Molecular breeding

Breeding efforts are and will be in the future critical to improve worldwide crop production for food, feed, non-food industrial and environmental aims. The recent development of "omics" sciences, in particular genomics, and bioinformatics give the great opportunity to be either integrated into traditional breeding schemes, or used to generate new breeding schemes and paradigms. There are important expectations from such technologies and from new genome-wide informations to enhance the effectiveness of plant breeding programs, starting from main crops such as tomato. When genotyping tools will not be anymore a limit, one issue crucial for future breeding will be the availability of well characterized germplasm collections. A detailed genetic analysis of the breeder's germplasm aided by DNA technologies will make more and more useful good programs of pre-breeding, to help in planning crosses and guiding the choice of inbred lines for hybrid combinations. As a side-aspect of this, DNA tools can be applied for DUS and hybrid purity testing. Molecular markers enable marker-assisted selection (MAS) for gene and QTL introgression, gene pyramiding and genetic ideotype breeding. MAS application presents several advantages such as increased reliability and efficiency provided by the fact that they can be scored at the seedling stage enabling indirect selection especially for quantitative traits with low heritabilities. MAS becomes particularly useful, or necessary when a phenotypic assay may be influenced by the environment, is particularly costly or technically difficult, MAS integration into classical breeding schemes, as well as the new possibilities are reviewed. Nowadays the cost of genotyping a plant rather than the cost of a datapoint, limited molecular marker polymorphism within cultivated tomato, and thus unavailability of closely-linked markers for all agronomically relevant traits, are the main limitations of MAS. However a trend towards an increased cost accessibility of genomics-based technologies is underway. On the other hand, in developing countries the unfamiliarity of many traditional plant breeders with the use of molecular markers and technologies still represents a major limitation. Eventually, for most crops MAS will be scaled up to the genomic level, consequently the breeder could practice whole genome selection. The expectations from genomics-assisted selection (GAS) are high for many species including tomato. The shifts to second and, soon, to third generation sequencing technologies will provide unique ways in which to conceive plant breeding programs. In addition, the development of phenomics and metabolomics should be taken into great consideration. Transgenic breeding, offers several advantages such as ability to overcome incompatibility barriers and the possibility to incorporate only the specific cloned gene into the recipient, thus avoiding the transfer of undesirable genes in introgressed chromosome regions from wild donors . Very strict release procedures unfortunately severely limit this opportunity, until the development of cisgenics or of other technical alternatives. Pyramiding of transgenes with either similar or complementary and/or additive effects is possible. It is here reviewed how tomato has been modified for improvement of different traits such as fruit quality, parthenocarpy, constitutive overproduction of antifungal compounds, bacterial and viral disease resistance and post-harvest and processing technology.

Breeding efforts are and will be in the future critical to improve worldwide crop production for food, feed, non-food industrial and environmental aims. The recent development of “omics” sciences, in particular genomics, and bioinformatics give the great opportunity to be either integrated into traditional breeding schemes, or used to generate new breeding schemes and paradigms. There are important expectations from such technologies and from new genome-wide information to enhance the effectiveness of plant breeding programs, starting from main crops such as Tomato. When genotyping tools will not be anymore a limit, one issue crucial for future breeding will be the availability of well characterized germplasm collections. A detailed genetic analysis of the breeder’s germplasm aided by DNA technologies will make more and more useful good programs of pre-breeding, to help in planning crosses and guiding the choice of inbred lines for hybrid combinations. As a side-aspect of this, DNA tools can be applied for DUS and hybrid purity testing. Molecular markers enable marker-assisted selection (MAS) for gene and QTL introgression, gene pyramiding and genetic ideotype breeding. MAS application presents several advantages such as increased reliability and efficiency provided by the fact that they can be scored at the seedling stage enabling indirect selection especially for quantitative traits with low heritabilities. MAS becomes particularly useful, or necessary when a phenotypic assay may be influenced by the environment, is particularly costly or technically difficult, MAS integration into classical breeding schemes, as well as the new possibilities are reviewed. Nowadays the cost of genotyping a plant rather than the cost of a data point, limited molecular marker polymorphism within cultivated Tomato, and thus unavailability of closely-linked markers for all agronomically relevant traits, are the main limitations of MAS. However a trend towards an increased cost accessibility of genomics-based technologies is underway. On the other hand, in developing countries the unfamiliarity of many traditional plant breeders with the use of molecular markers and technologies still represents a major limitation. Eventually, for most crops MAS will be scaled up to the genomic level, consequently the breeder could practice whole genome selection. The expectations from genomics-assisted selection (GAS) are high for many species including Tomato. The shifts to second and, soon, to third generation sequencing technologies will provide unique ways in which to conceive plant breeding programs. In addition, the development of phenomics and metabolomics should be taken into great consideration. Transgenic breeding, offers several advantages such as ability to overcome incompatibility barriers and the possibility to incorporate only the specific cloned gene into the recipient, thus avoiding the transfer of undesirable genes in introgressed chromosome regions from wild donors. Very strict release procedures unfortunately severely limit this opportunity, until the development of cisgenics or of other technical alternatives. Pyramiding of transgenes with either similar or complementary and/or additive effects is possible. It is here reviewed how Tomato has been modified for improvement of different traits such as fruit quality, parthenocarpy, constitutive overproduction of antifungal compounds, bacterial and viral disease resistance and post-harvest and processing technology.