Development and use of introgression populations for the detection of QTL related to important agronomic traits in eggplant

Tesis por compendio[ES] La berenjena (Solanum melongena L.) es uno de los cultivos comerciales de hortalizas solanáceas más importantes que se cultiva ampliamente en Asia y la región del Mediterráneo. A pesar de su importancia económica, la disponibilidad de poblaciones experimentales y herramientas genómicas para el mejoramiento es aún muy limitada en comparación con otros cultivos importantes. Debido a la alteración progresiva del ecosistema global por el cambio climático, las plantas están constantemente expuestas a condiciones ambientales estresantes que impactan negativamente en su productividad. El cuello de botella genético ocurrido durante la domesticación de la berenjena, que limita la disponibilidad de recursos genéticos para su mejoramiento genético, hace que este cultivo sea extremadamente vulnerable al cambio climático, por lo que se requieren nuevas estrategias para reducir su erosión genética. En este contexto, los parientes silvestres de los cultivos (CWRs) han demostrado ser un recurso genético válido para la mejora vegetal, ya que su uso permite ampliar la diversidad genética de los cultivos y, en paralelo, desarrollar variedades mejoradas adaptadas al cambio climático. Para lograr este objetivo, en esta tesis doctoral informamos sobre el desarrollo y la evaluación de materiales avanzados de berenjena obtenidos mediante el uso de parientes silvestres. En el primer capítulo, realizamos una evaluación fenotípica en dos ambientes de un conjunto de 16 ILs de berenjena con introgresión de S. incanum, un pariente silvestre. Se evaluaron diecisiete caracteres agronómicos para comparar el rendimiento de las ILs con el parental recurrente e identificar QTLs para los caracteres investigados. Encontramos diferencias morfológicas significativas entre los parentales, y el híbrido resultó heterótico para los caracteres de vigor. A pesar de que la interacción entre genotipo y ambiente (G x E) resultó significativa para la mayoría de los caracteres, en general las ILs mostraron pocas diferencias fenotípicas con el progenitor receptor, incluso en presencia de grandes fragmentos de introgresión del progenitor silvestre. Se encontraron valores de heredabilidad bajos a moderados para los caracteres agronómicos. En total, detectamos diez QTLs estables, dos de los cuales estaban relacionados con caracteres de planta y cuatro para caracteres de flor y fruto. En general, las introgresiones de S. incanum mejoraron los valores medios de la mayoría de los caracteres de planta y flor, y disminuyeron el de los caracteres de fruto. Para tres QTLs relacionados con la longitud del pedicelo del fruto y con el peso del fruto, encontramos evidencia de sintenia con otros QTLs identificados previamente en poblaciones de berenjena. Siete QTLs eran nuevos, de los cuales cuatro relacionados con la altura de la planta, con la espinosidad del cáliz de la flor y con la longitud del pedicelo del fruto no colocalizaron con ningún QTL previamente identificado en las poblaciones de berenjena, y tres relacionados con el diámetro del tallo, con la longitud del pedúnculo y del estigma, fueron los primeros identificados en berenjena para estos caracteres. En el segundo capítulo, el conjunto de IL de berenjena con introgresiones de S. incanum se evaluó para la forma del fruto en dos ambientes. Específicamente, realizamos un fenotipado detallado de los frutos de los parentales, del híbrido y de las ILs utilizando 32 descriptores morfológicos de la herramienta fenómica Tomato Analyzer. Se encontraron grandes diferencias morfológicas en los frutos de los parentales, y el híbrido presentó valores negativos de heterosis para muchos de los caracteres de forma del fruto, siendo fenotípicamente más cercano al parental S. incanum. Para la mayoría de los descriptores de forma del fruto observamos diferencias significativas entre las ILs y el parental receptor, incluso en presencia de pequeños fragmentos de introgresión del parental silvestre. A pesar de que la contribución del ambiente y la...