximum likelihood method, considering different models i.e. sire (−maternal grandsire), animal, univariate and bivariate models. Gestation length was fitted as a correlated indicator trait and, for all three traits, genetic correlations between first and later parities were estimated. Potential bias in estimates was avoided by acknowledging a possible environmental direct-maternal covariance. The total heritable variance was estimated for each trait to discuss its theoretical importance and practical value. Prediction error variances and accuracies were calculated to compare the models.</p> <p>Results and discussion</p> <p>On average, direct and maternal heritabilities for calving traits were low, except for direct gestation length. Calving ease in first parity had a significant and negative direct-maternal genetic correlation. Gestation length was maternally correlated to stillbirth in first parity and directly correlated to calving ease in later parities. Multi-trait models had a slightly greater predictive ability than univariate models, especially for the lowly heritable traits. The computation time needed for sire (−maternal grandsire) models was much smaller than for animal models with only small differences in accuracy. The sire (−maternal grandsire) model was robust when additional genetic components were estimated, while the equivalent animal model had difficulties reaching convergence.</p> <p>Conclusions</p> <p>For the evaluation of calving traits, multi-trait models show a slight advantage over univariate models. Extended sire models (−maternal grandsire) are more practical and robust than animal models. Estimated genetic parameters for calving traits of UK Holstein cattle are consistent with literature. Calculating an aggregate estimated breeding value including direct and maternal values should encourage breeders to consider both direct and maternal effects in selection decisions.</p

Association and Haplotype Analyses of Positional Candidate Genes in Five Genomic Regions Linked to Scrotal Hernia in Commercial Pig Lines

Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully. Using a family-based analysis we found that four regions surrounding ELF5, KIF18A, COL23A1 on chromosome 2, and NPTX1 on chromosome 12, respectively, may contain the genetic variants important for the development of the scrotal hernia in pigs. These findings were replicated in another case-control dataset. The SNPs around the ELF5 region were in high linkage disequilibrium with each other, and a haplotype containing SNPs from ELF5 and CAT was highly significantly associated with hernia development. Extensive re-sequencing work focused on the KIF18A gene did not detect any further SNPs with extensive association signals. These genes may be involved in the estrogen receptor signaling pathway (KIF18A and NPTX1), the epithelial-mesenchymal transition (ELF5) and the collagen metabolism pathway (COL23A1), which are associated with the important molecular characteristics of hernia pathophysiology. Further investigation on the molecular mechanisms of these genes may provide more molecular clues on hernia development in pigs