Search results for "single nucleotide polymorphism"
showing 10 items of 69 documents
Parentage Atlas of Italian Grapevine Varieties as Inferred From SNP Genotyping.
2021
The Italian grape germplasm is characterized by a high level of richness in terms of varieties number, with nearly 600 wine grape varieties listed in the Italian National Register of Grapevine Varieties and with a plethora of autochthonous grapes. In the present study an extended SNP genotyping has been carried out on Italian germplasm of cultivated Vitis vinifera subsp. sativa and Vitis hybrids. Several hundred Italian varieties maintained in the repositories of scientific Institutions and about one thousand additional varieties derived from previous studies on European, Southern Italy, Magna Graecia and Georgian germplasm were considered. The large genotyping data obtained were used to ch…
High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily
2016
The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars by using morphological and microsatellite markers. In this study, simple sequence repeat (SSR) were utilized to verify the true-to-typeness of a large clone collection (101) belonging to 21 biotypes of the most 10 cultivated Sicilian cultivars. Afterwards, 42 Organization Internationale de la Vigne…
Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range
2021
Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individu…
50,000 years of ice and seals: Impacts of the Last Glacial Maximum on Antarctic fur seals
2021
Abstract Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice‐associated prey and ice‐free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range. Population size trends and divergence events were investigated using continuous‐time size estimation analysis and divergence time estimation models. The combined results indicated that a panmictic population …
The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild
2013
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.
A population genomics analysis of the native Irish Galway sheep breed.
2019
SUMMARYThe Galway sheep population is the only native Irish sheep breed and represents an important livestock genetic resource, which is currently categorised as “at-risk”. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway breed and suggest more recent gene flow from the Suffolk sheep breed. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding a…
Association study between beta-defensin gene polymorphisms and mastitis resistance in Valle del Belice dairy sheep breed
2016
Abstract Mastitis is generally caused by bacteria, and it is the most common disease in livestock species. Defensins are peptides with a broad spectrum of antimicrobial activity and β-defensin genes have been studied in several livestock species due to their important role in the innate immune response. The aim of this study was to establish an association between polymorphisms in the β-defensin 1 and 2 genes and mastitis resistance in the Valle del Belice dairy sheep. Data consisted of 1855 and 2804 observations for case and control group, respectively. Six single nucleotide polymorphisms and seven haplotypes were selected for association studies with mastitis. In particular, polymorphism …
Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds
2018
The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del B…
Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures
2019
Genome-wide association studies (GWASes) have become a powerful tool for identifying genomic regions associated with important traits in livestock. Milk production traits in dairy sheep are measured at different time points during their life span. Using phenotypic data generated from longitudinal traits could improve the power of association studies but until now have received less attention in GWASes as a methodology and has not been implemented. The aim of this study was to carry out a GWAS for milk production traits in Valle del Belice sheep using repeated measures. After quality control, 469 ewes and 37 228 SNPs were retained for the analysis, and phenotypic data included 5586 test-day …
MicroRNAs and Drinking : Association between the Pre-miR-27a rs895819 Polymorphism and Alcohol Consumption in a Mediterranean Population
2016
Recently, microRNAs (miRNA) have been proposed as regulators in the different processes involved in alcohol intake, and differences have been found in the miRNA expression profile in alcoholics. However, no study has focused on analyzing polymorphisms in genes encoding miRNAs and daily alcohol consumption at the population level. Our aim was to investigate the association between a functional polymorphism in the pre-miR-27a (rs895819 A>G) gene and alcohol consumption in an elderly population. We undertook a cross-sectional study of PREvención con DIeta MEDiterránea (PREDIMED)-Valencia participants (n = 1007, including men and women aged 67 7 years) and measured their alcohol consumption (to…