Genome-wide association mapping of flowering and ripening periods in apple

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9% and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs

Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns

[EN] Between February 2018 and April 2018, flowers were collected from eight Rosaceae species. Flowers were kept in a freezer at -20 degrees C for three freezing times (Treatment 1, two months; Treatment 2, four months; Treatment 3, six months). After extracting pollen, in vitro germination was induced in a culture medium and incubated at six different temperatures for 72 h. The percentage of pollen germination, average pollen tube length and maximum pollen tube length were measured. Pollen germination was maximum for all species between 15 degrees C and 30 degrees C. Cydonia oblonga, Malus sylvestris, Prunus avium, Prunus domestica, Prunus dulcis, Prunus persica and Pyrus communis obtained 30-52% pollen germination between 15 degrees C and 20 degrees C. Prunus cerasifera had 40% pollen germination at 30 degrees C. All species studied reached the maximum pollen tube length between 10 degrees C and 25 degrees C. Germination did not change significantly for any of the species with freezing time, but we found significant differences in the three parameters measured between treatments. The highest germination percentages were obtained in Treatment 2 (four months frozen at -20 degrees C), while the maximum pollen tube length was reached in Treatment 1 (two months frozen at -20 degrees C). According to our results, freezing time affected the germination-temperature patterns. This could indicate that studies on the effect of temperature on pollen germination should always be carried out with fresh pollen to obtain more conclusive data.This work was supported by the Asociacion Club de Variedades Vegetales Protegidas as a part of a project with the Universitat Politecnica de Valencia (UPV 20170673). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Beltrán, R.; Valls, A.; Cebrián, N.; Zornoza, C.; García-Breijo, F.; Reig Armiñana, J.; Garmendia, A.... (2019). Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns. PeerJ. 7:1-18. https://doi.org/10.7717/peerj.8195S1187Acar, I., & Kakani, V. G. (2010). The effects of temperature on in vitro pollen germination and pollen tube growth of Pistacia spp. Scientia Horticulturae, 125(4), 569-572. doi:10.1016/j.scienta.2010.04.040Boavida, L. C., & McCormick, S. (2007). TECHNICAL ADVANCE: Temperature as a determinant factor for increased and reproducible in vitro pollen germination in Arabidopsis thaliana. The Plant Journal, 52(3), 570-582. doi:10.1111/j.1365-313x.2007.03248.xBrewbaker, J. L., & Kwack, B. H. (1963). THE ESSENTIAL ROLE OF CALCIUM ION IN POLLEN GERMINATION AND POLLEN TUBE GROWTH. American Journal of Botany, 50(9), 859-865. doi:10.1002/j.1537-2197.1963.tb06564.xBurke, J. J., Velten, J., & Oliver, M. J. (2004). In Vitro Analysis of Cotton Pollen Germination. Agronomy Journal, 96(2), 359-368. doi:10.2134/agronj2004.3590Castède, S., Campoy, J. A., García, J. Q., Dantec, L., Lafargue, M., Barreneche, T., … Dirlewanger, E. (2014). Genetic determinism of phenological traits highly affected by climate change in Prunus avium: flowering date dissected into chilling and heat requirements. New Phytologist, 202(2), 703-715. doi:10.1111/nph.12658Cerovlć, R., & Ružić, D. (1992). Pollen tube growth in sour cherry (Prunus cerasusL.) at different temperatures. Journal of Horticultural Science, 67(3), 333-340. doi:10.1080/00221589.1992.11516256Egea, J., Burgos, L., Zoroa, N., & Egea, L. (1992). Influence of temperature on thein vitrogermination of pollen of apricot(Prunus armeniaca, L.). Journal of Horticultural Science, 67(2), 247-250. doi:10.1080/00221589.1992.11516244Fan, L.