[CAT] L'albergínia (Solanum melongena L.) és un dels cultius comercials d'hortalisses solanácees més importants que es cultiva àmpliament a Àsia i la regió del Mediterrani. Malgrat la seua importància econòmica, la disponibilitat de poblacions experimentals i eines genòmiques per al millorament és encara molt limitada en comparació amb altres cultius importants. A causa de l'alteració progressiva de l'ecosistema global pel canvi climàtic, les plantes estan constantment exposades a condicions ambientals estressants que impacten negativament en la seua productivitat. El coll de botella genètic ocorregut durant la domesticació de l'albergínia, que limita la disponibilitat de recursos genètics per al seu millorament genètic, fa que aquest cultiu siga extremadament vulnerable al canvi climàtic, per la qual cosa es requereixen noves estratègies per a reduir la seua erosió genètica. En aquest context, els parents silvestres dels cultius (CWRs) han demostrat ser un recurs genètic vàlid per a la millora vegetal, ja que el seu ús permet ampliar la diversitat genètica dels cultius i, en paral·lel, desenvolupar varietats millorades adaptades al canvi climàtic. Per a aconseguir aquest objectiu, en aquesta tesi doctoral presentem el desenvolupament i l'avaluació de materials avançats d'albergínia obtinguts mitjançant l'ús de parents silvestres. En el primer capítol, realitzem una avaluació fenotípica en dos ambients d'un conjunt de 16 IL d'albergínia amb introgresions de S. incanum, un parent silvestre. Es van puntuar dèsset caràcters agronòmics per a avaluar el rendiment de les ILs en comparació amb el parental recurrent i identificar els QTL per als caràcters investigats. Trobarem diferències morfològiques significatives entre els parentals, i l'híbrid va resultar heteròtic per als caràcters de vigor. A pesar que la interacció entre genotip i ambient (G x E) va resultar significativa per a la majoria dels caràcters, en general les ILs van mostrar poques diferències fenotípiques amb el progenitor receptor, fins i tot en presència de grans fragments d'introgresió del progenitor silvestre. Es van trobar valors de heredabilitat baixos a moderats per als caràcters agronòmics. En total, detectarem deu QTL estables, dos dels quals estaven relacionats a caràcters de planta i quatre per a caràcters de flor i fruit. En general, les introgresions de S. incanum van millorar els valors mitjos de la majoria dels caràcters de planta i flor, i van disminuir el dels caràcters de fruit. Per a tres QTL relacionats amb la longitud del pedicel del fruit i amb el pes del fruit, trobem evidència de sintenia amb altres QTLs identificats prèviament en poblacions d'albergínia. Set QTL eren nous, dels quals quatre estaven relacionats amb l'altura de la planta, amb la espinositat del calze de la flor i amb la llargària del pedicel del fruit no van colocalitzar amb cap QTL prèviament identificat en les poblacions d'albergínia, i tres relacionats amb el diàmetre de la tija, amb la llargària del peduncle i de l'estigma, van ser els primers reportats en albergínia per a aquests caràcters. En el segon capítol, el conjunt de IL d'albergínia amb introgresions de S. incanum es va avaluar per a la forma del fruit en dos ambients. Específicament, realitzarem un fenotipado detallat dels fruits dels parentals, de l'híbrid i de les ILs utilitzant 32 descriptors morfològics de l'eina fenómica Tomato Analyzer. Es van trobar grans diferències morfològiques en els fruits dels parentals, i l'híbrid va presentar valors negatius de heterosis per a molts dels caràcters de forma del fruit, sent fenotípicamente més pròxim al parental S. incanum. Per a la majoria dels descriptors de forma del fruit observarem diferències significatives entre les ILs i el parental recipient, fins i tot en presència de xicotets fragments d'introgresió del parental silvestre. A pesar que la contribució de l'ambient i la interacció G × E van ser significatives per a quasi tots els descriptors, trobem que els seus...