Amalia Barone

RFLP maps of potato and their alignment with the homoeologous tomato genome

SummaryAn RFLP linkage map of the potato is presented which comprises 304 loci derived from 230 DNA probes and one morphological marker (tuber skin color). The self-incompatibility locus of potato was mapped to chromosome I, which is homoeologous to tomato chromosome I. By mapping chromosome-specific tomato RFLP markers in potato and, vice versa, potato markers in tomato, the different potato and tomato RFLP maps were aligned to each other and the similarity of the potato and tomato genome was confirmed. The numbers given to the 12 potato chromosomes are now in accordance with the established tomato nomenclature. Comparisons between potato RFLP maps derived from different genetic backgrounds revealed conservation of marker order but differences in chromosome and total map length. In particular, significant reduction of map length was observed in interspecific compared to intraspecific crosses. The distribution of regions with distorted segregation ratios in the genome was analyzed for four potato parents. The most prominent distortion of recombination was found to be caused by the self-incompatibility locus.

RFLP mapping on potato chromosomes of two genes controlling extreme resistance to potato virus X (PVX)

SummaryTwo different chromosomal locations of major genes controlling extreme resistance to potato virus X (PVX) were found by restriction fragment length polymorphism (RFLP) analysis of two populations segregating for the resistance. The resistance geneRx1 mapped to the distal end of chromosome XII, whereasRx2 was located at an intermediate position on linkage group V in a region where reduced recombination and segregation distortion have also been observed. These linkage anomalies were due to abnormal behaviour of the chromosome contributed by the resistant parent P34. The results presented were obtained using two different strategies for mapping genes of unknown location. One approach was the use of probes revealing polymorphic loci spread throughout the genome and resulted in the mapping ofRx1. The second approach was based on the assumption of possible linkage between the resistance gene and clone-specific DNA fragments introduced from a wild potato species.Rx2 was mapped by adopting this strategy.

The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation

BackgroundHigh levels of ascorbic acid (AsA) in tomato fruits provide health benefits for humans and also play an important role in several aspects of plant life. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. The transcriptional control of AsA levels in fruits can be investigated by combining the advanced genetic and genomic resources currently available for tomato. A comparative transcriptomic analysis of fruit tissues was carried out on an introgression line containing a QTL promoting AsA accumulation in the fruit, using a parental cultivar with lower AsA levels as a reference.ResultsIntrogression line IL 12-4 (S. pennellii in a S. lycopersicum background) was selected for transcriptomic analysis because it maintained differences in AsA levels compared to the parental genotypes M82 and S. pennellii over three consecutive trials. Comparative microarray analysis of IL 12-4 and M82 fruits over a 2-year period allowed 253 differentially-expressed genes to be identified, suggesting that AsA accumulation in IL 12-4 may be caused by a combination of increased metabolic flux and reduced utilization of AsA. In particular, the upregulation of a pectinesterase and two polygalacturonases suggests that AsA accumulation in IL12-4 fruit is mainly achieved by increasing flux through the L-galactonic acid pathway, which is driven by pectin degradation and may be triggered by ethylene.ConclusionsBased on functional annotation, gene ontology classification and hierarchical clustering, a subset of the 253 differentially-expressed transcripts was used to develop a model to explain the higher AsA content in IL 12-4 fruits in terms of metabolic flux, precursor availability, demand for antioxidants, abundance of reactive oxygen species and ethylene signaling.

Molecular Marker-assisted Selection for Potato Breeding

The use of molecular markers in potato breeding offers new opportunities for the selection of genotypes. To date, many markers linked to useful traits have been found. Indeed, the potato molecular map is saturated with more than 350 markers uniformly distributed on 12 chromosomes. More than 25 single dominant genes have been localized on the potato map, most of them being pest-resistance genes, together with some quantitative trait loci (QTL) controlling yield and tuber quality traits. Molecular markers linked to these genes are now available for rapid, efficient assisted selection (positive assisted selection). Moreover, in order to transfer useful genes, interspecific crosses between wild and cultivated genotypes are often performed, and in this case the use of species-specific molecular markers would allow the wild genomic content to be reduced in few backcross generations (negative assisted selection). The following review discusses the progress achieved in potato breeding through molecular marker-assisted selection.ResumenEl uso de marcadores moleculares en el mejoramiento de la papa ofrece nuevas oportunidades para la selección de genotipos. Hasta ahora se han encontrado muchos marcadores ligados a características útiles. Realmente el mapa molecular de la papa está saturado con más de 350 marcadores uniformemente distribuidos en 12 cromosomas. Más de 25 genes dominantes simples han sido identificados en el mapa de la papa, siendo la mayoria genes de resistencia a plagas y enfermedades conjuntamente con algunos Loci de Caracteres Cuantitativos (QTLs) que controlan las características de rendimiento y calidad. Ahora se encuentran disponibles, marcadores moleculares ligados a estos genes, para una más rápida y eficiente selección asistida (selección positiva asistida). Más aún, con el objeto de transferor genes útiles, generalmente se hacen cruzamientos interespecíficos entre genotipos silvestres y cultivados, y en este caso el uso de marcadores moleculares permitirán que el contenido genómico de especies silvestres se reduzca después de algunas generaciones de retrocruza (selección negativa asistida). La siguiente revisión discute el progreso alcanzado en el mejoramiento de la papa a través de la selección asistida por marcadores moleculares.

