Application of genomic technologies to the breeding of trees

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species

Structure and Expression of Bud Dormancy-Associated MADS-Box Genes (DAM) in European Plum

Bud dormancy in temperate perennials ensures the survival of growing meristems under the harsh environmental conditions of autumn and winter, and facilitates an optimal growth and development resumption in the spring. Although the molecular pathways controlling the dormancy process are still unclear, DORMANCY-ASSOCIATED MADS-BOX genes (DAM) have emerged as key regulators of the dormancy cycle in different species. In the present study, we have characterized the orthologs of DAM genes in European plum (Prunus domestica L.). Their expression patterns together with sequence similarities are consistent with a role of PdoDAMs in dormancy maintenance mechanisms in European plum. Furthermore, other genes related to dormancy, flowering, and stress response have been identified in order to obtain a molecular framework of these three different processes taking place within the dormant flower bud in this species. This research provides a set of candidate genes to be genetically modified in future research, in order to better understand dormancy regulation in perennial species

An integrative "omics" apprach identifies new candidate genes to impact aroma volatiles in peach fruit

[EN] Background: Ever since the recent completion of the peach genome, the focus of genetic research in this area has turned to the identification of genes related to important traits, such as fruit aroma volatiles. Of the over 100 volatile compounds described in peach, lactones most likely have the strongest effect on fruit aroma, while esters, terpenoids, and aldehydes have minor, yet significant effects. The identification of key genes underlying the production of aroma compounds is of interest for any fruit-quality improvement strategy. Results: Volatile (52 compounds) and gene expression (4348 genes) levels were profiled in peach fruit from a maturity time-course series belonging to two peach genotypes that showed considerable differences in maturation characteristics and postharvest ripening. This data set was analyzed by complementary correlation-based approaches to discover the genes related to the main aroma-contributing compounds: lactones, esters, and phenolic volatiles, among others. As a case study, one of the candidate genes was cloned and expressed in yeast to show specificity as an omega-6 Oleate desaturase, which may be involved in the production of a precursor of lactones/esters. Conclusions: Our approach revealed a set of genes (an alcohol acyl transferase, fatty acid desaturases, transcription factors, protein kinases, cytochromes, etc.) that are highly associated with peach fruit volatiles, and which could prove useful in breeding or for biotechnological purposes.We are grateful to Cristina Besada, PhD (Instituto Valenciano de Investigaciones Agrarias, IVIA, Spain) for her help with the fruit quality parameter analyses. We are also thankful to Cristina Marti and Clara Pons (Instituto de Biologia Molecular y Celular de Plantas, IBMCP, Spain) for their advice on microarray analyses. Jesus Garcia Brunton, PhD for providing the fruits used in this study (Instituto Murciano de Investigacion y Desarrollo Agrario, IMIDA, Spain). HS-SPME-GC-MS analyses were performed at the Metabolomic lab facilities at the IBMCP (CSIC) in Spain. GS has financial support from INTA (Instituto Nacional de Tecnologia Agropecuaria, Argentine). This project has been funded by the Ministry of Economy and Competitivity grant AGL2010-20595.Sánchez, G.; Venegas Calerón, M.; Salas, J.; Monforte Gilabert, AJ.; Badenes, M.; Granell Richart, A. (2013). An integrative "omics" apprach identifies new candidate genes to impact aroma volatiles in peach fruit. BMC Genomics. 14(343):1-23. https://doi.org/10.1186/1471-2164-14-343S1231434