[EN] Eggplant (Solanum melongena L.) is one of the most important commercial solanaceous vegetable crops grown widely in Asia and Mediterranean region. Despite its economic importance, the availability of experimental populations and genomic tools for breeding is still very limited compared to other major crops. Due to the progressive alteration of global ecosystem by climate change, plants are constantly exposed to stressful environmental conditions that impact negatively on their productivity. The genetic bottleneck occurred during eggplant domestication, which limits the availability of genetic resources for its genetic improvement, makes this crop extremely vulnerable to climate change, and, therefore, new strategies are needed for reducing its genetic erosion. In this context, crop wild relatives (CWRs) have demonstrated to be a valid genetic resources for plant breeding, as their use allows to broaden the genetic diversity of the crop and, in parallel, develop improved varieties adapted to climate change. To achieve this objective, in this doctoral thesis we reported on the development and evaluation of eggplant advanced materials obtained by using crop wild relatives. In the first chapter, we have conducted a phenotypic evaluation in two environments of a set of 16 eggplant ILs with introgression from S. incanum, a close wild relative. Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and identify QTLs for the investigated traits. We found significant morphological differences between parents, and the hybrid was heterotic for vigour related traits. Although significant genotype x environment interaction (G x E) was detected for most traits, the ILs generally exhibited few phenotypic differences with recipient parent, even in the presence of large introgression fragments from the wild parent. Low to moderate heritability values were found for the agronomic traits. In total, we detected ten stable QTLs, two of which were for plant-related traits and four for both flower- and fruit-related traits. In general, S. incanum introgressions improved the performance of most plant- and flower-related traits and decreased that of fruit-related traits. For three QTLs related to fruit pedicel length and fruit weight, we found evidence of synteny to other QTLs previously reported in eggplant populations. Seven QTLs were new, of which four related to plant height, flower calyx prickles, and fruit pedicel length, did not colocalized with any previous identified QTLs in eggplant populations, and three related to stem diameter, peduncle length, and stigma length, were the first reported in eggplant for these traits. In the second chapter, the set of eggplant ILs with introgression from S. incanum was evaluated for fruit shape in two environments. Specifically, we performed a detailed phenotyping of the fruits of the parents, hybrid, and ILs using 32 morphological descriptors of the phenomics tool Tomato Analyzer. Large differences in fruit morphology were found between ILs parents, and the hybrid exhibited negative values of heterosis for many fruit shape traits, being phenotypically closer to S. incanum parent. For most fruit shape descriptors, we observed significant differences between ILs and recipient parent, even in the presence of small wild donor fragments. Although the contribution of the environment and G × E interaction were significant for almost all descriptors, we found that their effects on fruit shape were relatively low, and the observed variations in fruit shape was mainly genetically regulated. Hierarchical clustering revealed nine clusters of highly correlated traits and six ILs groups. A total of 41 QTLs were mapped. Of these, sixteen associated to Basic Measurement and Fruit Shape Index descriptors were syntenic to other previously reported in several intraspecific and interspecific eggplant populations, while twenty-five QTLs related to Blockiness, Homogeneity....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, 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 was also received from Spanish Ministerio de Economía, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER); from Ministerio de Ciencia, Innovación y Universidades, Agencia Estatal de Investigación and Fondo Europeo de Desarrollo Regional (grant RTI-2018-094592-B-100 from MCIU/AEI/FEDER, UE); from 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 Vicerrectorado de Investigación, Innovación y Transferencia de la Universitat Politècnica de València (Ayuda a Primeros Proyectos de Investigación; PAID-06-18). Giulio Mangino is grateful to Generalitat Valenciana for a predoctoral grant within the Santiago Grisolía programme (GRISOLIAP/2016/012).Mangino, G. (2022). Development and use of introgression populations for the detection of QTL related to important agronomic traits in eggplant [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/188916Compendi

Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs

[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 Norway. The 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 was also received from Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER); from Ministerio de Ciencia, Innovacion y Universidades, Agencia Estatal de Investigacion and Fondo Europeo de Desarrollo Regional (grant RTI-2018-094592-B-100 from MCIU/AEI/FEDER, UE); from 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 Vicerrectorado de Investigacion, Innovacion y Transferencia de la Universitat Politecnica de Valencia (Ayuda a Primeros Proyectos de Investigacion; PAID-06-18). Giulio Mangino is grateful to Generalitat Valenciana for a predoctoral grant within the Santiago Grisolia programme (GRISOLIAP/2016/012). Pietro Gramazio is grateful to Japan Society for the Promotion of Science for a postdoctoral grant (P19105, FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)).Mangino, G.; Plazas Ávila, MDLO.; Vilanova Navarro, S.; Prohens Tomás, J.; Gramazio, P. (2020). Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs. Agronomy. 10(4):1-15. https://doi.org/10.3390/agronomy10040467S115104FAOSTAThttp://www.fao.org/faostat/Gebhardt, C. (2016). The historical role of species from the Solanaceae plant family in genetic research. Theoretical and Applied Genetics, 129(12), 2281-2294. doi:10.1007/s00122-016-2804-1Hirakawa, H., Shirasawa, K., Miyatake, K., Nunome, T., Negoro, S., Ohyama, A., … Fukuoka, H. (2014). Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World. 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L., Hamilton, R. S., Xie, F., Reinke, R. F., & Fitzgerald, M. A. (2015). Identification of stable QTLs causing chalk in rice grains in nine environments. Theoretical and Applied Genetics, 129(1), 141-153. doi:10.1007/s00122-015-2616-8Ranil, R. H. G., Niran, H. M. L., Plazas, M., Fonseka, R. M., Fonseka, H. H., Vilanova, S., … Prohens, J. (2015). Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design. Scientia Horticulturae, 193, 174-181. doi:10.1016/j.scienta.2015.07.030Balakrishnan, D., Surapaneni, M., Mesapogu, S., & Neelamraju, S. (2018). Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theoretical and Applied Genetics, 132(1), 1-25. doi:10.1007/s00122-018-3219-yWang, J.-X., Gao, T.-G., & Knapp, S. (2008). Ancient Chinese Literature Reveals Pathways of Eggplant Domestication. 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Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant

[EN] Multi-parent advanced generation inter-cross (MAGIC) populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3 Magic EGGplant InCanum, S3MEGGIC; 8-way), constituted by the 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanin presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-insensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence single-nucleotide polymorphisms (SNPs) confirmed a low residual heterozygosity (6.87%), a lack of genetic structure in the S3MEGGIC population, and no differentiation among subpopulations carrying a cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of the founder genomes, suggesting a cryptic selection in favour or against specific parental genomes. Genome-wide association study (GWAS) analysis for PA, FA, and PUC detected strong associations with two myeloblastosis (MYB) genes similar to MYB113 involved in the anthocyanin biosynthesis pathway, and with a COP1 gene which encodes for a photo-regulatory protein and may be responsible for the PUC trait. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1 compared with the tomato genome. Parental genotypes for the three genes were in agreement with the identification of the candidate genes performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.This work was supported by the Ministerio de Ciencia, Innovacion y Universidades, Agencia Estatal de Investigacion and Fondo Europeo de Desarrollo Regional (grant RTI2018-094592-B-I00 from MCIU/AEI/FEDER, UE) and European Unions Horizon, 2020 Research and Innovation Programme under grant agreement no. 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops). AA is grateful to Spanish Ministerio de Ciencia, Innovacion y Universidades for a pre-doctoral (FPU18/01742) contract. MP is grateful to Spanish Ministerio de Ciencia e Innovacion for a post-doctoral grant (IJC2019-039091-I/AEI/10.13039/501100011033). PG is grateful to Spanish Ministerio de Ciencia e Innovacion for a post-doctoral grant (FJC2019-038921-I/AEI/10.13039/501100011033). Funding for open access charge: Universitat Politecnica de Valencia.Mangino, G.; Arrones-Olmo, A.; Plazas Ávila, MDLO.; Pook, T.; Prohens Tomás, J.; Gramazio, P.; Vilanova Navarro, S. (2022). Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant. Frontiers in Plant Science. 13:1-15. https://doi.org/10.3389/fpls.2022.8477891151

Genomic tools for the enhancement of vegetable crops: a case in eggplant

[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 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 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 Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO / FEDER). Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Juan de la Cierva programme (FCJI-2015-24835). Giulio Mangino is grateful to Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana for a pre-doctoral grant within the Santiago Grisolia programme (GRISOLIAP / 2016/012).Gramazio, P.; Prohens Tomás, J.; Plazas Ávila, MDLO.; Mangino, G.; Herraiz García, FJ.; García-Fortea, E.; Vilanova Navarro, S. (2018). Genomic tools for the enhancement of vegetable crops: a case in eggplant. Notulae Botanicae Horti Agrobotanici Cluj-Napoca. 46(1):1-13. https://doi.org/10.15835/nbha46110936S11346

Influence of Egr-1 in cardiac tissue-derived mesenchymal stem cells in response to glucose variations

