Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits

Abstract Background Nuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits. Results A mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping. Conclusions The QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop.The authors thank Quival-Frutos Secos El Nogal (Pontevedra, Spain) for technical support and Diputación de Pontevedra for farm facilities. We also thank Rosana Pereira Vianello Brondani from Embrapa Arroz e Feijão, CNPq (Brasil) for supplying some microsatellite primers. MDLF was supported by a research contract of the Xunta de Galicia. This work has been funded by grants PET2008_0167, EUI2009-04052 and AGL2011-25562 of the Ministerio de Ciencia e Innovación and PGIDI03RAG16E of the Xunta de Galicia.Peer Reviewe

Nuevo cultivar con frutos y sépalos convertidos en frutos de alto interés para su consumo fresco y procesado industrial

Número de publicación: 2 341 527 21 Número de solicitud: 200900003 51 Int. Cl.: C12N 15/82 (2006.01) A01H 5/00 (2006.01Nuevo cultivar con frutos y sépalos convertidos en frutos de alto interés para su consumo fresco y procesado industrial. En la presente invención se describen secuencias de nucleótidos capaces de incrementar la expresión de un gen de desarrollo reproductivo lo que tiene como resultado la generación de cultivares con un fruto de alto interés para su consumo fresco y procesado industrial caracterizado por poseer características mejoradas respecto de los cultivares conocidos de variedades comerciales. Estos nuevos cultivares tienen el cáliz de la flor carnoso y convertido en fruto. El fruto verdadero y el cáliz tienen mayores niveles de azúcares y licopeno y un mayor contenido en grados Brix. Además, exhiben una mayor tasa de cuajado de fruto y tienen inhibida la zona de abscisión del fruto, lo que facilita la recolección mecánica.Universidad de Almerí

Identification, introgression, and validation of fruit volatile QTLs from a red-fruited wild tomato species

[EN] Volatile organic compounds (VOCs) are major determinants of fruit flavor, a primary objective in tomato breeding. A recombinant inbred line (RIL) population consisting of 169 lines derived from a cross between Solanum lycopersicum and a red-fruited wild tomato species Solanum pimpinellifolium accession (SP) was characterized for VOCs in three different seasons. Correlation and hierarchical cluster analyses were performed on the 52 VOCs identified, providing a tool for the putative assignation of individual compounds to metabolic pathways. Quantitative trait locus (QTL) analysis, based on a genetic linkage map comprising 297 single nucleotide polymorphisms (SNPs), revealed 102 QTLs (75% not described previously) corresponding to 39 different VOCs. The SP alleles exerted a positive effect on most of the underlying apocarotenoid volatile QTLs-regarded as desirable for liking tomato-indicating that alleles inherited from SP are a valuable resource for flavor breeding. An introgression line (IL) population developed from the same parental genotypes provided 12 ILs carrying a single SP introgression and covering 85 VOC QTLs, which were characterized at three locations. The results showed that almost half of the QTLs previously identified in the RILs maintained their effect in an IL form, reinforcing the value of these QTLs for flavor/aroma breeding in cultivated tomato.We thank Erika Moro for valuable help in volatile analysis of the ILs. WB was supported by a fellowship granted by the Universidad de Costa Rica and CSIC-Spain by way of a collaboration agreement between CSIC/UCR. Volatile profiling was performed in the Metabolomic facilities of the IBMCP, CSIC (Spain). This work was supported in part by the Spanish MINECO Project AGL2015-65246-R co-financed by EU FEDER, MINECO Project AGL2011-26957, and the Bilateral agreements of Scientific and Technological Cooperation between the Spanish National Research Council (CSIC) and the Italian National Research Council (CNR). Funding for this project was provided through TRADITOM. TRADITOM has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 634561. Networking activities were supported by COST action Fruit Quality FA 1106.Rambla Nebot, JL.; Medina, A.; Fernández Del Carmen, MA.; Barrantes, W.; Grandillo, S.; Cammareri, M.; López Casado, G.... (2016). Identification, introgression, and validation of fruit volatile QTLs from a red-fruited wild tomato species. Journal of Experimental Botany. 68(3):429-442. https://doi.org/10.1093/jxb/erw455S429442683Alba, J. M., Montserrat, M., & Fernández-Muñoz, R. (2008). 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Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: A tool for gene mapping and gene discovery. Genome, 43(5), 803-813. doi:10.1139/gen-43-5-803Orzaez, D., Medina, A., Torre, S., Fernández-Moreno, J. P., Rambla, J. L., Fernández-del-Carmen, A., … Granell, A. (2009). A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation. Plant Physiology, 150(3), 1122-1134. doi:10.1104/pp.109.139006Rambla, J. L., Alfaro, C., Medina, A., Zarzo, M., Primo, J., & Granell, A. (2015). Tomato fruit volatile profiles are highly dependent on sample processing and capturing methods. Metabolomics, 11(6), 1708-1720. doi:10.1007/s11306-015-0824-5Rambla, J. L., Tikunov, Y. M., Monforte, A. J., Bovy, A. G., & Granell, A. (2013). The expanded tomato fruit volatile landscape. 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Ritmos y relojes circadianos de las plantas

Las plantas necesitan coordinar toda su fisiología, y por ende su reproducción, con la información del ambiente que las rodea. Los ritmos biológicos permiten a las plantas anticiparse a ciertas condiciones exteriores cambiantes como luz y temperatura. Los encargados de generar los ritmos son los relojes biológicos, que a su vez utilizan la información del ambiente que rodea a la planta para actualizar su propio funcionamiento. Entre los ritmos biológicos los de mayor trascendencia para plantas y animales son los que ocurren con periodos cercanos a un día o ritmos circadianos. En los últimos años hemos asistido a una gran cantidad de descubrimientos acerca de la naturaleza del reloj circadiano de las plantas y de cómo éste controla proceso anuales tan importantes como la floración y la tuberización. Sin embargo aún estamos lejos de comprender, y por tanto manipular, este importante mecanismo biológico clave para la ecología y la producción de los vegetales

Non-random distribution of transposable elements in the nuclear genome of plants

We have studied the genomic distribution of five different families of plant transposable elements by analyzing their location in DNA fractions from maize and tobacco genomes fractionated according to base composition. The results show that each family of elements Is preferentially Integrated In one specific fraction of Its respective host genome. This demonstrates that the distribution of transposable elements In the nuclear genome of plants Is not random but compartimentalized, i.e., the elements are located In specific genomic compartments characterized by having a specific G + C content and representing a small proportion of the genomes. Furthermore, these compartments seem to correspond to the genomic regions where most of the plant genes are also located, suggesting a preferential Integration of transposable elements In the transcriptlonally active regions of the plant genome. The implications of these results on the current applications of transposon tagging techniques are discussed.Peer reviewe

Two homologous low temperature inducible genes from Arabidopsis encode highly hydrophobic proteins

We have characterized two related cDNAs (RCIM and RC12B) corresponding to genes from Arabidopsis thaliana, the expression of which i s transiently induced by low, nonfreezing temperatures. R C l Z A and R C D B encode small(54 amino acids), highly hydropho- bic proteins that bear two potential transmembrane domains. They show similarity to proteins encoded by genes from barley (Hordeum vulgare L.) and wheatgrass (Lophophyrum elongatum) that are reg- ulated by different stress conditions. Their high leve1 of sequence homology (78%) and their genomic location in a single restriction fragment suggest that both genes originated as a result of a tandem duplication. However, their regulatory sequences have diverged enough to confer on them different expression patterns. Like most of the cold-inducible plant genes characterized, the expression of RC12A and R C / Z B i s also promoted by abscisic acid (ABA) and dehydration but i s nota general response to stress conditions, since it i s not induced by salt stress or by anaerobiosis. Furthermore, low temperatures are able to induce RC12A and RC12B expression in ABA-deficient and -insensitive genetic backgrounds, indicating that both ABA-dependent and 4ndependent pathways regulate the low- temperature responsiveness of these two genes.We wish to thank Dr. M. Koorneef for providing us with seeds of ABA-related mutants a n d Dr. M.J. Jorquera for her technical assistance.Peer reviewe

Two related low-temperature-inducible genes of Arabidopsis encode proteins showing high homology to 14-3-3 proteins, a family of putative kinase regulators

We have isolated two Rare Cold-Inducible (RCI1 and RCI2) cDNAs by screening a cDNA library prepared from cold-acclimated etiolated seedlings of Arabidopsis thaliana with a subtracted probe. RNA-blot hybridizations revealed that the expression of both RCI1 and RCI2 genes is induced by low temperature independently of the plant organ or the developmental stage considered. However, RCI1 mRNA accumulates faster and at higher levels than the RCI2 one indicating that these genes have differential responsiveness to cold stress. Additionally, when plants are returned to room temperature, RCI1 mRNA decreases faster than RCI2. In contrast to most of the cold-inducible plant genes characterized, the expression of RCI1 and RCI2 is not induced by ABA or water stress. The nucleotide sequences of RCI1 and RCI2 cDNAs predict two acidic polypeptides of 255 and 251 amino acids with molecular weights of 29 and 28 kDa respectively. The alignment of these polypeptides indicates that they have 181 identical amino acids suggesting that the corresponding genes have a common origin. Sequence comparisons reveal no similarities between the RCI proteins and any other cold-regulated plant protein so far described. Instead, they demonstrate that the RCI proteins are highly homologous to a family of proteins, known as 14-3-3 proteins, which are thought to be involved in the regulation of multifunctional protein kinases.Project INIA 9062 y EEC PTP BIOT CT93-0400Peer reviewe

