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

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). Resistance to the two-spotted spider mite (Tetranychus urticae) by acylsucroses of wild tomato (Solanum pimpinellifolium) trichomes studied in a recombinant inbred line population. Experimental and Applied Acarology, 47(1), 35-47. doi:10.1007/s10493-008-9192-4Abegaz, E. G., Tandon, K. S., Scott, J. W., Baldwin, E. A., & Shewfelt, R. L. (2004). Partitioning taste from aromatic flavor notes of fresh tomato (Lycopersicon esculentum, Mill) to develop predictive models as a function of volatile and nonvolatile components. Postharvest Biology and Technology, 34(3), 227-235. doi:10.1016/j.postharvbio.2004.05.023Baldwin, E. A., Goodner, K., & Plotto, A. (2008). Interaction of Volatiles, Sugars, and Acids on Perception of Tomato Aroma and Flavor Descriptors. Journal of Food Science, 73(6), S294-S307. doi:10.1111/j.1750-3841.2008.00825.xBarrantes, W., Fernández-del-Carmen, A., López-Casado, G., González-Sánchez, M. Á., Fernández-Muñoz, R., Granell, A., & Monforte, A. J. (2014). Highly efficient genomics-assisted development of a library of introgression lines of Solanum pimpinellifolium. Molecular Breeding, 34(4), 1817-1831. doi:10.1007/s11032-014-0141-0Buttery, R. G., & Ling, L. C. (1993). Volatile Components of Tomato Fruit and Plant Parts. Bioactive Volatile Compounds from Plants, 23-34. doi:10.1021/bk-1993-0525.ch003Capel, C., Fernández del Carmen, A., Alba, J. M., Lima-Silva, V., Hernández-Gras, F., Salinas, M., … Lozano, R. (2015). Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L. Theoretical and Applied Genetics, 128(10), 2019-2035. doi:10.1007/s00122-015-2563-4Chen, G., Hackett, R., Walker, D., Taylor, A., Lin, Z., & Grierson, D. (2004). Identification of a Specific Isoform of Tomato Lipoxygenase (TomloxC) Involved in the Generation of Fatty Acid-Derived Flavor Compounds. Plant Physiology, 136(1), 2641-2651. doi:10.1104/pp.104.041608Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences, 95(25), 14863-14868. doi:10.1073/pnas.95.25.14863Fowlkes, E. B., & Mallows, C. L. (1983). A Method for Comparing Two Hierarchical Clusterings. Journal of the American Statistical Association, 78(383), 553. doi:10.2307/2288117Goulet, C., Kamiyoshihara, Y., Lam, N. B., Richard, T., Taylor, M. G., Tieman, D. M., & Klee, H. J. (2015). Divergence in the Enzymatic Activities of a Tomato and Solanum pennellii Alcohol Acyltransferase Impacts Fruit Volatile Ester Composition. Molecular Plant, 8(1), 153-162. doi:10.1016/j.molp.2014.11.007Goulet, C., Mageroy, M. H., Lam, N. B., Floystad, A., Tieman, D. M., & Klee, H. J. (2012). Role of an esterase in flavor volatile variation within the tomato clade. Proceedings of the National Academy of Sciences, 109(46), 19009-19014. doi:10.1073/pnas.1216515109Klee, H. J., & Tieman, D. M. (2013). Genetic challenges of flavor improvement in tomato. Trends in Genetics, 29(4), 257-262. doi:10.1016/j.tig.2012.12.003Kochevenko, A., Araújo, W. L., Maloney, G. S., Tieman, D. M., Do, P. T., Taylor, M. G., … Fernie, A. R. (2012). Catabolism of Branched Chain Amino Acids Supports Respiration but Not Volatile Synthesis in Tomato Fruits. Molecular Plant, 5(2), 366-375. doi:10.1093/mp/ssr108Louveau, T., Leitao, C., Green, S., Hamiaux, C., van der Rest, B., Dechy-Cabaret, O., … Chervin, C. (2010). Predicting the substrate specificity of a glycosyltransferase implicated in the production of phenolic volatiles in tomato fruit. FEBS Journal, 278(2), 390-400. doi:10.1111/j.1742-4658.2010.07962.xMageroy, M. H., Tieman, D. M., Floystad, A., Taylor, M. G., & Klee, H. J. (2011). A Solanum lycopersicum catechol-O-methyltransferase involved in synthesis of the flavor molecule guaiacol. The Plant Journal, 69(6), 