Mesenchymal stem cells (MSCs) represent a promising cell population for cell therapy and regenerative medicine applications. However, how variations in glucose are perceived by MSC pool is still unclear. Since, glucose metabolism is cell type and tissue dependent, this must be considered when MSCs are derived from alternative sources such as the heart. The zinc finger transcription factor Egr-1 is an important early response gene, likely to play a key role in the glucose-induced response. Our aim was to investigate how short-term changes in in vitro glucose concentrations affect multipotent cardiac tissue-derived MSCs (cMSCs) in a mouse model of Egr-1 KO (Egr-1-/-). Results showed that loss of Egr-1 does not significantly influence cMSC proliferation. In contrast, responses to glucose variations were observed in wt but not in Egr-1 -/- cMSCs by clonogenic assay. Phenotype analysis by RT-PCR showed that cMSCs Egr-1-/- lost the ability to regulate the glucose transporters GLUT-1 and GLUT-4 and, as expected, the Egr-1 target genes VEGF, TGFβ-1, and p300. Acetylated protein levels of H3 histone were impaired in Egr-1-/- compared to wt cMSCs. We propose that Egr-1 acts as immediate glucose biological sensor in cMSCs after a short period of stimuli, likely inducing epigenetic modifications. © 2014 Daniela Bastianelli et al

Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette

[EN] Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.This work has been funded by grants RTI-2018-094592-BI00 and PID2021-128148OB-I00 funded by MCIN/AEI/10.13039/501100011033/and by "ERDF A way of making Europe", and by 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). AA is grateful to Spanish Ministerio de Ciencia, Innovacio ' n y Universidades for a predoctoral (FPU18/01742) contract. PG is grateful to Spanish Ministerio de Ciencia e Innovacion for a post-doctoral grant (FJC2019-038921-I/AEI/10.13039/501100011033). Funding for open access charge: Universitat Politecnica de Valencia.Arrones-Olmo, A.; Mangino, G.; Alonso-Martín, D.; Plazas Ávila, MDLO.; Prohens Tomás, J.; Portis, E.; Barchi, L.... (2022). Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette. Frontiers in Plant Science. 13:1-14. https://doi.org/10.3389/fpls.2022.10259511141

Fruit Composition of Eggplant Lines with Introgressions from the Wild Relative S. incanum: Interest for Breeding and Safety for Consumption

[EN] The wild species Solanum incanum has been used as a donor parent for the development of a set of eggplant introgression lines (ILs), which are of interest for breeding for stress tolerances and relevant morpho-agronomic traits but could also be useful for breeding for fruit quality, due to the generally higher content in health-promoting compounds of S. incanum. The use of eggplant ILs with introgressions from S. incanum requires ensuring that glycoalkaloids levels are below safety limits. We evaluated 25 fruit composition traits, including proximate composition, sugars, acids, phenolics, glycoalkaloids, and minerals in a set of 16 eggplant ILs with S. incanum, both parents and the F-1, grown under two environments (open field and screenhouse). The results demonstrated that the parents were significantly different regarding most fruit composition traits. Large variation was found among the 16 ILs for all traits analyzed and a strong influence of the environment accounted for the variation of 17 out of the 25 traits evaluated. Although the S. incanum parent produced fruits with high levels of glycoalkaloids, the 16 ILs showed mean values of total glycoalkaloids below the currently accepted safety limit for human consumption (200 mg kg(-1) fresh weight). Overall, the ILs produced fruits that are safe for consumption, with nutritional and functional quality similar to the recipient parent. Furthermore, six putative QTLs were detected spread over chromosomes 3 for crude protein, 5 for malic and total acids, and 7 for chlorogenic acid and solamargine, and potential candidate genes were spotted for most of them, which provide new relevant information for eggplant breeding.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, 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 was also received from grants AGL2015-64755-R funded by MCIN/AEI/10.13039/501100011033 and by "ERDF A way of making Europe" and RTI-2018-094592-B-100 funded by MCIN/AEI/10.13039/501100011033, and from 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). M.P. is grateful to the Spanish Ministerio de Ciencia e Innovacion for a post-doctoral grant with the Juan de la Cierva program (grant number IJC2019-039091-I from MCIN/AEI/10.1309/501100011033). P.G. is grateful to the Japan Society for the Promotion of Science for a post-doctoral grant (P19105, FY2019 JSPS Postdoctoral Fellowship for Research in Japan). E.R.-M. is grateful to the Spanish Ministerio de Economia, Industria y Competitividad for a pre-doctoral grant (grant number BES-2016-077482 from MCIN/AEI/10.1309/501100011033).Rosa-Martínez, E.; Adalid-Martinez, AM.; García-Martínez, MD.; Mangino, G.; Raigón Jiménez, MD.; Plazas Ávila, MDLO.; Gramazio, P.... (2022). Fruit Composition of Eggplant Lines with Introgressions from the Wild Relative S. incanum: Interest for Breeding and Safety for Consumption. Agronomy. 12(2):1-12. https://doi.org/10.3390/agronomy1202026611212

