Suchergebnisse

[EN] Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8x and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding. ; This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no. 677379 (G2P-SOL project: Linking genetic resources, genomes, and phenotypes of Solanaceous crops), by the Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant AGL2015-64755-R), and by the Spanish Ministerio ...

[EN] Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype x environment interaction (G x E) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments. ; This work was undertaken as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting, and Preparing Crop Wild Relatives", which is supported by the Government of ...

[EN] Evaluation and prediction of the performance of hybrids is important in eggplant (Solanum melongena) breeding. A set of 10 morphologically highly diverse eggplant parents, including nine inbred S. melongena and one weedy S. insanum accessions, were intercrossed according to a half-diallel mating design without reciprocals to obtain 45 hybrids. Parents and hybrids were evaluated for 14 morphological and agronomic conventional descriptors and 14 fruit morphometric traits using Tomato Analyzer. Genetic distances among parents were estimated with 7,335 polymorphic SNP markers. Wide ranges of variation and significant differences were observed in the set of 55 genotypes for all traits, although the hybrids group had significantly higher vigour and yield than parents. General and specific combining abilities (GCA and SCA) were significant for most (GCA) or all (SCA) traits, although a wide variation was obtained for GCA/SCA ratios. Many relevant traits associated to vigour and yield had low GCA/SCA ratios and narrow-sense heritability (h(2)) values, while the reverse occurred for most fruit shape descriptors. Broad-sense heritability (H-2) values were generally high, irrespective of GCA/SCA ratios. Significant correlations were found between traits related to size of leaf, flower and fruit, as well as among many fruit morphometric traits. Genetic distances (GD) among parents were coherent with their phylogenetic relationships, but few significant and generally low correlations were found between GD and hybrid means, heterosis or SCA. The results provide relevant information for developing appropriate strategies for parent selection and hybrid development in eggplant and suggest that GD among parents have limited value to predict hybrid performance in this crop. ; This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and from Spanish Ministerio de ...

[EN] Islands provide unique opportunities to integrated research approaches to study evolution and conservation because boundaries are circumscribed, geological ages are often precise, and many taxa are greatly imperiled. We combined morphological and hybridization studies with high-throughput genotyping platforms to streamline relationships in the endangered monophyletic and highly diverse lineage ofSolanumin the Canarian archipelago, where three endemic taxa are currently recognized. Inter-taxa hybridizations were performed, and morphological expression was assessed with a common-garden approach. Using the eggplant Single Primer Enrichment Technology (SPET) platform with 5,093 probes, 74 individuals of three endemic taxa (Solanum lidii,S. vespertiliosubsp.vespertilio, andS. vespertiliosubsp.doramae) were sampled for SNPs. While morphological and breeding studies showed clear distinctions and some continuous variation, inter-taxon hybrids were fertile and heterotic for vigor traits. SPET genotyping revealed 1,421 high-quality SNPs and supported four, not three, distinct taxonomic entities associated with post-emergence geological, ecological and geographic factors of the islands. Given the lack of barriers to hybridization among all the taxa and their molecular differences, great care must be taken in population management. Conservation strategies must take account of the sexual and breeding systems and genotypic distribution among populations to successfully conserve and restore threatened/endangered island taxa, as exemplified bySolanumon the Canary Islands. ; This work was supported by funds from project DEMIURGO to the Jardin Botanico Canario "Viera y Clavijo" -Unidad Asociada al CSIC of the Cabildo de Gran Canaria. Consumables and genotyping were funded by the Jardin Botanico Canario "Viera y Clavijo" -Unidad Asociada al CSIC. Participation of authors from Universitat Politecnica de Valencia has been partially funded by the European Union's Horizon 2020 Research and Innovation Programme under the Grant ...

