Genomic analyses provide insights into the history of tomato breeding

Lin, Tao; Zhu, Guangtao; Zhang, Mengjie; Xu, Xiangyang; Yu, Qinghui; Zheng, Zheng; Zhang, Zhonghua; Lun, Yaoyao; Li, Shuai; Wang, Xiaoxuan; Huang, Zejun; Li, Junming; Zhang, Chengqi; Wang, Taotao; Zhang, Yuyang; Wang, Aoxue; Zhang, Yancong; Lin, Kui; Li, Chuanyou; Xiong, Guosheng; Xue, Yongbiao; Mazzucato, Andrea; Causse, Mathilde; Fei, Zhangjun; Giovannoni, James J.; Chetelat, Roger T.; Zamir, Dani; Städler, Thomas; Li, Jin-Fu; Ye, Zhibiao; Du, Yan; Huang, Sanwen

doi:10.1038/ng.3117

Cited by 752 publications

(847 citation statements)

References 49 publications

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“…Mapping of these genes on the reference genome of S. lycopersicum 'Heinz 1706' showed that considering the number of genes on each chromosome there was a relatively higher concentration of these defence genes on chromosomes 1, 5, 8, 9 and 10. Intriguingly, there was no overlap with previously analysed genomic locations of domestication sweeps, but on chromosomes 1 (2), 2 (3) and 8 (4) there was an overlap with the genomic locations of improvement sweeps analysed and described in another recent study (Lin et al, 2014) (Fig. 2A).…”

Section: Selection Of Genes Involved In Tomato Defence Responsessupporting

confidence: 53%

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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Section: Selection Of Genes Involved In Tomato Defence Responsessupporting

confidence: 53%

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

Satková

Starý

Plešková

et al. 2016

Ann Bot

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“…Ripening involved genes, such as GR or HP1, are clearly independent of the common symbiotic pathway (Oldroyd 2013) and are probably a more recent evolutive acquisition originated by the selection for fleshy fruit characteristics. Such an interpretation, if validated, may suggest that plants selected for fruit traits of human interest, as fruit weight (Lin et al 2014), were also positively selected for their mycorrhizal systemic responsiveness. This could pave the way to investigate the role of AMF in tomato crop selection history.…”

Section: Resultsmentioning

confidence: 97%

Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening

Chialva

Zouari

Salvioli

et al. 2016

Planta

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Main conclusion Systemic responses to an arbuscular mycorrhizal fungus reveal opposite phenological patterns in two tomato ripening mutants depending whether ethylene or light reception is involved. The availability of tomato ripening mutants has revealed many aspects of the genetics behind fleshy fruit ripening, plant hormones and light signal reception. Since previous analyses revealed that arbuscular mycorrhizal symbiosis influences tomato berry ripening, we wanted to test the hypothesis that an interplay might occur between root symbiosis and fruit ripening. With this aim, we screened seven tomato mutants affected in the ripening process for their responsiveness to the arbuscular mycorrhizal fungus Funneliformis mosseae. Following their phenological responses we selected two mutants for a deeper analysis: Green ripe (Gr), deficient in fruit ethylene perception and high-pigment-1 (hp-1), displaying enhanced light signal perception throughout the plant. We investigated the putative interactions between ripening processes, mycorrhizal establishment and systemic effects using biochemical and gene expression tools. Our experiments showed that both mutants, notwithstanding a normal mycorrhizal phenotype at root level, exhibit altered arbuscule functionality. Furthermore, in contrast to wild type, mycorrhization did not lead to a higher phosphate concentration in berries of both mutants. These results suggest that the mutations considered interfere with arbuscular mycorrhiza inducing systemic changes in plant phenology and fruits metabolism. We hypothesize a cross talk mechanism between AM and ripening processes that involves genes related to ethylene and light signaling.

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“…(iv) Neolycopersicon group containing only Solanum penellii, which was considered to be sister to the rest of the section based on its lack of the sterile anther that occurs as a morphological synapomorphy in S. habrochaites and the rest of the core tomatoes 8 . More recent studies using conserved orthologous sequence markers (COSII) 11 , genome-wide single nucleotide polymorphisms (SNPs) 7,12 and genomic repeat elements 13 have largely supported previous hypotheses with respect to major clades within the tomatoes, although individual species relationships are less clear cut for some taxa. Thus, given the general acceptance of this informal classification, in the present study we will often use it as reference in order to better clarify the results here presented.…”

Section: Introductionmentioning

confidence: 92%

Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

Cattáneo¹,

Diambra²,

McCarthy³

2017

Preprint

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Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k -mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

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Genomic analyses provide insights into the history of tomato breeding

Cited by 752 publications

References 49 publications

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

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

Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening

Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

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