http://www.cnr.it/ontology/cnr/individuo/prodotto/ID293388
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
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