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 collections.Using this methodology,we...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 collections.Using 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 Spain.The rest of the materials originate from different countries and include landraces for fresh consumption,elite cultivars,heirlooms,and breeding lines.Apart from their LSL trait,‘da serbo’landraces are of remarkable interest for their resilience.We identified 32,799 high-quality SNPs,which were used for model ancestry population structure and non-parametric hierarchical clustering.Six 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 provenance.Linkage disequilibrium(LD)in the collection decayed very rapidly within<5 kb.We 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 JAR1.Finally,a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits.Our findings suggest the presence of a genetic footprint of the‘da serbo’germplasm selected in the Mediterranean basin.Moreover,we provide novel insights on LSL‘da serbo’germplasm as a promising source of alleles for tolerance to stresses.展开更多
The wild Solanum pimpinellifolium(SP)and the weedy S.lycopersicum var.cerasiforme(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(...The wild Solanum pimpinellifolium(SP)and the weedy S.lycopersicum var.cerasiforme(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(S.lycopersicum var.lycopersicum).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 taxa.These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross(MAGIC)population.The morphoagronomic characterization was carried out with 39 descriptors to assess plant,inflorescence,fruit and agronomic traits,revealing the broad range of diversity captured.Part 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 environment.Whole-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 variants.The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC.This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa.The 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 breeding.The 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.展开更多
文摘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 collections.Using 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 Spain.The rest of the materials originate from different countries and include landraces for fresh consumption,elite cultivars,heirlooms,and breeding lines.Apart from their LSL trait,‘da serbo’landraces are of remarkable interest for their resilience.We identified 32,799 high-quality SNPs,which were used for model ancestry population structure and non-parametric hierarchical clustering.Six 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 provenance.Linkage disequilibrium(LD)in the collection decayed very rapidly within<5 kb.We 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 JAR1.Finally,a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits.Our findings suggest the presence of a genetic footprint of the‘da serbo’germplasm selected in the Mediterranean basin.Moreover,we provide novel insights on LSL‘da serbo’germplasm as a promising source of alleles for tolerance to stresses.
文摘The wild Solanum pimpinellifolium(SP)and the weedy S.lycopersicum var.cerasiforme(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(S.lycopersicum var.lycopersicum).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 taxa.These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross(MAGIC)population.The morphoagronomic characterization was carried out with 39 descriptors to assess plant,inflorescence,fruit and agronomic traits,revealing the broad range of diversity captured.Part 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 environment.Whole-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 variants.The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC.This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa.The 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 breeding.The 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.