1043-1051. doi:10.1111/j.1365-313x.2011.04854.xMathieu, S., Cin, V. D., Fei, Z., Li, H., Bliss, P., Taylor, M. G., … Tieman, D. M. (2008). Flavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. Journal of Experimental Botany, 60(1), 325-337. doi:10.1093/jxb/ern294Matsui, K., Ishii, M., Sasaki, M., Rabinowitch, H. D., & Ben-Oliel, G. (2007). Identification of an Allele Attributable to Formation of Cucumber-like Flavor in Wild Tomato Species (Solanum pennellii) That Was Inactivated during Domestication. Journal of Agricultural and Food Chemistry, 55(10), 4080-4086. doi:10.1021/jf063756bMATSUI, K., MIYAHARA, C., WILKINSON, J., HIATT, B., KNAUF, V., & KAJIWARA, T. (2000). Fatty Acid Hydroperoxide Lyase in Tomato Fruits: Cloning and Properties of a Recombinant Enzyme Expressed inEscherichia coli. Bioscience, Biotechnology, and Biochemistry, 64(6), 1189-1196. doi:10.1271/bbb.64.1189Monforte, A. J., & Tanksley, S. D. (2000). 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. Journal of Experimental Botany, 65(16), 4613-4623. doi:10.1093/jxb/eru128Saliba-Colombani, V., Causse, M., Langlois, D., Philouze, J., & Buret, M. (2001). Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits. Theoretical and Applied Genetics, 102(2-3), 259-272. doi:10.1007/s001220051643Salinas, M., Capel, C., Alba, J. M., Mora, B., Cuartero, J., Fernández-Muñoz, R., … Capel, J. (2012). Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch). Theoretical and Applied Genetics, 126(1), 83-92. doi:10.1007/s00122-012-1961-0Sefton, M. A., Skouroumounis, G. K., Elsey, G. M., & Taylor, D. K. (2011). Occurrence, Sensory Impact, Formation, and Fate of Damascenone in Grapes, Wines, and Other Foods and Beverages. Journal of Agricultural and Food Chemistry, 59(18), 9717-9746. doi:10.1021/jf201450qShen, J., Tieman, D., Jones, J. B., Taylor, M. G., Schmelz, E., Huffaker, A., … Klee, H. J. (2014). A 13-lipoxygenase, TomloxC, is essential for synthesis of C5 flavour volatiles in tomato. Journal of Experimental Botany, 65(2), 419-428. doi:10.1093/jxb/ert382Sim, S.-C., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M. W., Van Deynze, A., … Francis, D. M. (2012). Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato. PLoS ONE, 7(7), e40563. doi:10.1371/journal.pone.0040563Simkin, A. J., Schwartz, S. H., Auldridge, M., Taylor, M. G., & Klee, H. J. (2004). The tomato carotenoid cleavage dioxygenase 1 genes contribute to the formation of the flavor volatiles β-ionone, pseudoionone, and geranylacetone. The Plant Journal, 40(6), 882-892. doi:10.1111/j.1365-313x.2004.02263.xSkouroumounis GK Massywestropp RA Sefton MA Williams PJ . 1993. beta-Damascenone formation in juices and wines. In: Schreier P Winterhalter P , eds. Progress in flavour precursor studies: analysis, generation, biotechnology. Proceedings of the International Conference, Würzburg, Germany, September 30–October 2, 1992, 275–278.Speirs, J., Lee, E., Holt, K., Yong-Duk, K., Steele Scott, N., Loveys, B., & Schuch, W. (1998). Genetic Manipulation of Alcohol Dehydrogenase Levels in Ripening Tomato Fruit Affects the Balance of Some Flavor Aldehydes and Alcohols. Plant Physiology, 117(3), 1047-1058. doi:10.1104/pp.117.3.1047Tadmor, Y., Fridman, E., Gur, A., Larkov, O., Lastochkin, E., Ravid, U., … Lewinsohn, E. (2002). Identification ofmalodorous, a Wild Species Allele Affecting Tomato Aroma That Was Selected against during Domestication. Journal of Agricultural and Food Chemistry, 50(7), 2005-2009. doi:10.1021/jf011237xTieman, D., Bliss, P., McIntyre, L. M., Blandon-Ubeda, A., Bies, D., Odabasi, A. Z., … Klee, H. J. (2012). The Chemical Interactions Underlying Tomato Flavor Preferences. Current Biology, 22(11), 1035-1039. doi:10.1016/j.cub.2012.04.016Tieman, D., Taylor, M., Schauer, N., Fernie, A. R., Hanson, A. D., & Klee, H. J. (2006). Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proceedings of the National Academy of Sciences, 103(21), 8287-8292. doi:10.1073/pnas.0602469103Tieman, D., Zeigler, M., Schmelz, E., Taylor, M. G., Rushing, S., Jones, J. B., & Klee, H. J. (2010). Functional analysis of a tomato salicylic acid methyl transferase and its role in synthesis of the flavor volatile methyl salicylate. The Plant Journal, 62(1), 113-123. doi:10.1111/j.1365-313x.2010.04128.xTieman, D. M., Loucas, H. M., Kim, J. Y., Clark, D. G., & Klee, H. J. (2007). Tomato phenylacetaldehyde reductases catalyze the last step in the synthesis of the aroma volatile 2-phenylethanol. Phytochemistry, 68(21), 2660-2669. doi:10.1016/j.phytochem.2007.06.005Tieman, D. M., Zeigler, M., Schmelz, E. A., Taylor, M. G., Bliss, P., Kirst, M., & Klee, H. J. (2006). Identification of loci affecting flavour volatile emissions in tomato fruits. Journal of Experimental Botany, 57(4), 887-896. doi:10.1093/jxb/erj074Tikunov, Y., Lommen, A., de Vos, C. H. R., Verhoeven, H. A., Bino, R. J., Hall, R. D., & Bovy, A. G. (2005). A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles. Plant Physiology, 139(3), 1125-1137. doi:10.1104/pp.105.068130Tikunov, Y. M., Molthoff, J., de Vos, R. C. H., Beekwilder, J., van Houwelingen, A., van der Hooft, J. J. J., … Bovy, A. G. (2013). NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit. The Plant Cell, 25(8), 3067-3078. doi:10.1105/tpc.113.114231Van Ooijen JW . 2006. JoinMap® 4. Software for the calculation of genetic linkage maps in experimental populations. Wageningen, The Netherlands: Kyazma BV.Vogel, J. T., Tieman, D. M., Sims, C. A., Odabasi, A. Z., Clark, D. G., & Klee, H. J. (2010). Carotenoid content impacts flavor acceptability in tomato (Solanum lycopersicum). Journal of the Science of Food and Agriculture, 90(13), 2233-2240. doi:10.1002/jsfa.4076Voorrips, R. E. (2002). MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs. Journal of Heredity, 93(1), 77-78. doi:10.1093/jhered/93.1.77Zanor, M. I., Rambla, J.-L., Chaïb, J., Steppa, A., Medina, A., Granell, A., … Causse, M. (2009). Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. Journal of Experimental Botany, 60(7), 2139-2154. doi:10.1093/jxb/erp086Zorrilla-Fontanesi, Y., Rambla, J.-L., Cabeza, A., Medina, J. J., Sánchez-Sevilla, J. F., Valpuesta, V., … Amaya, I. (2012). Genetic Analysis of Strawberry Fruit Aroma and Identification of O-Methyltransferase FaOMT as the Locus Controlling Natural Variation in Mesifurane Content. Plant Physiology, 159(2), 851-870. doi:10.1104/pp.111.18831

RB1037-5

Peer reviewedA2 Solicitud de patente sin informe sobre el estado de la técnic

An examination of QTL architecture underlying pod shattering resistance in common bean

Póster presentado en la "8th International Conference on Legume Genetics and Genomics (ICLGG)", que tuvo lugar en Siófok, Hungría, entre el 18 y el 22 de septiembre de 2017.The domesticated common bean (Phaseolus vulgaris) originated in the Mesoamerican and Andean regions independently. Similar to other legume crops, the reduction of pod shattering represents a key domestication syndrome in the domesticated common bean. Understanding the genetic variation of common bean in relation to pod shattering is important for elucidating the underlying genetic mechanisms of parallel evolution (Don and Wang, 2015) and also because this will provide breeders with key tools to improve this trait, thus reducing yield loss (Santalla et al., 2004). Most of these studies have been conducted in cereals (Lin et al., 2012), while in legumes, the identification of pod-shattering genes lag far behind those of the cereal crops (Li and Olsen, 2016). In this study, we identified quantitative trait loci (QTLs) controlling pod fiber in the ventral suture (string) and