Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

Sim, Sung-Chur; Robbins, Matthew D.; Deynze, Allen Van; Michel, Andy; Francis, David M.

doi:10.1038/hdy.2010.139

Cited by 74 publications

(71 citation statements)

References 54 publications

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“…Commercial tomato species exhibit a reduced ability to cope with attack by a wide range of pests and pathogens due to extensive selection through history (Sim et al 2011). An effective strategy for increasing the resistance of commercial food crops is the introduction of genes that confer enhanced resistance to a target pest, as has been achieved for several insect/crop systems such as B. tabaci and cassava (Carabali et al 2013).…”

Section: Resultsmentioning

confidence: 99%

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Novel resistance mechanisms of a wild tomato against the glasshouse whitefly

McDaniel

Tosh

Gatehouse

et al. 2016

Agron. Sustain. Dev.

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The glasshouse whitefly, Trialeurodes vaporariorum, is an important pest of many crop plants including tomato, Solanum lycopersicum. Many wild tomato species exhibit a higher resistance to whiteflies. Therefore, locating the source of this enhanced resistance and breeding it into commercial tomato species is an important strategy to reduce the impact of pests on crops. Here, we assessed the pest resistance of Lycopersicon pimpinellifolium by comparing oviposition and feeding data from T. vaporariorum on this wild tomato species with data collected from a susceptible commercial tomato, S. lycopersicum var. 'Elegance'. The location of resistance factors was examined by use of electrical penetration graph (EPG) studies on these tomato species. Results show that whiteflies preferentially settled on the commercial tomato more often in 80 % of the replicates when given free choice between the two tomato species and laid significantly fewer eggs on L. pimpinellifolium. Whiteflies exhibited a shorter duration of the second feeding bout, reduced pathway phase probing, longer salivation in the phloem and more non-probing activities in the early stages of the EPG on the wild tomato species compared to the commercial tomato. These findings evidence that a dual mode of resistance is present in this wild tomato against T. vaporariorum: a post-penetration, pre-phloem resistance mechanism and a phloem-located factor, which to the best of our knowledge is the first time that evidence for this has been presented. These findings can be used to inform future breeding strategies to increase the resistance of commercial tomato varieties against this important pest.

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Section: Resultsmentioning

confidence: 99%

“…This selection process has potentially left the cultivated tomato bereft of the genetic variation required to allow it to cope with a range of environmental and biological stresses, including attack by T. vaporariorum (Sim et al 2011). Therefore, attempts have been made to increase the innate genetic resistance of the cultivated tomato.…”

Section: Introductionmentioning

confidence: 99%

Novel resistance mechanisms of a wild tomato against the glasshouse whitefly

McDaniel

Tosh

Gatehouse

et al. 2016

Agron. Sustain. Dev.

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“…Through domestication, breeding and research activities of the ancestral wild Solanum species, originating from the Andean region, many morphologically different cultivars and forms have been created. During this process, the genomes of cultivated tomatoes have passed through a progressive genetic bottleneck, reducing the genetic diversity in cultivated varieties compared to their wild relatives (Sim et al, 2011). Breeding selection has focused almost exclusively on traits related to desirable agricultural characteristics such as fruit yield and quality, loss of germination inhibition or compact growth habit.…”

Section: Introductionmentioning

confidence: 99%

Diverse responses of wild and cultivated tomato to BABA, oligandrin andOidium neolycopersiciinfection

Satková

Starý

Plešková

et al. 2016

Ann Bot

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Background and Aims Current strategies for increased crop protection of susceptible tomato plants against pathogen infections include treatment with synthetic chemicals, application of natural pathogen-derived compounds or transfer of resistance genes from wild tomato species within breeding programmes. In this study, a series of 45 genes potentially involved in defence mechanisms was retrieved from the genome sequence of inbred reference tomato cultivar Solanum lycopersicum 'Heinz 1706'. The aim of the study was to analyse expression of these selected genes in wild and cultivated tomato plants contrasting in resistance to the biotrophic pathogen Oidium neolycopersici, the causative agent of powdery mildew. Plants were treated either solely with potential resistance inducers or by inducers together with the pathogen.Methods The resistance against O. neolycopersici infection as well as RT-PCR-based analysis of gene expression in response to the oomycete elicitor oligandrin and chemical agent b-aminobutyric acid (BABA) were investigated in the highly susceptible domesticated inbred genotype Solanum lycopersicum 'Amateur' and resistant wild genotype Solanum habrochaites.Key Results Differences in basal expression levels of defensins, germins, b-1,3-glucanases, heveins, chitinases, osmotins and PR1 proteins in non-infected and non-elicited plants were observed between the highly resistant and susceptible genotypes. Moreover, these defence genes showed an extensive up-regulation following O. neolycopersici infection in both genotypes. Application of BABA and elicitin induced expression of multiple defence-related transcripts and, through different mechanisms, enhanced resistance against powdery mildew in the susceptible tomato genotype.Conclusions The results indicate that non-specific resistance in the resistant genotype S. habrochaites resulted from high basal levels of transcripts with proven roles in defence processes. In the susceptible genotype S. lycopersicum 'Amateur', oligandrin-and BABA-induced resistance involved different signalling pathways, with BABAtreated leaves displaying direct activation of the ethylene-dependent signalling pathway, in contrast to previously reported jasmonic acid-mediated signalling for elicitins.

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“…SNPs were discovered in cultivated tomato via sequencing (Hamilton et al, 2012) and showed a higher degree of polymorphism among the tomato cultivars (Sim et al, 2011).…”

Section: Molecular Markersmentioning

confidence: 99%

“…DNA markers help us to understand genetic variation at the DNA level. Therefore, several molecular marker systems have been applied to the study of genetic diversity in crops, including restriction fragment length polymorphism (RFLP) (Garcia-Mas et al, 2000), random-amplified polymorphic DNA (Korkmaz and Dogan, 2015), amplified fragment length polymorphism (van Berloo et al, 2008), simple sequence repeats (SSR) (Zhou et al, 2015b), single nucleotide polymorphism (SNP), and insertiondeletion (Sim et al, 2011) markers.…”

Section: Introductionmentioning

confidence: 99%

Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers

Wang

Zou

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Knowledge of genetic diversity is important to assist breeders in the selection of parental materials and in the design of breeding programs. In this study, we genotyped 348 inbred tomato lines, representing vintage and contemporary fresh-market varieties, by using 52 single nucleotide polymorphisms (SNPs); 45 of these were found to be polymorphic. The average minor allele frequency and unbiased expected heterozygosity were 0.315 and 0.356, respectively. Population structure analysis revealed that contemporary germplasm could be distinctly divided into six subpopulations representing three market classes and breeding programs (pink, green, and red). Vintage germplasm could be separated into at least two subpopulations, and more admixtures were found in vintage lines than in contemporary lines. These findings indicate that contemporary inbred lines are more diversified than vintage inbred lines. AMOVA of vintage and contemporary lines was performed. A significant difference was found (P < 0.01), which explained 17.4% of the total genetic variance. Subsequently, we constructed a core collection using 45 polymorphic SNP markers. The data showed that all alleles were captured by only 2% of lines, indicating that more alleles, as well as rare alleles, could enable more variation to be captured in the core collection. These data allow us to discard redundant inbred tomato lines and to select elite inbred lines, which will accelerate the breeding process.

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Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

Cited by 74 publications

References 54 publications

Novel resistance mechanisms of a wild tomato against the glasshouse whitefly

Novel resistance mechanisms of a wild tomato against the glasshouse whitefly

Diverse responses of wild and cultivated tomato to BABA, oligandrin andOidium neolycopersiciinfection

Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers

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