Garcia-Pedrajas N.,University of Cordoba, Spain |
Ortiz-Boyer D.,University of Cordoba, Spain |
Garcia-Pedrajas M.D.,Experimental Station la Mayora |
Fyfe C.,University of West of Scotland
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2010
Translation initiation sites (TIS) recognition is one of the first steps in gene structure prediction, and one of the common components in any gene recognition system. Many methods have been described in the literature to identify TIS in transcripts such as mRNA, EST and cDNA sequences. However, the recognition of TIS in DNA sequences is a far more challenging task, and the methods described so far for transcripts achieve poor results in DNA sequences. Most methods approach this problem taking into account its biological features. In this work we try a different view, considering this classification problem from a purely machine learning perspective. From the point of view of machine learning, TIS recognition is a class imbalance problem. Thus, in this paper we approach TIS recognition from this angle, and apply the different methods that have been developed to deal with imbalance datasets. Results show an advantage of class imbalance methods with respect to the same methods applied without considering the class imbalance nature of the problem. The applied methods are also able to improve the results obtained with the best method in the literature, which is based on looking for the next in-frame stop codon from the putative TIS that must be predicted. © 2010 Springer-Verlag.
Palomares-Rius F.J.,Experimental Station La Mayora |
Lopez-Sese A.I.,Experimental Station La Mayora |
Gomez-Guillamon M.L.,Experimental Station La Mayora
Acta Horticulturae | Year: 2010
The Zimbabwean genotype TGR-1551 had been found to be resistant to Bemisia tabaci Genn. in previous studies. In order to have a better knowledge of this resistance and determine the most suitable character to evaluate the genetic resistance to B. tabaci, three whitefly life-parameters have been tested in a RIL population (F7) derived from a cross between 'TGR-1551' and the susceptible Spanish cultivar 'Bola de Oro'. Plants of each parent, their F 1 and 62 RIL were grown in a greenhouse under natural conditions of whitefly infestation. In each plant, the number of adults of B. tabaci, ovoposition and number of empty pupal cases were recorded. Significant differences were found between parents for each whitefly lifeparameter: TGR-1551 showed a high level of resistance whatever the parameter was considered, and 'Bola de Oro' behaved as highly susceptible to B. tabaci. The low number of adults and low ovoposition found on leaves of TGR-1551 suggested the presence of non-preference mechanisms in this genotype. In the F1 population, the number of adult whiteflies and the ovoposition was similar to 'Bola de Oro', while the number of empty pupal cases was similar to the number found in TGR-1551. These results pointed to the existence of antibiotic mechanisms in the resistant genotype which impede B. tabaci to reach its adult stage. Highly significant differences among RIL were observed for the three parameters, mainly for the number of empty pupal cases, explaining the 43 % of the variance observed. Some RIL behaved like TGR-1551 and some like the F1, which suggested a different genetic control of antixenosis and antibiosis mechanisms in TGR-1551. Dominance effects seem to be involved in antibiosis, while antixenosis, measured as ovoposition, should be regulated by recessive factors. These results confirm the usefulness of the number of empty pupal cases in the selection of B. tabaci resistance and for genetic studies.
Yuste-Lisbona F.J.,Experimental Station La Mayora |
Capel C.,University of Almeria |
Sarria E.,Experimental Station La Mayora |
Gomez-Guillamon M.L.,Experimental Station La Mayora |
And 3 more authors.
Acta Horticulturae | Year: 2010
Melon (Cucumis melo L.) is a valuable crop grown in temperate and tropical regions worldwide. Powdery mildew caused by Podosphaera xanthii is one of the most frequent diseases of melon. The genotype TGR-1551 is resistant to races 1, 2, and 5 of powdery mildew. We constructed a genetic linkage map using an F 2 population derived from a cross between TGR-1551 and the susceptible Spanish cultivar 'Bola de Oro'. The software JoinMap® 4.0 was used to locate on the linkage map a total of 429 loci: 241 AFLP, 55 RAPD, 117 SSR, 14 SCAR/CAPS/dCAPS, and 2 phenotypic traits (Vat and a loci), which were distributed among 12 linkage groups with a LOD score ≥6.0. The map spans 1318.2 cM, with an average of 3.1 cM/marker. Powdery mildew resistance was evaluated as a quantitative trait and then, QTL analyses were performed using interval mapping and multiple QTL model mapping with MapQTL ® 5.0 software. Both methods detected a dominant QTL for resistance to either 1, 2 or 5 races of powdery mildew, all located at the same genomic region of G4. Therefore, these QTL were considered as a unique QTL designated as Pm-R. This QTL was supported by LOD scores of 26.5, 33.3, and 36.2, explaining 53.6, 61.9, and 64.9% of the phenotypic variance in the mapping population for resistance to powdery mildew races 1, 2, and 5, respectively. In addition, four codominant markers, previously described as linked to the dominant powdery mildew resistance gene, were linked to the Pm-R QTL, which suggests the correspondence between this QTL and the dominant resistance gene. One of those codominant markers, PM3-CAPS, cosegregated with the Pm-R QTL, and the markers PM2-CAPS and PM4-dCAPS flanked this QTL. These markers could be used to select resistance to powdery mildew in melon breeding.