An association mapping approach to identify favourable alleles for tomato fruit quality breeding

BMC Plant Biology

Research Article

Antonietta D’Alessandro¹  Mario Parisi¹  Giuseppe Mennella¹  Gianluca Francese¹  Teodoro Cardi¹  Marco Milone¹  Amalia Barone²  Maria Manuela Rigano²  Valentino Ruggieri²  Adriana Sacco² 

[1] Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l’Orticoltura (CRA-ORT), Via Cavalleggeri 25, 84098, Pontecagnano, SA, Italy;Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy;

关键词: Candidate genes;    Fruit quality;    Genome-wide association;    Metabolite analysis;    Mixed Linear Model;    Solanum lycopersicum;    SolCAP Infinium array;   

DOI  :  10.1186/s12870-014-0337-9

 received in 2014-07-09, accepted in 2014-11-17,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundGenome Wide Association Studies (GWAS) have been recently used to dissect complex quantitative traits and identify candidate genes affecting phenotype variation of polygenic traits. In order to map loci controlling variation in tomato marketable and nutritional fruit traits, we used a collection of 96 cultivated genotypes, including Italian, Latin American, and other worldwide-spread landraces and varieties. Phenotyping was carried out by measuring ten quality traits and metabolites in red ripe fruits. In parallel, genotyping was carried out by using the Illumina Infinium SolCAP array, which allows data to be collected from 7,720 single nucleotide polymorphism (SNP) markers.ResultsThe Mixed Linear Model used to detect associations between markers and traits allowed population structure and relatedness to be evidenced within our collection, which have been taken into consideration for association analysis. GWAS identified 20 SNPs that were significantly associated with seven out of ten traits considered. In particular, our analysis revealed two markers associated with phenolic compounds, three with ascorbic acid, β-carotene and trans-lycopene, six with titratable acidity, and only one with pH and fresh weight. Co-localization of a group of associated loci with candidate genes/QTLs previously reported in other studies validated the approach. Moreover, 19 putative genes in linkage disequilibrium with markers were found. These genes might be involved in the biosynthetic pathways of the traits analyzed or might be implied in their transcriptional regulation. Finally, favourable allelic combinations between associated loci were identified that could be pyramided to obtain new improved genotypes.ConclusionsOur results led to the identification of promising candidate loci controlling fruit quality that, in the future, might be transferred into tomato genotypes by Marker Assisted Selection or genetic engineering, and highlighted that intraspecific variability might be still exploited for enhancing tomato fruit quality.

【 授权许可】

Unknown   
© Ruggieri et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.