Genomics-Assisted Breeding for Tomato Fruit Quality in the Next-Generation Omics Age - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 193

Chapter 12

Genomics-Assisted Breeding for Tomato Fruit
Quality in the Next-Generation Omics Age

MatthewP.Kinkadeand MajidR.Foolad

Abstract

The cultivated tomato, Solanum lycopersicum L., is the most consumed and most popular vegetable
crop in the world. It is the primary source of the carotenoid lycopene, a highly beneficial dietary
antioxidant whose consumption may reduce the incidence of certain cancer and heart diseases in
humans. Tomato is also an important model system for genetics and genomics studies that have
led to many discoveries, including identification and development of some of the earliest molecular
markers and genetic maps, fine mapping and cloning of the first plant disease resistance gene, and
fine mapping and cloning of the first QTL. Marker-assisted selection (MAS) has been employed
extensively in tomato for improving many simple traits. However, MAS has not been frequently used
to advance complex traits in tomato, although many QTLs have been identified for various quantitative
traits. In this chapter we look beyond the heavily reviewed QTL analysis approaches and focus mainly
on the use of new “omics” technology and its potential use for tomato breeding, in particular for
improving fruit quality. With the dawn of the genomics and next-generation sequencing ages, the role
of genomic tools in applied tomato breeding is changing. The tomato genome has been sequenced and
the information is freely available. Genomic and transcriptomic resources and bioinformatic methods
have become available, metabolomic methods have been established, segregating populations have
been analyzed for alterations in key metabolic traits on an “omic” scale, and large, multi-faceted
omics databases have been constructed. Reverse genetics approaches, such as TILLING, have recently
been employed to produce novel disease resistance and fruit quality traits in tomato. Mutagenized
populations have been developed for use in TILLING approaches, and the bioinformatic workflows
to handle high-throughput identification of mutations in candidate genes have been published. Thus,
the pillars now exist upon which a genomics-assisted breeding scheme could be devised for tomato.
The challenge is how to seamlessly incorporate these types of analyses, selection methods, and tools
into a practical breeding program, and determine whether or not the time and expense required for
such studies can be justified for use in contemporary tomato variety development programs.