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Molecular Mapping of Quantitative Trait Loci in Tomato

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The Tomato Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

A major objective in modern biology is deciphering the genetic and molecular bases of natural phenotypic variation. Over the past three decades, the tomato clade (Solanum sect. Lycopersicon) has been a model system not only for the identification and positional cloning of quantitative trait loci (QTL), but also for the development of new molecular breeding strategies aimed at a more efficient exploration and exploitation of the rich biodiversity stored in wild germplasm for hundreds of biologically and agronomically relevant quantitative traits. The numerous QTL mapping studies conducted so far have resulted in the detection of several thousands of QTL. Despite this wealth of genetic information, the molecular bases have been revealed for only a handful of major QTL. The release of the tomato genome sequences, along with the rapid development of cost-effective next-generation sequencing (NGS) technologies, new mapping resources, and the evergrowing ‘‘omic’’ platforms, are holding the promise to reverse this trend. This deluge of genomic resources are undoubtedly reshaping QTL analyses also in this crop, allowing a reexamination of the variation and inheritance of complex traits at the intraspecific level, increasing the spectrum of potentially valuable alleles available for breeding. In this framework, precision phenotyping, advanced bioinformatics tools, as well as public phenotype “warehousing” databases are foreseen as the necessary tools to boost our understanding of the genetic and molecular architecture of quantitative traits, and to guarantee sustainable crop improvements in the face of an evergrowing human population and changing climates.

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Abbreviations

AB:

Advanced backcross

AM:

Association mapping

BC:

Backcross

BIL:

Backcross inbred line

cM:

CentiMorgans

COSII:

Conserverd ortholog set II

GWAS:

Genome-wide Association Studies

IL:

Introgression line

ILH:

Introgression line hybrid

LD:

Linkage disequilibrium

MAF:

Minor frequency slleles

MAS:

Marker-assisted selection

MLMM:

Multilocus mixed model

NGS:

Next-generation sequencing

NIL:

Near isogenic line

PCR:

Polymerase chain reaction

QTL:

Quantitative trait loci

QTN:

Quantitative trait nucleotide

RFLP:

Restriction fragment length polymorphism

RIL:

Recombinant inbred line

RNAi:

RNA interference

RS:

Reproductive stage

SG:

Seed germination

SGe:

Selective genotyping

SGN:

SOL genomics network

SNP:

Single nucleotide polymorphism

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Acknowledgments

The authors thank all the colleagues who provided unpublished information and apologize to those authors whose work we could not highlight because of space limitations. Research in the laboratory of S. Grandillo and M. Cammareri was supported in part by the EUSOL project PL 016214-2, the Italian Ministry of University and Research (MIUR) project GenoPOM-PRO, a dedicated grant from the Italian Ministry of Economy and Finance to the National Research Council for the project “Innovazione e Sviluppo del Mezzogiorno—Conoscenze Integrate per Sostenibilità ed Innovazione del Made in Italy Agroalimentare—Legge n. 191/2009,” and the PON R&C 2007–2013 grant financed by the Italian MIUR in cooperation with the European Funds for the Regional Development (FESR).

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  1. Research Division Portici, Italian National Research Council, Institute of Bioscience and BioResources (CNR-IBBR), Via Università 133, 80055, Portici, Naples, Italy

    Silvana Grandillo & Maria Cammareri

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  1. Silvana Grandillo
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  2. Maria Cammareri
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Correspondence to Silvana Grandillo .

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Editors and Affiliations

  1. GAFL, INRA, Montfavet Cedex, France

    Mathilde Causse

  2. Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA

    Jim Giovannoni

  3. INRA-INP Toulouse, Castanet Tolosan, France

    Mondher Bouzayen

  4. INRA-INP Toulouse, Castanet Tolosan, France

    Mohamed Zouine

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Grandillo, S., Cammareri, M. (2016). Molecular Mapping of Quantitative Trait Loci in Tomato. In: Causse, M., Giovannoni, J., Bouzayen, M., Zouine, M. (eds) The Tomato Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-53389-5_4

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