-M. (2001). In vitro Arabidopsis pollen germination and characterization of the inward potassium currents in Arabidopsis pollen grain protoplasts. Journal of Experimental Botany, 52(361), 1603-1614. doi:10.1093/jexbot/52.361.1603Feij�, J. A., Malh�, R., & Obermeyer, G. (1995). Ion dynamics and its possible role during in vitro pollen germination and tube growth. Protoplasma, 187(1-4), 155-167. doi:10.1007/bf01280244Goldwin, G. K., & Webster, A. D. (1983). The cumulative effects of hormone mixtures containing GA3, DPU plus NOXA, NAA or 2,4,5-TP on the cropping and flowering of sweet cherry cultivars,Prunus aviumL. Journal of Horticultural Science, 58(4), 505-516. doi:10.1080/00221589.1983.11515149Hebbar, K. B., Rose, H. M., Nair, A. R., Kannan, S., Niral, V., Arivalagan, M., … Vara Prasad, P. V. (2018). Differences in in vitro pollen germination and pollen tube growth of coconut (Cocos nucifera L.) cultivars in response to high temperature stress. Environmental and Experimental Botany, 153, 35-44. doi:10.1016/j.envexpbot.2018.04.014Hedhly, A., Hormaza, J. I., & Herrero, M. (2004). Effect of temperature on pollen tube kinetics and dynamics in sweet cherry,Prunus avium(Rosaceae). American Journal of Botany, 91(4), 558-564. doi:10.3732/ajb.91.4.558Hedhly, A., Hormaza, J. I., & Herrero, M. (2005). The Effect of Temperature on Pollen Germination, Pollen Tube Growth, and Stigmatic Receptivity in Peach. Plant Biology, 7(5), 476-483. doi:10.1055/s-2005-865850Hegedűs, A., & Halász, J. (2006). Self-incompatibility in plums (Prunus salicina Lindl., Prunus cerasifera Ehrh. and Prunus domestica L.). A minireview. International Journal of Horticultural Science, 12(2). doi:10.31421/ijhs/12/2/646Hegedűs, A., Lénárt, J., & Halász, J. (2012). Sexual incompatibility in Rosaceae fruit tree species: molecular interactions and evolutionary dynamics. Biologia plantarum, 56(2), 201-209. doi:10.1007/s10535-012-0077-3Heide, O. M., & Prestrud, A. K. (2005). Low temperature, but not photoperiod, controls growth cessation and dormancy induction and release in apple and pear. Tree Physiology, 25(1), 109-114. doi:10.1093/treephys/25.1.109Iglesias, A., Garrote, L., Quiroga, S., & Moneo, M. (2011). A regional comparison of the effects of climate change on agricultural crops in Europe. Climatic Change, 112(1), 29-46. doi:10.1007/s10584-011-0338-8KAKANI, V. G., PRASAD, P. V. V., CRAUFURD, P. Q., & WHEELER, T. R. (2002). Response of in vitro pollen germination and pollen tube growth of groundnut (Arachis hypogaea L.) genotypes to temperature. Plant, Cell & Environment, 25(12), 1651-1661. doi:10.1046/j.1365-3040.2002.00943.xKAKANI, V. G., REDDY, K. R., KOTI, S., WALLACE, T. P., PRASAD, P. V. V., REDDY, V. R., & ZHAO, D. (2005). Differences in in vitro Pollen Germination and Pollen Tube Growth of Cotton Cultivars in Response to High Temperature. Annals of Botany, 96(1), 59-67. doi:10.1093/aob/mci149Mesejo, C., Martínez-Fuentes, A., Reig, C., Rivas, F., & Agustí, M. (2006). The inhibitory effect of CuSO4 on Citrus pollen germination and pollen tube growth and its application for the production of seedless fruit. Plant Science, 170(1), 