ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

BACKGROUND: Brown trout is one of the most widespread fresh-water fish species in Europe. The evolutionary history of and phylogenetic relationships between brown trout populations are complex, and this is especially true for Italian populations, which are heavily influenced in different ways by stocking practices. The characterization of the genetic structure of Italian brown trout populations may give information on the risk of losing endemic Italian populations due to lack of genetic diversity or to admixture with stocking populations. The identification of signatures of selection, and the information deriving from dense genotyping data will help genotype-informed breeding programs. We used a ddRAD-seq approach to obtain more than 100,000 single nucleotide polymorphisms (SNPs), and to characterize the population structure and signatures of selection in 90 brown trout samples. RESULTS: Italian brown trout populations are genetically differentiated, although the stocking practices have introduced strong admixture in endemic Italian trout, especially with the Atlantic lineage. Most of the analysed populations showed high levels of kinship and inbreeding. We detected putative signatures of selection using different approaches, and investigated if the regions were enriched for functional categories. Several regions putatively under selection and characterized by a reduction in heterozygosity across all the studied populations are enriched for genes involved in the response to viral infections. CONCLUSIONS: Our results, which show evidence of admixture with the Atlantic lineage (commonly used for stocking), confirm the need for controlling stocking practices, in order to avoid the erosion of the endemic gene pool; given the apparently high levels of kinship and inbreeding in local populations, our results also show the need to take action for increasing gene diversity. In addition, we used the genetically-distinct lineages to detect signatures of selection and we identified putative signatures of selection in several regions associated with resistance to infectious diseases. These constitute candidate regions for the study of resistance to infections in wild and farmed trout.

Kernel oil content and oil composition in walnut (Juglans regia L.) accessions from north-eastern Italy.

BACKGROUND: Walnut oil use is currently limited by its poor oxidative stability due to the high percentage of polyunsaturated fatty acids. Modifying the oil composition may be a goal in walnut breeding to increase interest in this crop. Exploring natural variability and identifying the main environmental factors affecting oil quality are necessary in crop selection. Therefore 190 wild accessions were collected and evaluated during 2013 and 2014 for oil content and its fatty acid profile and compared with five commercial cultivars as references. RESULTS: High variation in kernel oil content and fatty acid composition was found in the native walnut. Kernel oil content ranged from 54.2 to 72.2% (w/w). The major fatty acids were linoleic (range 46.9-68.6%), oleic (10.0-25.1%), linolenic (6.9-17.6%), palmitic (3.9-11.4%) and stearic (1.1-5.2%) acids. Some accessions had oil with a fatty acid ratio very different from the reference commercial cultivars, especially the oleic acid/polyunsaturated fatty acid (PUFA) ratio. A significant linear relationship and positive correlation between the daily minimum temperature and oleic acid content was observed in the wild walnuts. CONCLUSION: The wide variation in fatty acid content and composition allows superior accessions to be selected for diffusion among growers. A suitable strategy would be to make a selection against PUFA content rather than just for high oleic acid. In addition, the selected high oleic accessions, before being utilized per se or as donor parents in breeding programs, have to demonstrate they are not adversely affected by the environment. © 2017 Society of Chemical Industry.