Detection, molecular characterisation and aspects involving the transmission of tomato chlorotic dwarf viroid in eggplant

"This is the peer reviewed version of the following article: Gramazio P, Lerma MD, Villanueva G, et al. Detection, molecular characterisation and aspects involving the transmission of tomato chlorotic dwarf viroid in eggplant. Ann Appl Biol. 2019;175:172 183. https://doi.org/10.1111/aab.12527, which has been published in final form at https://doi.org/10.1111/aab.12527. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."[EN] Tomato chlorotic dwarf viroid (TCDVd) is a pospiviroid that causes severe disease symptoms in tomato. TCDVd is also naturally found in other crops and plants, in most occasions being asymptomatic. Apart from the natural hosts reported up to now, artificial inoculations have revealed that TCDVd can infect other plants, including eggplant (Solanum melongena). In a screening of seedlings of eggplant from a breeding programme we detected a pospiviroid, which we identified as TCDVd, representing the first report of natural infection of eggplant by TCDVd. The new TCDVd isolate of eggplant was detected by reverse transcription polymerase chain reaction (RT¿PCR) using primers TG21/CT20, initially designed to detect potato spindle tuber viroid. The new isolate sequence is close to a Brugmansia sanguinea isolate of TCDVd from the Netherlands, and most of the nucleotidic changes with respect to this isolate and to the reference genome sequence of TCDVd are found in the TR region. Naturally infected plants of eggplant with this TCDVd isolate did not display any disease symptoms. We demonstrated that in eggplant TCDVd is mechanically transmitted with low to moderate efficiency with cultivation practices, but not by plant¿to¿plant contact. Tomato plants artificially inoculated with the eggplant isolate of TCDVd tested positive for the presence of the viroid at 50¿days after inoculation, but did not display any disease symptoms. Seed transmission to germinated seedlings of eggplant was variable among progenies from infected plants, ranging from 7.7% to 100.0%. Disinfection of seeds with chemical treatments with sodium hypochlorite and trisodium phosphate solutions plus thermotherapy at 80°C for 24¿hr or 90°C for 6 hr was ineffective in reducing the rate of transmission by seed. We did not find evidence of horizontal transmission of TCDVd by pollen, but vertical transmission was highly efficient when healthy eggplant plants were pollinated with infected pollen. Our results indicate that asymptomatic infection of eggplant by TCDVd and high seed and pollen transmission rates may contribute to the spread of this viroid. The information we obtained is useful in order to implement measures for the prevention, control and eradication of TCDVd in eggplant crops, as well as to avoid their transmission to other hosts.P.G. is grateful to Universitat Politècnica de València and to Japan Society for the Promotion of Science for their respective postdoctoral grants (PAID-10-18 and FY2019 JSPS Postdoctoral Fellowship for Research in Japan [Standard]). A.A. and D.A. are grateful to Universitat Politècnica de València for their respective predoctoral (PAID-01-18 and PAID-01-16) contracts within the Programa de Ayudas de Investigación y Desarrollo initiative. E.G.-F. is grateful to Ministerio de Educación, Cultura y Deporte para la Formación de Profesorado Universitario for a predoctoral grant (FPU17/02389). G.M. is grateful to Generalitat Valenciana for a predoctoral grant within the Santiago Grisolía programme (GRISOLIAP/2016/012). M.P. is grateful to Generalitat Valenciana and Fondo Social Europeo for a postdoctoral grant (APOSTD/2018/014).Gramazio, P.; Lerma Lerma, MD.; Villanueva-Párraga, G.; Vilanova Navarro, S.; García-Fortea, E.; Mangino, G.; Figás-Moreno, MDR.... (2019). Detection, molecular characterisation and aspects involving the transmission of tomato chlorotic dwarf viroid in eggplant. Annals of Applied Biology. 175(2):172-183. https://doi.org/10.1111/aab.12527S1721831752Bakker, D., Bruinsma, M., Dekter, R. W., Toonen, M. A. J., Verhoeven, J. T. J., & Koenraadt, H. M. S. (2015). Detection of PSTVd and TCDVd in seeds of tomato using real-time RT-PCR. EPPO Bulletin, 45(1), 14-21. doi:10.1111/epp.12195Barba, M., & James, D. (2017). Quarantine and Certification for Viroids and Viroid Diseases. Viroids and Satellites, 415-424. doi:10.1016/b978-0-12-801498-1.00039-5Broadbent, L. (1976). Epidemiology and Control of Tomato Mosaic Virus. 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First successful backcrossing towards eggplant (Solanum melongena) of a New World species, the silverleaf nightshade (S-elaeagnifolium), and characterization of interspecific hybrids and backcrosses

