Maria Federico

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Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS)(More)
Single nucleotide polymorphisms (SNPs) have rapidly become the molecular marker of choice in plant and animal association mapping (AM) studies. In this work, a genome-wide association study (GWAS) and candidate quantitative trait loci (cQTL) approaches were used to identify SNP markers associated with seed quality traits, in a Brassica napus L. association(More)
Subfunctionalization is the process by which a pair of duplicated genes, or paralogs, experiences a reduction of individual expression patterns or function while still reproducing the complete expression pattern and function of the ancestral gene. Two germin-like protein (GLP)-encoding genes, GerB and GerF, are paralogs that belong to a small gene family in(More)
The extent of genome redundancy exhibited by Brassica species provides a model to study the evolutionary fate of multi-copy genes and the effects of polyploidy in economically important crops. Phytoene synthase (PSY) catalyzes the first committed reaction of the carotenoid biosynthetic pathway, which has been shown to be rate-limiting in Brassica napus(More)
The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs) that are bound by a given Transcription Factor to regulate gene expression or repression. In turn, DNA structured motifs are a mathematical counterpart that models sets of TFBSs that work in concert in the gene(More)
With a growing number of online videos, many producers feel the need to use video captions in order to expand content accessibility and face two main issues: production and alignment of the textual transcript. Both activities are expensive either for the high labor of human resources or for the employment of dedicated software. In this paper, we focus on(More)
This paper presents new optimizations designed to improve an algorithm at the state-of-the-art for filtering sequences as a preprocessing step to the task of finding multiple repeats allowing a given pairwise edit distance between pairs of occurrences. The target application is to find possibly long repeats having two or more occurrences, such that each(More)
Phytoene synthase (PSY) has been shown to catalyze the first committed and rate-limiting step of carotenogenesis in several crop species, including Brassica napus L. Due to its pivotal role, PSY has been a prime target for breeding and metabolic engineering the carotenoid content of seeds, tubers, fruits and flowers. In Arabidopsis thaliana, PSY is encoded(More)