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ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean‘da serbo’type long shelf-life germplasm

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Horticulture Research 2020年第1期7卷 1047-1060页

作者： Salvatore Esposito Teodoro Cardi Gabriele Campanelli Sara Sestili María JoséDíez salvador soler Jaime Prohens Pasquale Tripodi CREA Research Centre for Vegetable and Ornamental Crops Pontecagnano(SA)Italy CREA Research Centre for Vegetable and Ornamental Crops Monsampolo del Tronto(AP)TrontoItaly Instituto de Conservación y Mejora de la Agrodiversidad Valenciana Universitat Politècnica de València46022 ValenciaSpain

Double digest restriction-site associated sequencing(ddRAD-seq)is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm *** this methodology,we investigated the genomic diversity of a panel of 288 diverse tomato(Solanum lycopersicum L.)accessions enriched in‘da serbo’(called‘de penjar’in Spain)long shelf life(LSL)materials(152 accessions)mostly originating from Italy and *** rest of the materials originate from different countries and include landraces for fresh consumption,elite cultivars,heirlooms,and breeding *** from their LSL trait,‘da serbo’landraces are of remarkable interest for their *** identified 32,799 high-quality SNPs,which were used for model ancestry population structure and non-parametric hierarchical *** genetic subgroups were revealed,clearly separating most‘da serbo’landraces,but also the Spanish germplasm,suggesting a subdivision of the population based on type and geographical *** disequilibrium(LD)in the collection decayed very rapidly within<5 *** then investigated SNPs showing contrasted minor frequency allele(MAF)in‘da serbo’materials,resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and ***,a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key *** findings suggest the presence of a genetic footprint of the‘da serbo’germplasm selected in the Mediterranean ***,we provide novel insights on LSL‘da serbo’germplasm as a promising source of alleles for tolerance to stresses.

关键词： germplasm breeding shelf

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Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy *** and *** *** accessions used for the first interspecific tomato MAGIC population

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Horticulture Research 2020年第1期7卷 477-492页

作者： Pietro Gramazio Leandro Pereira-Dias Santiago Vilanova Jaime Prohens salvador soler Javier Esteras Alfonso Garmendia María JoséDíez Faculty of Life and Environmental Sciences University of Tsukuba1-1-1 Tennodai305-8572 TsukubaJapan Instituto de Conservación y Mejora de la Agrodiversidad Valenciana Universitat Politècnica de ValènciaCamino de Vera 1446022 ValenciaSpain Departamento de Ecosistemas Agroforestales Universitat Politècnica de ValènciaCamino de Vera 1446022 ValenciaSpain Instituto Agroforestal Mediterráneo Universitat Politècnica de ValènciaCamino de Vera 1446022 ValenciaSpain

The wild Solanum pimpinellifolium(SP)and the weedy *** ***(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(*** ***).We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions,selected to maximize the range of variation of both *** eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross(MAGIC)*** morphoagronomic characterization was carried out with 39 descriptors to assess plant,inflorescence,fruit and agronomic traits,revealing the broad range of diversity *** of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments,while in the case of SLC to both human activity and adaptation to the ***-genome resequencing of the eight accessions revealed over 12 million variants,ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP,being 46.3%of them(4,897,803)private *** genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of *** was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two *** functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and *** comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.

关键词： agronomic breeding MAGIC

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