[EN] Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers are amongst the most common markers of choice for studies of diversity and relationships in horticultural species. We have used 11 SSR and 35 SNP markers derived from transcriptome sequencing projects to fingerprint 48 accessions of a collection of brinjal (Solanum melongena), gboma (S. macrocarpon) and scarlet (S. aethiopicum) eggplant complexes, which also include their respective wild relatives S. incanum, S. dasyphyllum and S. anguivi. All SSR and SNP markers were polymorphic and 34 and 36 different genetic fingerprints were obtained with SSRs and SNPs, respectively. When combining both markers all accessions but two had different genetic profiles. Although on average SSRs were more informative than SNPs, with a higher number of alleles, genotypes and polymorphic information content (PIC), and expected heterozygosity (He) values, SNPs have proved highly informative in our materials. Low observed heterozygosity (Ho) and high fixation index (f) values confirm the high degree of homozygosity of eggplants. Genetic identities within groups of each complex were higher than with groups of other complexes, although differences in the ranks of genetic identity values among groups were observed between SSR and SNP markers. For low and intermediate values of pair-wise SNP genetic distances, a moderate correlation between SSR and SNP genetic distances was observed (r(2) = 0.592), but for high SNP genetic distances the correlation was low (r(2) = 0.080). The differences among markers resulted in different phenogram topologies, with a different eggplant complex being basal (gboma eggplant for SSRs and brinjal eggplant for SNPs) to the two others. Overall the results reveal that both types of markers are complementary for eggplant fingerprinting and that interpretation of relationships among groups may be greatly affected by the type of marker used. ; This work has been funded by European Union's Horizon 2020 Research and Innovation ...

[EN] Increasing the content in bioactive phenolics in the eggplant (Satanum melongena) fruit is of interest, but may result in enhanced browning. We evaluated six varieties of S. melongena, 22 accessions of wild related species and 42 interspecific hybrids between cultivated eggplant and wild relatives for phenolics content, fruit flesh colour, polyphenol oxidase (PPO) activity, and fruit flesh browning. Wild relatives generally had a higher content in phenolics and a broader range of variation than cultivated eggplant. Chlorogenic acid was the predominant ( > 65.0%) phenolic acid in cultivated eggplant and its primary genepool wild ancestor S. insanum, while for the other wild species on average represented 50% of the chromatogram peak area. Fruit flesh colour was lighter in S. melongena than in the wild species, while PPO activity and browning was much higher in wild species of the secondary and tertiary genepools. Interspecific hybrids between S. melongena and S. insanum were intermediate in their characteristics, while those with secondary and tertiary genepool species were more similar to the wild species. No significant correlations were found between total phenolics or chlorogenic acid contents and fruit flesh browning, but PPO activity was correlated to both the degree of browning (r = 0.404) and colour difference (r = 0.458). The results indicate that wild species can contribute to improving the bioactive properties of eggplant without affecting negatively fruit flesh colour and browning. ; This work has been funded in part by the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway (GS13044 and GS17011). This project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website: ...

[EN] Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario. ; This work has been funded in part by the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives," which is supported by the Government of Norway. This project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website: http://www.cwrdiversity.org/. Funding has also been received from the European Union's Horizon 2020 ...

[EN] Dramatic advances in genomics during the last decades have led to a revolution in the field of vegetable crops breeding. Some vegetables, like tomato, have served as model crops in the application of genomic tools to plant breeding but other important crops, like eggplant (Solanum melongena), lagged behind. The advent of next generation sequencing (NGS) technologies and the continuous decrease of the sequencing costs have allowed to develop genomic tools with a greatly benefit for no-model plants such as eggplant. In this review we present the currently available genomic resources in eggplant and discuss their interest for breeding. The first draft of eggplant genome sequence and the new upcoming improved assembly, as well as the transcriptomes and RNA-based studies represent important genomic tools. The transcriptomes of cultivated eggplant and several wild relatives of eggplant are also available and have provided relevant information for the development of markers and understanding biological processes in eggplant. In addition, a historical overview of the eggplant genetic mapping studies, performed with different types of markers and experimental populations, provides a picture of the increase over time of the precision and resolution in the identification of candidate genes and QTLs for a wide range of stresses, and morphoagronomic and domestication traits. Finally, we discuss how the development of new genetic and genomic tools in eggplant can pave the way for increasing the efficiency of eggplant breeding for developing improved varieties able to cope with the old and new challenges in horticultural production. ; This work has been funded in part by the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene ...

e0180774 12 7 ; S ; [EN] Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying ...

