Dataset Information

Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information.

ABSTRACT: Fruit weight (FW) and shelf life (SL) are important traits in commercial fresh market tomatoes. A tomato RIL population was developed by antagonistic and divergent selection for both traits from an interspecific cross between the Solanum lycopersicum L. cv. "Caimanta" and the S. pimpinellifolium L. accession "LA0722". The objective of this work was to evaluate phenotypic and genetic components for FW and SL. Phenotypic data from RILs were collected during 3-year trials. Sixteen SSR, 62 InDels developed based on the genome sequences of "Caimanta" and "LA0722", and four functional markers for fruit size genes were used. FW and SL had a significant genetic variability, and both traits showed a genotype by year interaction. Genome-wide molecular characterization of the population demonstrated that is genetically structured according to FW. Marker data was used to study changes on allelic frequencies at loci between the phenotypic extreme group of RILs for FW and SL. Twenty four markers were associated to FW, the LC gene in chromosome 2 and other six markers in chromosomes 1, 2, 6, and 11 presented the most significant associations. Finally, we reported three new genomic regions located on chromosomes 9, 10 and 12 that underlie SL in tomato.

SUBMITTER: Cambiaso V

PROVIDER: S-EPMC6776149 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information.

Cambiaso Vladimir V Gimenez Magalí Diana MD da Costa Javier Hernán Pereira JHP Vazquez Dana Valeria DV Picardi Liliana Amelia LA Pratta Guillermo Raúl GR Rodríguez Gustavo Rubén GR

Breeding science 20190704 3

Fruit weight (FW) and shelf life (SL) are important traits in commercial fresh market tomatoes. A tomato RIL population was developed by antagonistic and divergent selection for both traits from an interspecific cross between the <i>Solanum lycopersicum</i> L. cv. "Caimanta" and the <i>S. pimpinellifolium</i> L. accession "LA0722". The objective of this work was to evaluate phenotypic and genetic components for FW and SL. Phenotypic data from RILs were collected during 3-year trials. Sixteen SSR ...[more]

PMID: 31598077

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Project description:The conservation and characterization of landraces have key roles in the safeguarding and valorization of agrobiodiversity. Indeed, these plant genetic resources represent an important crop heritage with quality and sensory characteristics that can be of great use to consumers and industry. In addition, the preservation of genetic resources from the risk of progressive genetic erosion, and the enhancement of their potential can contribute to food security and improve the nutritional value of food. Accordingly, this study aimed to investigate a collection of Sardinian tomato landraces for parameters that have determinant roles in evaluating their responses to conservation, and therefore to consumer acceptance. Six Sardinian landraces and two commercial varieties were cultivated in a two-years off-season trial, harvested at two different maturity stages (turning, red-ripe) and characterized using 14 fruit-related quality parameters that define the marketability, nutritional value, and flavor of the fruit. Data were collected at intervals of 10 days, starting from the harvest date and over 30 days of storage under refrigeration. The simultaneous analysis of all the qualitative characteristics for the different genotypes allowed to clearly differentiate the local varieties from the commercial varieties and a few landraces emerged for their satisfactory performances, e.g. "Tamatta kaki" ad "Tamatta groga de appiccai". In particular, the "Tamatta groga de appiccai" showed satisfactory lycopene content at marketable stages (average 5.65 mg 100g-1 FF), a peculiar orange-pink color with the highest hue angle values (range: H°T0 = 72.55-H°T30 = 48.26), and the highest firmness among the landraces of the red-ripe group (range: EpT0 = 1.64-EpT30 = 0.54 N mm-1). These results highlight the potential of some of the Sardinian tomato landraces for developing new varieties or promoting their direct valorization in local markets and could considerably increase the effectiveness and efficiency of agrobiodiversity conservation strategies.

Project description:Key messageSix novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs. The size and weight of edible organs have been strongly selected during crop domestication. Concurrently, human have also focused on nutritional and cultural characteristics of fruits and vegetables, at times countering selective pressures on beneficial size and weight alleles. Therefore, it is likely that novel improvement alleles for organ weight still segregate in ancestral germplasm. To date, five domestication and diversification genes affecting tomato fruit weight have been identified, yet the genetic basis for increases in weight has not been fully accounted for. We found that fruit weight increased gradually during domestication and diversification, and semi-domesticated subpopulations featured high phenotypic and nucleotide diversity. Columella and septum fruit tissues were proportionally increased, suggesting targeted selection. We developed twenty-one F2 populations with parents fixed for the known fruit weight genes, corresponding to putative key transitions from wild to fully domesticated tomatoes. These parents also showed differences in fruit weight attributes as well as the developmental timing of size increase. A subset of populations was targeted for QTL-seq, leading to the identification of six uncloned fruit weight QTLs. Three QTLs, located on chromosomes 1, 2 and 3, were subsequently validated by progeny testing. By exploring the segregation of the known fruit weight genes and the identified QTLs, we estimated that most beneficial alleles in the newly identified loci arose in semi-domesticated subpopulations from South America and were not likely transmitted to fully domesticated landraces. Therefore, these alleles could be incorporated into breeding programs using the germplasm and genetic resources identified in this study.

Dataset Information

Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information.

Publications

Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information.

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