pod shattering in a recombinant inbred line (RIL) population derived from a cross between a cultivated common bean and wild nuña bean. F2:7 flines were grown under short-day conditions and pod string and pod shattering were analysed at several developmental stages. Correlation analysis showed positive relationship among pod string and shattering. Multi-environment QTL mapping revealed that a major QTL on linkage group 2 (LG02) controlled pod string and co-localized to pod shattering. In addition, minor QTLs related to pod string and pod shattering were identified on LGs01, 03, 04 and 07. Genes underlying the pleiotropic QTL regions could be potential targets for improving shattering resistance performance through marker assisted selection. These QTLs not only provide useful information for isolating candidate genes involved in pod development but also mean potential targets for improving pod shattering resistance by marker assisted selection.This work was financially supported by the Ministerio de Economía y Competitividad (AGL2014-51809-R and AGL2015-64991-C3-1-R) and UE-FEDER Program.Peer 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

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

Uncovering the genetic architecture of Colletotrichum lindemuthianum resistance through QTL mapping and epistatic interaction analysis in common bean

This Document is Protected by copyright and was first published by Frontiers. All rights reserved. it is reproduced with permission.Colletotrichum lindemuthianum is a hemibiotrophic fungal pathogen that causes anthracnose disease in common bean. Despite the genetics of anthracnose resistance has been studied for a long time, few quantitative trait loci (QTLs) studies have been conducted on this species. The present work examines the genetic basis of quantitative resistance to races 23 and 1545 of C. lindemuthianum in different organs (stem, leaf and petiole). A population of 185 recombinant inbred lines (RIL) derived from the cross PMB0225 × PHA1037 was evaluated for anthracnose resistance under natural and artificial photoperiod growth conditions. Using multi-environment QTL mapping approach, 10 and 16 main effect QTLs were identified for resistance to anthracnose races 23 and 1545, respectively. The homologous genomic regions corresponding to 17 of the 26 main effect QTLs detected were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins. Among them, it is worth noting that the main effect QTLs detected on linkage group 05 for resistance to race 1545 in stem, petiole and leaf were located within a 1.2 Mb region. The NL gene Phvul.005G117900 is located in this region, which can be considered an important candidate gene for the non-organ-specific QTL identified here. Furthermore, a total of 39 epistatic QTL (E-QTLs) (21 for resistance to race 23 and 18 for resistance to race 1545) involved in 20 epistatic interactions (eleven and nine interactions for resistance to races 23 and 1545, respectively) were identified. None of the main and epistatic QTLs detected displayed significant environment interaction effects. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for anthracnose resistance improvement in common bean through application of marker-assisted selection (MAS).This work was financially supported by the Ministerio de Economía y Competitividad (AGL2011-25562) and UE-FEDER Program. The authors would like to thank Junta de Andalucía (grant number P10-AGR-06931) and Campus de Excelencia Internacional Agroalimentario-CeiA3 for partially supporting this work financially.MECUE-FEDERJunta de AndalucíaCampus de Excelencia Internacional Agroalimentario-CeiA3Peer reviewe

Cartografía genética de QTLs asociados a caracteres de grano en el acervo genético andino de judía (Phaseolus vulgaris L.)