37-43. doi:10.1016/j.plantsci.2005.07.023Pham, V. T., Herrero, M., & Hormaza, J. I. (2015). Effect of temperature on pollen germination and pollen tube growth in longan ( Dimocarpus longan Lour.). Scientia Horticulturae, 197, 470-475. doi:10.1016/j.scienta.2015.10.007Reddy, K. R., & Kakani, V. G. (2007). Screening Capsicum species of different origins for high temperature tolerance by in vitro pollen germination and pollen tube length. Scientia Horticulturae, 112(2), 130-135. doi:10.1016/j.scienta.2006.12.014Rosell, P., Herrero, M., & Galán Saúco, V. (1999). Pollen germination of cherimoya (Annona cherimola Mill.). Scientia Horticulturae, 81(3), 251-265. doi:10.1016/s0304-4238(99)00012-6Sanzol, J., & Herrero, M. (2001). The «effective pollination period» in fruit trees. Scientia Horticulturae, 90(1-2), 1-17. doi:10.1016/s0304-4238(00)00252-1Saxe, H., Cannell, M. G. R., Johnsen, Ø., Ryan, M. G., & Vourlitis, G. (2001). Tree and forest functioning in response to global warming. New Phytologist, 149(3), 369-399. doi:10.1046/j.1469-8137.2001.00057.xSedgley, M. (1977). The Effect of Temperature on Floral Behaviour, Pollen Tube Growth and Fruit Set in the Avocado. Journal of Horticultural Science, 52(1), 135-141. doi:10.1080/00221589.1977.11514739Silva, G. J., Souza, T. M., Barbieri, R. L., & Costa de Oliveira, A. (2014). Origin, Domestication, and Dispersing of Pear (Pyrusspp.). Advances in Agriculture, 2014, 1-8. doi:10.1155/2014/541097Sorkheh, K., Azimkhani, R., Mehri, N., Chaleshtori, M. H., Halász, J., Ercisli, S., & Koubouris, G. C. (2018). Interactive effects of temperature and genotype on almond ( Prunus dulcis L.) pollen germination and tube length. Scientia Horticulturae, 227, 162-168. doi:10.1016/j.scienta.2017.09.037Sorkheh, K., Shiran, B., Rouhi, V., & Khodambashi, M. (2011). Influence of temperature on the in vitro pollen germination and pollen tube growth of various native Iranian almonds (Prunus L. spp.) species. Trees, 25(5), 809-822. doi:10.1007/s00468-011-0557-7Sorkheh, K., Shiran, B., Rouhi, V., Khodambashi, M., Wolukau, J. N., & Ercisli, S. (2011). Response of in vitro pollen germination and pollen tube growth of almond (Prunus dulcis Mill.) to temperature, polyamines and polyamine synthesis inhibitor. Biochemical Systematics and Ecology, 39(4-6), 749-757. doi:10.1016/j.bse.2011.06.015Stern, R. A., Goldway, M., Zisovich, A. H., Shafir, S., & Dag, A. (2004). Sequential introduction of honeybee colonies increases cross-pollination, fruit-set and yield of ‘Spadona’ pear (Pyrus communisL.). The Journal of Horticultural Science and Biotechnology, 79(4), 652-658. doi:10.1080/14620316.2004.11511821Webster, A. D., & Goldwin, G. K. (1981). The hormonal requirements for improved fruit setting of plum,Prunus domesticaL. cv Victoria. Journal of Horticultural Science, 56(1), 27-40. doi:10.1080/00221589.1981.11514962Weinbaum, S. A., Parfitt, D. E., & Polito, V. S. (1984). Differential cold sensitivity of pollen grain germination in two Prunus species. Euphytica, 33(2), 419-426. doi:10.1007/bf00021139Wickham, H. (2016). ggplot2. Use R! doi:10.1007/978-3-319-24277-4Wolukau, J. N., Zhang, S., Xu, G., & Chen, D. (2004). The effect of temperature, polyamines and polyamine synthesis inhibitor on in vitro pollen germination and pollen tube growth of Prunus mume. Scientia Horticulturae, 99(3-4), 289-299. doi:10.1016/s0304-4238(03)00112-

I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees

Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees