Search results for "genotyping"
showing 10 items of 250 documents
An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
2016
[EN] Background: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. Results: We report the Genoty…
Assessment of genetic diversity and relatedness in the Latvian potato genetic resources collection by DArT genotyping
2015
Potato (Solanum tuberosumL.) has been cultivated in Latvia since the 17th century, and formal breeding programmes have been established since the start of the 20th century. The Latvian potato genetic resource collection consists of 83 accessions of Latvian origin, including landraces, old cultivars released starting from the 1930's, modern cultivars and breeding material. These are maintained in field andin vitrocollections. Pedigree information about the potato cultivars is often limited, and the use of hybrids of local cultivars as parents is common in the Latvian potato breeding programme. Ninety-four Latvian potato varieties and breeding lines and some commonly used foreign accessions w…
Discovery of a Major QTL Controlling Trichome IV Density in Tomato Using K-Seq Genotyping
2021
[EN] Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, breeding programs could incorporate some natural defense mechanisms, such as those afforded by trichomes, present in certain Solanum species. We have identified a S. pimpinellifolium accession with very high density of this type of trichomes. This accession was crossed with a S. lycopersicum var. cerasiforme and a S. lycopersicum var. lycopersicum accessions, and the two resulting F2 …
Single-Spore Extraction for Genetic Analyses of Arbuscular Mycorrhizal Fungi
2020
International audience; Biomass of arbuscular mycorrhizal fungi (AMF, Glomeromycota) is often only available in small quantities as these fungi are obligate biotrophs and many species are difficult to cultivate under controlled conditions. Here, I describe a simple, efficient approach to produce crude extracts from single or a small number of spores that can be used for genotyping AMF.
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…
A genomic map of climate adaptation in Mediterranean cattle breeds
2019
International audience; Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate sub-types. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional…
Variation in gene expression within clones of the earthworm Dendrobaena octaedra
2017
Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones) is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured…
Morphological and molecular variability within the fig cultivar 'Dottato' in the Italian protected designation origin area "fichi di Cosenza"
2017
The morphological and molecular diversity among fig accessions of 'Dottato', found in the PDO "Fichi di Cosenza" area was studied by evaluating 24 morphological traits and by genotyping with 18 microsatellite markers. The microsatellite allelic profiles among the putative clones of 'Dottato' indicated a moderate genetic variability, discriminating unambiguously most of the accessions. Only two groups of identity were found. The average expected and observed heterozygosity were 0.43 and 0.62, respectively. The mean polymorphic information content (PIC) was 0.4, varying from 0.08 (LMFC26) to 0.067 (FCUP 38-6). The morphological clustering allowed the distinction of all genotypes. Some genotyp…
Cytological and molecular characterization of three gametoclones of Citrus clementina
2013
Abstract Background Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). Results Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a sing…