4 páginas.-Trabajo presentado en las "IV Jornadas de la AEL - V Seminario de judía", celebradas bajo el lema "Legumbres y salud" en Pontevedra el año 2012.[EN] A comprehensive QTL analysis was performed from a novel genetic linkage map generated in the Andean intra-gene pool. The results revealed that seed related traits are controlled by several QTLS, which have only individual effects, or may also be involved in epistatic or environmental interactions, indicating that seed related traits are inherited as a polygenic trait, and that epistasis could play a key role.[ES] Se ha construido un nuevo mapa de ligamiento del acervo genético Andino de judía, el cual ha sido utilizado para realizar un análisis integrado de QTLS en esta especie. Los resultados mostraron que algunos caracteres de semilla están controlados por QTLS que tienen únicamente efectos individuales, mientras otros pueden estar involucrados así mismo en interacciones epistáticas o ambientales, indicando que el control genético de estos caracteres es poligénioo, y que la epistasis juega un papel esencial.Trabajo financiado por los proyectos PET2OO8-0167, EUI2009—O4052, AGL2011-25562 (Ministerio de Ciencia e Innovación) y PGIDIO3RAG16E (Xunta de Galicia).Peer reviewe

Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L

[EN] QTL and candidate genes associated to fruit quality traits have been identified in a tomato genetic map derived from Solanum pimpinellifolium L., providing molecular tools for marker-assisted breeding. The study of genetic, physiological, and molecular pathways involved in fruit development and ripening has considered tomato as the model fleshy-fruited species par excellence. Fruit quality traits regarding organoleptic and nutritional properties are major goals for tomato breeding programs since they largely decide the acceptance of tomato in both fresh and processing markets. Here we report the genetic mapping of single-locus and epistatic quantitative trait loci (QTL) associated to the fruit size and content of sugars, acids, vitamins, and carotenoids from the characterization of a RIL population derived from the wild-relative Solanum pimpinellifolium TO-937. A genetic map composed of 353 molecular markers including 13 genes regulating fruit and developmental traits was generated, which spanned 1007 cM with an average distance between markers of 2.8 cM. Genetic analyses indicated that fruit quality traits analyzed in this work exhibited transgressive segregation and that additive and epistatic effects are the major genetic basis of fruit quality traits. Moreover, most mapped QTL showed environment interaction effects. FrW7.1 fruit size QTL co-localized with QTL involved in soluble solid, vitamin C, and glucose contents, dry weight/fresh weight, and most importantly with the Sucrose Phosphate Synthase gene, suggesting that polymorphisms in this gene could influence genetic variation in several fruit quality traits. In addition, 1-deoxy-D-xylulose 5-phosphate synthase and Tocopherol cyclase genes were identified as candidate genes underlying QTL variation in beta-carotene and vitamin C. Together, our results provide useful genetic and molecular information regarding fruit quality and new chances for tomato breeding by implementing marker-assisted selection.Thanks are due to Dr. Fernando Yuste-Lisbona and Dr. Antonio Monforte for critical review of the manuscript. This work was funded by the ESPSOL project from the Fundacion Genoma of the Spanish Ministerio de Ciencia y Tecnologia. We also thank research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3).Capel, C.; Fernandez Del Carmen, MA.; Alba, J.; Lima-Silva, V.; Hernandez-Gras, F.; Salinas, M.; Boronat, A.... (2015). Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L. TAG Theoretical and Applied Genetics. 