GENOME-WIDE ASSOCIATION STUDY (GWAS) IN TOMATO 'DA SERBO' GERMPLASM, AN IMPORTANT SOURCE OF BIODIVERSITY (Contributo in atti di convegno)

Type
Label
  • GENOME-WIDE ASSOCIATION STUDY (GWAS) IN TOMATO 'DA SERBO' GERMPLASM, AN IMPORTANT SOURCE OF BIODIVERSITY (Contributo in atti di convegno) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Alternative label
  • TRANCHIDA-LOMBARDO V.*, MERCATI F.**, LONGO C.**, POMA D.***, MONFORTE A.****, GRANELL A.****, TUCCI M. *, GRILLO S. *, SUNSERI F.** (2014)
    GENOME-WIDE ASSOCIATION STUDY (GWAS) IN TOMATO 'DA SERBO' GERMPLASM, AN IMPORTANT SOURCE OF BIODIVERSITY
    in 58th Italian Society of Agricultural Genetics Annual Congress, Alghero, Italy, 15/18 September, 2014
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • TRANCHIDA-LOMBARDO V.*, MERCATI F.**, LONGO C.**, POMA D.***, MONFORTE A.****, GRANELL A.****, TUCCI M. *, GRILLO S. *, SUNSERI F.** (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • *) Institute of Biosciences and Bioresources (IBBR) - CNR, Research Division Portici **) Department of AGRARIA, University Mediterranea of Reggio Calabria ***) Department of Agraria, University of Palermo ****) Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia (Spain) (literal)
Titolo
  • GENOME-WIDE ASSOCIATION STUDY (GWAS) IN TOMATO 'DA SERBO' GERMPLASM, AN IMPORTANT SOURCE OF BIODIVERSITY (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#isbn
  • 978-88-904570-4-3 (literal)
Abstract
  • Tomato (Solanum lycopersicum L.) shows a noteworthy morphological diversification in different geographical regions. Particularly, Italy and Spain have been recognized as secondary centres of diversification being tomato cultivation characterized by a wealth of landraces with different fruit sizes and shapes. Among the germplasm collections, long shelf-life (LSL) tomatoes typical of the Mediterranean region, the so-called tomato 'da serbo', form a group of drought tolerant landraces that can grow without irrigation. The mutant phenotype is characterized by small round tomatoes with excellent nutritional properties due to the elevated concentration of sugars and antioxidant substances. The valorisation of this ancient tomato germplasm is important to extend the genetic basis of the tomato genome and to limit the genetic erosion caused by the employment of modern cultivars, thus conserving an important source of biodiversity. The present study provided a Genome-Wide Association Study using an important LSL tomato collection from south Italy and Spain, in order to identify SNPs associated to genome of the analysed collection. Genome-wide SNP genotyping was performed using the Infinium assay that was developed by the Solanaceae Coordinated Agricultural Project (SolCAP). The data obtained from the assays were analysed using the Genotyping Module of the GenomeStudio software (Illumina Inc.). The SNP dataset was accurately inspected and properly modified according to the following criteria: i) samples with low SNP call quality (p50GC<0.54) were removed; ii) SNPs with a GenTrain score higher than 0.6 were retained; iii) 100% monomorphic markers were removed; iv) markers with a number of NCs higher than 20% were removed, as well as the 100% NC markers; v) among duplicated genotypes, the SNP profiles showing the lowest percentage of NC markers were retained. The GWAS was carried out using GAPIT, the R package Genome Association and Prediction Integrated Tool. A Mixed Linear Model was performed and a kinship (k) matrix was calculated to define the variance-covariance structure of the random effects among individuals for association mapping. SNPs with Minor Allele Frequencies (MAFs) less than 0.05 were removed from the analysis, the Benjamini-Hochberg procedure adjusts for the multiple testing problem by controlling the false discovery rate (FDR) at 0.05. In order to discover private markers associated to the germplasm collection and identified by GWAS analysis, a Manhattan plot was developed by GAPIT package, where the genomic position of the SNPs in the genome was in the X-axis, whilst the Y-axis represented the negative log base 10 of the P values. Associations are expressed as -log10(P) and SNPs with stronger association with the trait had a large Y-coordinate value. The GWAS approach was able to identify several SNPs associated to the LSL tomato genome useful to develop molecular markers linked to traits of interest for future breeding programmes. The identification of SNPs that directly affect protein and gene functions related to LSL could represent a useful tool to develop a candidate gene isolating program in tomato. This work was supported by the Project CISIA of the National Research Council of Italy to S.G. (literal)
Prodotto di
Autore CNR
Insieme di parole chiave

Incoming links:


Prodotto
Autore CNR di
Insieme di parole chiave di
data.CNR.it