[EN] Solanum insanum L. (Solanaceaeae) is the wild progenitor of common eggplant (S. melongena L.) and is naturally distributed in south and southeast Asia, Madagascar and Mauritius. Despite interest in its potential for eggplant breeding it has not been studied extensively. Solanum insanum has been subjected to various taxonomic treatments, with several discussions and arguments on its delimitation as a species, due to its close similarities with the cultivated S. melongena and the wild species S. incanum L. from the Middle East and northern Africa. Solanum insanum has long been used in a variety of medicinal and culinary preparations across many different Asian ethnolinguistic groups. Limited studies carried out on its chemical composition and pharmacognostical properties coupled with ethnobotanic studies reveal that S. insanum has potential for eggplant improvement with respect to phytochemical properties of interest for human health. Further study of morphological and genetic diversity in S. insanum is essential to promote its utilization in eggplant breeding, in light of its potential to hybridize with cultivated eggplant successfully. Here we compile and review the taxonomy, phytogeography, ecology and habitat characteristics, cytology, ethnobotany, breeding and phytochemical analysis of S. insanum. A comprehensive botanical description and illustrations for S. insanum are provided. A detailed comparison of S. insanum and its closely allied species, S. melongena and S. incanum is also made. The potential of S. insanum for crop improvement and future research priorities are discussed. ; This work was undertaken as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives" (http://www.cwrdiversity.org/) that is supported by the Government of Norway, managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens Kew, and implemented in partnership with national and international gene banks and plant breeding ...

[EN] Introgression breeding can contribute to broadening the genetic background of eggplant (Solanum melongena). We used six eggplant varieties and 44 interspecific hybrids between these eggplant accessions and 10 accessions of wild relatives from the primary genepool species S. insanum and secondary genepool species S. anguivi, S. dasyphyllum, S. incanum, S. lichtensteinii, and S. tomentosum to obtain first backcross generations to S. melongena. Pollen viability in cultivated and wild parents and interspecific hybrids with S. insanum was high, while for interspecific hybrids with secondary genepool species it was variable. First backcross generations to S. melongena were obtained with interspecific hybrids of all the wild species, with the best results being obtained in crosses with hybrids between S. melongena and S. insanum. However, ample differences were observed among eggplant varieties in the success of the crosses. Additionally, the six eggplant varieties were crossed with secondary genepool species S. campylacanthum, S. lidii and S. vespertilio and with tertiary genepool species S. bonariense, S. elaeagnifolium and S. sisymbriifolium with the aim of obtaining new interspecific hybrids. Successful interspecific hybridization was achieved with the three new secondary genepool species tested and, using embryo rescue, with the tertiary genepool species S. elaeagnifolium. The new backcross generations and interspecific hybrids obtained will contribute to broadening the genetic background of the eggplant and to the genetic enhancement of this crop. ; This work was undertaken as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. The project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Mew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information ...

[EN] Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks. ; This work has been funded by the European Union's Horizon 2020 ...

1 19 213 7 ; S ; [EN] The need to boost agricultural production in the coming decades in a climate change scenario requires new approaches for the development of new crop varieties that are more resilient and more efficient in the use of resources. Crop wild relatives (CWRs) are a source of variation for many traits of interest in breeding, in particular tolerance to abiotic and biotic stresses. However, their potential in plant breeding has largely remained unexploited. CWRs can make an effective contribution to broadening the genetic base of crops and to introgressing traits of interest, but their direct use by breeders in breeding programs is usually not feasible due to the presence of undesirable traits in CWRs (linkage drag) and frequent breeding barriers with the crop. Here we call for a new approach, which we tentatively call 'introgressiomics', which consists of mass scale development of plant materials and populations with introgressions from CWRs into the genetic background of crops. Introgressiomics is a form of pre-emptive breeding and can be focused, when looking for specific phenotypes, or un-focused, when it is aimed at creating highly diverse intro-gressed populations. Exploring germplasm collections and identifying adequate species and accessions from different genepools encompassing a high diversity, using different strategies like the creation of germplasm diversity sets, Focused identification of germplasm strategy (FIGS) or gap analysis, is a first step in introgressiomics. Interspecific hybridization and backcrossing is often a major barrier for introgressiomics, but a number of techniques can be used to potentially overcome these and produce introgression populations. The generation of chromosome substitution lines (CSLs), introgression lines (ILs), or multiparent advanced inter-cross (MAGIC) populations by means of marker-assisted selection allows not only the genetic analysis of traits present in CWRs, but also developing genetically characterized elite materials that can be easily ...