128(10):2019-2035. doi:10.1007/s00122-015-2563-4S2019203512810Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, Bakker F, Dirks R, Breit T, Gravendeel B, Huits H, Struss D, Swanson-Wagner R, van Leeuwen H, van Ham RC, Fito L, Guignier L, Sevilla M, Ellul P, Ganko E, Kapur A, Reclus E, de Geus B, van de Geest H, Te Lintel Hekkert B, van Haarst J, Smits L, Koops A, Sanchez-Perez G, van Heusden AW, Visser R, Quan Z, Min J, Liao L, Wang X, Wang G, Yue Z, Yang X, Xu N, Schranz E, Smets E, Vos R, Rauwerda J, Ursem R, Schuit C, Kerns M, van den Berg J, Vriezen W, Janssen A, Datema E, Jahrman T, Moquet F, Bonnet J, Peters S (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148Agarwal A, Rao AV (2000) Tomato lycopene and its role in human health and chronic diseases. Can Med Assoc J 163:739–744Alba JM, Montserrat M, Fernández-Muñoz R (2009) Resistance to the two-spotted spider mite (Tetranychus urticae) by acylsucroses of wild tomato (Solanum pimpinellifolium) trichomes studied in a recombinant inbred line population. Exp Appl Acarol 47:35–47Ament K, Van Schie CC, Bouwmeester HJ, Haring MA, Schuurink RC (2006) Induction of a least specific genranygeranyl pyrophosphate synthase and emission of (E, E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene in tomato are dependent on both jasmonic acid and salicylic acid signaling pathways. Planta 224:1197–1208Areshchenkova T, Ganal MW (1999) Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42:536–544Ashrafi H, Kinkade M, Foolad MR (2009) A new genetic linkage map of tomato based on a Solanum lycopersicum × S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes. Genome 52:935–956Baldwin EA, Nisperos-Carriedo MO, Moshonas MG (1991) Quantitative analysis of flavor and other volatiles and for certain constituents of two tomato cultivars during ripening. J Am Soc Hort Sci 116:265–269Borguini R, Torres E (2009) Tomatoes and tomato products as dietary sources of antioxidant. Food Rev Int 25:313–325Burr B, Burr FA (1991) Recombinant inbreeds for molecular mapping in maize: theoretical and practical considerations. Trends Genet 7:55–60Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemarie-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTL involved in tomato fruit size and composition. J Exp Bot 55:1671–1685Chen FQ, Foolad MR (1999) A molecular linkage map of tomato based on a cross between Lycopersicon esculentum and L. pimpinellifolium and its comparison with other molecular maps of tomato. Genome 42:94–103Chen FQ, Foolad MR, Hyman J, St Clair DA, Beelaman RB (1999) Mapping of QTL for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTL across tomato species. Mol Breed 5:283–299Crozier A, Jaganath IB, Clifford MN (2009) Dietary phenolics: chemistry, bioavailability and effects on health. Nat Prod Rep 26:1001–1043Cunningham FX Jr, Pogson B, McDonald KA, DellaPenna D, Gantt E (1996) Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation. Plant Cell 8:1613–1626Di Matteo A, Sacco A, Anacleria M, Pezzotti M, Delledonne M, Ferrarini A, Frusciante L, Barone A (2010) The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation. BMC Plant Biol 10:163Doganlar S, Frary A, Ku HM, Tanksley SD (2002) Mapping quantitative traits loci in inbred backcross lines of Lycopersicon pimpinellifolium LA1589. Genome 456:1189–1202Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162Fernandez-Muñoz R, Dominguez E, Cuartero J (2000) A novel source of resistance to the two-spotted spider mite in Lycopersicon pimpinellifolium Jusl. Mill.: its genetics as affected by interplot interference. Euphytica 111:169–173Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007:64358Frary A, Nesbitt TC, Frary A, Grandillo S, Van der Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88Frary A, Doganlar S, Frampton A, Fulton T, Uhlig J, Yates H, Tanksley S (2003) Fine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1. Genome 46:235–243Fraser PD, Pinto ME, Holloway DE, Bramley PM (2000) Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant J 24:551–558Fulton TM, Bucheli P, Voirol E, López J, Pétiard V, Tanksley SD (2002) Quantitative trait loci QTL affecting sugars, organic acids and other biochemical properties possibly contributing to flavour, identified in four advanced backcross populations of tomato. Euphytica 127:163–177Grandillo S, Tanksley SD (1996) Genetic analysis of RFLPs, GATA microsatellites and RAPDs in a croos between L. esculentum and L. pimpinellifolium. Theor Appl Genet 92:957–965Grandillo S, Ku HM, Tanksley SD (1999) Identifying loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99:978–987Heber D, Lu QY (2002) Overview of mechanisms of action of lycopene. Exp Biol Med 227:920–923Holland JB (2001) Epistasis and plant breeding. Plant Breed Rev 21:27–82Kader AA, Stevens MA, Albright-Holton M, Morris LL, Algazi M (1977) Effect of fruit ripeness when picked on flavor and composition in fresh market tomatoes. J Am Soc Hort Sci 102:724–731Kanwischer M, Porfirova S, Bergmuller E, Dormann P (2005) Alterations in tocopherol cyclase activity in transgenic and mutant plants of Arabidopsis affect tocopherol content, tocopherol composition, and oxidative stress. Plant Physiol 137:713–723Khialparast F, Abdemishani S, Yazdisamadi B, Naghavi MR, Foolad MR (2013) Identification and characterization of quantitative trait loci related to chemical traits in tomato (Lycopersicon esculentum Mill.). Crop Breed J 3:13–18Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175Kotkov Z, Hejtmnkov A, Lachman A (2009) Determination of the influence of variety and level of maturity of the content and development of carotenoids in tomatoes. Czech J Food Sci 27:S200–S203Lin T, Zhu G, ZhangJ XuX, YuQ Zheng Z, Zhang Z, LunY Li S, Wang X, Huang H, Li J, Chunzhi Z, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Städler T, Li J, Ye Z, Du Y, Huang S (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226Lippman Z, Tanksley SD (2001) Dissecting the genetic pathway to extreme fruit size in tomato using a cross between Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 1581:413–422Lois LM, Rodriguez-Concepción M, Gallego F, Campos N, Boronat A (2000) Carotenoid biosynthesis during tomato fruit development: regulatory role of 1-deoxy-d-xylulose 5-phosphate synthase. Plant J 22:503–513Meadows GG (2012) Diet, nutrients, phytochemicals, and cancer metastasis suppressor genes. Cancer Metastasis Rev 31:441–454Miron D, Shaffer AA (1991) Sucrose Phosphate Synthase, Sucrose Synthase, and Invertase activities in developing fruit of Lycopersicum esculemtum Mill. and the sucrose accumulating Lycopersicum hirsutum Humb. and Bonpl. Plant Physiol 95:623–627Moco S, Bino RJ, Vorst O, Verhoeven HA, de Groot J, van Beek TA, Vervoort J, de Vos JHR (2006) A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol 141:1205–1218Monforte AJ, Tanksley SD (2000) 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 43:803–813Montgomery J, Wittwer CT, Palais R, Zhou L (2007) Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nat Protoc 2:59–66Nesbitt TC, Tanksley SD (2001) fw2.2 directly affects the size of developing tomato fruit, with secondary effects on fruit number and photosyntate distribution. Plant Physiol 127:575–583Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M, Zamir D, Lifschitz E (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125:1979–1989Powell ALT, Nguyen CV, Hill T, Cheng KL, Figueroa-Balderas R, Aktas K, Ashrafi H, Pons C, Fernández-Muñoz R, Vicente A, Lopez-Baltazar