2n gametes in the potato: essential ingredients for breeding and germplasm transfer.

Abstract 2n gametes are the result of meiotic mutations occurring during micro – and mega-sporogenesis. They have been identified in several plant species of different taxa. The potato is probably the crop plant where they have been most intensively studied and also more appropriately used for the genetic improvement of cultivated genotypes. This paper reviews how 2n gametes allow potato breeders to broaden the genetic basis of the cultivated Solanum tuberosum, introducing both new genes for the improvement of traits of interest and allelic diversity to maximize heterozygosity. We provide molecular and breeding evidence that, in the potato, 2n gametes represent a unique tool to transfer target genes from wild forms to the cultivated tetraploid gene pool. In fact, species directly crossable to S. tuberosum haploids can be exploited through sexual polyploidization crossing schemes. For those which have developed crossability barriers, specific crossing schemes based on ploidy bridges can be designed. In this paper we also give possible hypotheses to explain conflicting results on the genetic control and meiotic mutations responsible for 2n-gamete formation in the potato.

Enhancing the Health-Promoting Effects of Tomato Fruit for Biofortified Food

Consumption of tomato fruits, like those of many other plant species that are part of the human diet, is considered to be associated with several positive effects on health. Indeed, tomato fruits are an important source of bioactive compounds with known beneficial effects including vitamins, antioxidants, and anticancer substances. In particular, antioxidant metabolites are a group of vitamins, carotenoids, phenolic compounds, and phenolic acid that can provide effective protection by neutralizing free radicals, which are unstable molecules linked to the development of a number of degenerative diseases and conditions. In this review, we will summarize the recent progress on tomatoes nutritional importance and mechanisms of action of different phytochemicals against inflammation processes and prevention of chronic noncommunicable diseases (e.g., obesity, diabetes, coronary heart disease, and hypertension). In addition, we will summarize the significant progress recently made to improve the nutritional quality of tomato fruits through metabolic engineering and/or breeding.

High-Throughput Genomics Enhances Tomato Breeding Efficiency

Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.

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

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.

Structural and Functional Genomics of Tomato

Tomato (Solanum lycopersicum L.) is the most intensively investigated Solanaceous species both in genetic and genomics studies. It is a diploid species with a haploid set of 12 chromosomes and a small genome (950 Mb). Based on the detailed knowledge on tomato structural genomics, the sequencing of the euchromatic regions started in the year 2005 as a common effort of different countries. The manuscript focuses on markers used for tomato, on mapping efforts mainly based on exploitation of natural biodiversity, and it gives an updated report on the international sequencing activities. The principal tools developed to explore the function of tomato genes are also summarized, including mutagenesis, genetic transformation, and transcriptome analysis. The current progress in bioinformatic strategies available to manage the overwhelming amount of data generated from different tomato “omics” approaches is reported, and emphasis is given to the effort of producing a computational workbench for the analysis of the organization, as well as the functionality and evolution of the Solanaceae family.

Heterozygosity in 2n gametes of potato evaluated by RFLP markers

The heterozygosity transmitted through 2n gametes in potato was evaluated by following the segregation of RFLP markers in tetraploid progeny from bilateral sexual polyploidization in a cross between two diploid (2x) interspecific hybrids which produce 2n SDR eggs or 2n FDR pollen. Out of 84 probe/enzyme combinations tested, 23 revealed polymorphism between the parents and were heterozygous in at least one of the parents. These probes characterized 13 loci distributed on five different chromosomes of the potato RFLP map. The heterozygosity transmitted through SDR and FDR gametes was estimated to be 31.8% and 71.4%, respectively. Two different indices (LH and RHI) were used to select plants showing a high level of heterozygosity in the tetraploid progeny. The recombination events and the centromere positions were estimated for chromosomes I, VI and VII, following the segregation ratios of SDR or FDR gametes produced by the parents. A different recombination rate was observed between the two interspecific hybrids.