[EN] Silverleaf nightshade (Solanum elaeagnifolium Cav.) is a drought tolerant invasive weed native to the New World. Despite its interest for common eggplant (S. melongena L.) breeding, up to now no success has been obtained in introgression breeding of eggplant with American Solanum species. Using an interspecific hybrid between common eggplant and S. elaeagnifolium as maternal parent we were able to obtain several fruits with viable seed after pollination with S. melongena pollen. Twenty individuals of the first backcross (BC1) generation were crossed again to the S. melongena parent and second backcross (BC2) seed was obtained for 17 of them, suggesting that most of the genome of S. elaeagnifolium is likely to be represented in the set of BC2 families. Five plants of each of the two parents, interspecific hybrid and BC1 generation were characterized with morphological descriptors and for pollen viability. The interspecific hybrid was intermediate among parents, although in overall morphological characteristics more similar to the S. elaeagnifolium parent. However, pollen viability of the hybrid was very low (2.6%). The BC1 generation was intermediate in characteristics between the hybrid and the S. melongena parent, with pollen viability increasing to an average of 19.4%. The root system of the inter specific hybrid indicated that it is able to explore larger areas of the soil than the S. melongena parent. The phenolics profile of the fruit of the two parents and hybrid revealed a higher diversity in phenolic constituents in S. elaeagnifolium compared to S. melongena, where the major phenolic compound was chlorogenic acid, while the interspecific hybrid was intermediate. By using flow cytometry it was found that S. elaeagnifolium, S. melongena, and their interspecific hybrid were diploid, although the genome size of S. elaeagnifolium was slightly smaller than that of S. melongena. Our results represent the first report of successful development of backcross generations of common eggplant with a New World Solarium species. This makes available a relatively unexplored, phylogenetically distant genepool for eggplant breeding. The backcross materials obtained can make a relevant contribution to developing new eggplant cultivars with new nutritional and environmental properties.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, 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 was also received from 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 Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Edgar Garcia-Fortea is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2017 call) contract. Giulio Mangino is grateful to Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana for a predoctoral grant within the Santiago Grisolia programme (GRISOLIAP/2016/012). Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a postdoctoral grant within the Juan de la Cierva programme (FCJI-2015-24835), and to Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana and Fons Social Europeu for a postdoctoral grant (APOSTD/2018/014).García-Fortea, E.; Gramazio, P.; Vilanova Navarro, S.; Fita, A.; Mangino, G.; Villanueva-Párraga, G.; Arrones-Olmo, A.... (2019). First successful backcrossing towards eggplant (Solanum melongena) of a New World species, the silverleaf nightshade (S-elaeagnifolium), and characterization of interspecific hybrids and backcrosses. Scientia Horticulturae. 246:563-573. https://doi.org/10.1016/j.scienta.2018.11.018S563573246Acosta, M. C., Bernardello, G., Guerra, M., & Moscone, E. A. (2005). Karyotype analysis in several South American species ofSolanumandLycianthes rantonnei(Solanaceae). TAXON, 54(3), 713-723. doi:10.2307/25065428Afful, N. 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