Tomato Flower Abnormalities Induced by Low Temperatures Are Associated with Changes of Expression of MADS-Box Genes

Flower and fruit development in tomato (Lycopersicon esculentum Mill.) were severely affected when plants were grown at low temperatures, displaying homeotic and meristic transformations and alterations in the fusion pattern of the organs. Most of these homeotic transformations modified the identity of stamens and carpels, giving rise to intermediate organs. Complete homeotic transformations were rarely found and always affected organs of the reproductive whorls. Meristic transformations were also commonly observed in the reproductive whorls, which developed with an excessive number of organs. Scanning electron microscopy revealed that meristic transformations take place very early in the development of the flower and are related to a significant increase in the floral meristem size. However, homeotic transformations should occur later during the development of the organ primordia. Steady-state levels of transcripts corresponding to tomato MADS-box genes TM4, TM5, TM6, and TAG1 were greatly increased by low temperatures and could be related to these flower abnormalities. Moreover, in situ hybridization analyses showed that low temperatures also altered the stage-specific expression of TM4

Mapping of single-locus and epistatic QTLs for seed morpho-agronomic traits from an adapted x exotic nuña bean population

Comunicación presentada en la First Legume Society Conference, celebrada en Novi Sad (Serbia) del 9 al 11 de mayo de 2013.Common bean (Phaseolus vulgaris L.) is a widely grown and important economic grain legume. Seed quality is a critical attribute in determining commercial acceptability of common bean. Thereby, to obtain insights into the genetics of seed quality, a population of 185 recombinant inbred lines (RILs) derived from an Andean intra-gene pool cross, involving PMB0225 (dry bean) and PHA1037 (nuña bean) parents, was evaluated for seven seed traits under six different environments (long-day and short-day natural photoperiod conditions). Multi-environment QTL analyses performed detected a total of 46 QTLs, which were mapped throughout all linkage groups: 21 had only additive effects, 17 had only epistatic effects and eight had both additive and epistatic effects. For seed dimension and weight traits, 19 single-locus QTLs and 13 epistatic QTLs involved in eight epistatic interactions were detected; while for seed color and brightness, 10 single-locus QTLs and 12 epistatic QTLs involved in seven epistatic interactions were identified. Interactions between QTLs and environment were also detected, but despite this fact, QTLs with differential effect on long-day and short-day environments were not found. It may be concluded that i) the genetics of seed quality is complex in nature, where not only additive effects but also epistasis are important components of the genetic variance in the Andean common bean background, and ii) the QTLs here reported will play a significant role in enhancing marker assisted selection efficiency for breeding nuña beans. The work was supported by the PET2008-0167 and AGL2011-25562 projects of the Ministerio de Economía y Competitividad from Spain.N

Genetic analysis of single-locus and epistatic QTLs for seed traits in an adapted × nuña RIL population of common bean (Phaseolus vulgaris L.)

Key message: The QTLs analyses here reported demonstrate the significant role of both individual additive and epistatic effects in the genetic control of seed quality traits in the Andean common bean. Common bean shows considerable variability in seed size and coat color, which are important agronomic traits determining farmer and consumer acceptability. Therefore, strategies must be devised to improve the genetic base of cultivated germplasm with new alleles that would contribute positively to breeding programs. For that purpose, a population of 185 recombinant inbred lines derived from an Andean intra-gene pool cross, involving an adapted common bean (PMB0225 parent) and an exotic nuña bean (PHA1037 parent), was evaluated under six different-short and long-day-environmental conditions for seed dimension, weight, color, and brightness traits, as well as the number of seed per pod. A multi-environment Quantitative Trait Loci (QTL) analysis was carried out and 59 QTLs were mapped on all linkage groups, 18 of which had only individual additive effects, while 27 showed only epistatic effects and 14 had both individual additive and epistatic effects. Multivariate models that included significant QTL explained from 8 to 68 % and 2 to 15 % of the additive and epistatic effects, respectively. Most of these QTLs were consistent over environment, though interactions between QTLs and environments were also detected. Despite this, QTLs with differential effect on long-day and short-day environments were not found. QTLs identified were positioned in cluster, suggesting that either pleiotropic QTLs control several traits or tightly linked QTLs for different traits map together in the same genomic regions. Overall, our results show that digenic epistatic interactions clearly play an important role in the genetic control of seed quality traits in the Andean common bean.The research has been funded by grant AGL2011-25562 from the Ministerio de Economía y Competitividad (Spain). We also thank Campus de Excelencia Internacional Agroalimentario (CeiA3) for supporting in part this work.MECCampus de Excelencia Internacional Agroalimentario (CeiA3)Peer Reviewe