J, Barry CS, Liu Y, Chetelat R, Granell A, Van Deynze A, Giovannoni JJ, Bennett AB (2012) Uniform ripening encodes a golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336:1711–1715Raiola A, Rigano MM, Calafiore R, Frusciante L, Barone A (2014) Enhancing the health-promoting effects of tomato fruit for biofortified food. Mediat Inflamm 2014:139873Rick CM (1974) High soluble-solids content in large-fruited tomato lines derived from a wild green-fruited species. Hilgardia 42:493–510Rodríguez-López MJ, Garzo E, Bonani JP, Fereres A, Fernández-Muñoz R, Moriones E (2011) Whitefly resistance traits derived from the wild tomato Solanum pimpinellifolium affect the preference and feeding behavior of Bemisia tabaci and reduce the spread of Tomato yellow leaf curl virus. Phytopathology 10:1191–1201Saliba-Colombani V, Causse M, Langlois D, Philouze J, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTL for physical and chemical traits. Theor Appl Genet 102:259–272Salinas M, Capel C, Alba JM, Mora B, Cuartero J, Fernández-Muñoz R, Lozano R, Capel J (2013) Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch). Theor Appl Genet 126:83–92Sharma A, Zhang L, Nino-Liu D, Ashrafi H, Foolad MR (2008) A Solanum lycopersicum × Solanum pimpinellifolium linkage map of tomato displaying genomic locations of R-Genes, RGAs, and candidate resistance/defense-response ESTs. Int J Plant Genomics 2008:926090Smulders MJM, Bredemeijer G, RusKortekaas W, Arens P, Vosman B (1997) Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 94:264–272Stevens MA, Rick CM (1986) Genetics and breeding. In: Athernon JG, Rudich J (eds) The tomato crop. A scientific basis for improvement. Chapman and Hall, London, pp 35–109Stevens MA, Kader AA, Albright-Holton M (1977) Intercultivar variation in composition of locular and pericarp portions of fresh market tomatoes. J Am Soc Horti Sci 102:689–692Stevens R, Buret M, Philippe D, Garchely C, Baldet P, Rothan C, Causse M (2007) Candidate genes and quantitative trait loci affecting fruit ascorbic acid content in three tomato populations. Plant Physiol 143:1943–1953The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641Vallverdú-Queral A, Medina-Remón A, Martínez-Huélamo M, Jaúregui O, Andres-Lacueva C, Lamuela-Raventos RM (2011) Phenolic profile and hydrophilic antioxidant capacity as chemotaxonomic markers of tomato varieties. J Agric Food Chem 59:3994–4001Van der Hoeven R, Ronnind C, Giovannoni JJ, Martin G, Tanksley SD (2002) Deductions about the number, organization and evolution of genes in the tomato geneme based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14:1441–1456van Ooijen JW (2006) JoinMap® 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenVillalta I, Reina-Sanchez A, Cuartero J, Carbonell EA, Asins MJ (2005) Comparative microsatellite linkage analysis and genetic structure of two populations of F6 lines derived from Lycopersicon pimpinellifolium and L. cheesmanii. Theor Appl Genet 110:881–894Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTL. J Hered 93:77–78Xu J, Ranc N, Muños S, Rolland S, Bouchet JP, Desplat N, Le Paslier MC, Liang Y, Brunel D, Causse M (2013) Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 126:567–581Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTL network: mapping and visualizing genetic architecture of complex trait in experimental populations. Bioinformatics 10:721–723Yates HE, Frary A, Doganlar S, Frampton A, Eannetta NT, Uhlig J, Tanksley SD (2004) Comparative fine mapping of fruit quality QTL on chromosome 4 introgressions derived from two wild tomato species. Euphytica 135:283–296Zou L, Li H, Ouyang B, Zhang J, Ye Z (2006) Cloning and mapping of genes involved in tomato ascorbic acid biosynthesis and metabolism. Plant Sci 170:120–12