The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population

Background: The improvement of fruit aroma is currently one of the most sought-after objectives in peach breeding programs. To better characterize and assess the genetic potential for increasing aroma quality by breeding, a quantity trait locus (QTL) analysis approach was carried out in an F-1 population segregating largely for fruit traits. Results: Linkage maps were constructed using the IPSC peach 9 K Infinium (R) II array, rendering dense genetic maps, except in the case of certain chromosomes, probably due to identity-by-descent of those chromosomes in the parental genotypes. The variability in compounds associated with aroma was analyzed by a metabolomic approach based on GC-MS to profile 81 volatiles across the population from two locations. Quality-related traits were also studied to assess possible pleiotropic effects. Correlation-based analysis of the volatile dataset revealed that the peach volatilome is organized into modules formed by compounds from the same biosynthetic origin or which share similar chemical structures. QTL mapping showed clustering of volatile QTL included in the same volatile modules, indicating that some are subjected to joint genetic control. The monoterpene module is controlled by a unique locus at the top of LG4, a locus previously shown to affect the levels of two terpenoid compounds. At the bottom of LG4, a locus controlling several volatiles but also melting/non-melting and maturity-related traits was found, suggesting putative pleiotropic effects. In addition, two novel loci controlling lactones and esters in linkage groups 5 and 6 were discovered. Conclusions: The results presented here give light on the mode of inheritance of the peach volatilome confirming previously loci controlling the aroma of peach but also identifying novel ones.GS has financial support from INTA (Instituto Nacional de Tecnologia Agropecuaria, Argentina). HS-SPME-GC-MS analyses were performed at the Metabolomic lab facilities at the IBMCP (CSIC) in Spain. This project has been funded by the Ministry of Economy and Competitivity grant AGL2010-20595.Sánchez, G.; Martinez, J.; Romeu, J.; Garcia, J.; Monforte Gilabert, AJ.; Badenes, M.; Granell Richart, A. (2014). The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population. BMC Plant Biology. 14(137):1-16. https://doi.org/10.1186/1471-2229-14-137S11614137Klee, H. J., & Giovannoni, J. J. (2011). Genetics and Control of Tomato Fruit Ripening and Quality Attributes. 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Journal of Agricultural and Food Chemistry, 55(13), 5221-5228. doi:10.1021/jf0705015Zhang, B., Shen, J., Wei, W., Xi, W., Xu, C.-J., Ferguson, I., & Chen, K. (2010). Expression of Genes Associated with Aroma Formation Derived from the Fatty Acid Pathway during Peach Fruit Ripening. Journal of Agricultural and Food Chemistry, 58(10), 6157-6165. doi:10.1021/jf100172eAubert, C., Günata, Z., Ambid, C., & Baumes, R. (2003). Changes in Physicochemical Characteristics and Volatile Constituents of Yellow- and White-Fleshed Nectarines during Maturation and Artificial Ripening. Journal of Agricultural and Food Chemistry, 51(10), 3083-3091. doi:10.1021/jf026153iXI, W.-P., ZHANG, B., LIANG, L., SHEN, J.-Y., WEI, W.-W., XU, C.-J., … CHEN, K.-S. (2011). Postharvest temperature influences volatile lactone production via regulation of acyl-CoA oxidases in peach fruit. Plant, Cell & Environment, 35(3), 534-545. doi:10.1111/j.1365-3040.2011.02433.xBrandi, F., Bar, E., Mourgues, F., Horváth, G., Turcsi, E., Giuliano, G., … Rosati, C. (2011). Study of «Redhaven» peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism. BMC Plant Biology, 11(1), 24. doi:10.1186/1471-2229-11-24Sánchez, G., Venegas-Calerón, M., Salas, J. J., Monforte, A., Badenes, M. L., & Granell, A. (2013). An integrative «omics» approach identifies new candidate genes to impact aroma volatiles in peach fruit. BMC Genomics, 14(1), 343. doi:10.1186/1471-2164-14-343Verde, I., Abbott, A. G., Scalabrin, S., Jung, S., Shu, S., … Grimwood, J. (2013). The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics, 45(5), 487-494. doi:10.1038/ng.2586Verde, I., Bassil, N., Scalabrin, S., Gilmore, B., Lawley, C. 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J., Sánchez, G., Granell, A., García-Brunton, J., Badenes, M. L., & Ríos, G. (2014). Quantitative trait loci affecting reproductive phenology in peach. BMC Plant Biology, 14(1), 52. doi:10.1186/1471-2229-14-52Lander, E. S., Green, P., Abrahamson, J., Barlow, A., Daly, M. J., Lincoln, S. E., & Newburg, L. (1987). MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1(2), 174-181. doi:10.1016/0888-7543(87)90010-3Voorrips, 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/93.1.77Tikunov, 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.105.068130Shannon, P. (2003). 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Quantitative trait loci affecting reproductive phenology in peach

Background: The reproductive phenology of perennial plants in temperate climates is largely conditioned by the duration of bud dormancy, and fruit developmental processes. Bud dormancy release and bud break depends on the perception of cumulative chilling and heat during the bud development. The objective of this work was to identify new quantitative trait loci (QTLs) associated to temperature requirements for bud dormancy release and flowering and to fruit harvest date, in a segregating population of peach. Results: We have identified QTLs for nine traits related to bud dormancy, flowering and fruit harvest in an intraspecific hybrid population of peach in two locations differing in chilling time accumulation. QTLs were located in a genetic linkage map of peach based on single nucleotide polymorphism (SNP) markers for eight linkage groups (LGs) of the peach genome sequence. QTLs for chilling requirements for dormancy release and blooming clustered in seven different genomic regions that partially coincided with loci identified in previous works. The most significant QTL for chilling requirements mapped to LG1, close to the evergrowing locus. QTLs for heat requirement related traits were distributed in nine genomic regions, four of them co-localizing with QTLs for chilling requirement trait. Two major loci in LG4 and LG6 determined fruit harvest time. Conclusions: We identified QTLs associated to nine traits related to the reproductive phenology in peach. A search of candidate genes for these QTLs rendered different genes related to flowering regulation, chromatin modification and hormone signalling. A better understanding of the genetic factors affecting crop phenology might help scientists and breeders to predict changes in genotype performance in a context of global climate change.We thank Matilde Gonzalez for technical assistance. This work was supported by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA)-FEDER (grant no. RTA2007-00060), and the Ministry of Science and Innovation of Spain (grant no. AGL2010-20595).Romeu, J.; Monforte Gilabert, AJ.; Sánchez, G.; Granell Richart, A.; Garcia-Brunton, J.; Badenes, M.; Rios Garcia, G. (2014). Quantitative trait loci affecting reproductive phenology in peach. BMC Plant Biology. 14(52):1-16. https://doi.org/10.1186/1471-2229-14-52S1161452Rohde, A., & Bhalerao, R. P. (2007). Plant dormancy in the perennial context. Trends in Plant Science, 12(5), 217-223. doi:10.1016/j.tplants.2007.03.012Coville, F. V. (1920). The Influence of Cold in Stimulating the Growth of Plants. Proceedings of the National Academy of Sciences, 6(7), 434-435. doi:10.1073/pnas.6.7.434Chuine, I. (2010). Why does phenology drive species distribution? 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A JWST near- and mid-infrared nebular spectrum of the type Ia supernova 2021aefx

We present JWST near-infrared (NIR) and mid-infrared (MIR) spectroscopic observations of the nearby normal Type Ia supernova (SN) SN 2021aefx in the nebular phase at +255 days past maximum light. Our Near Infrared Spectrograph (NIRSpec) and Mid Infrared Instrument observations, combined with ground-based optical data from the South African Large Telescope, constitute the first complete optical+NIR+MIR nebular SN Ia spectrum covering 0.3–14 μm. This spectrum unveils the previously unobserved 2.5−5 μm region, revealing strong nebular iron and stable nickel emission, indicative of high-density burning that can constrain the progenitor mass. The data show a significant improvement in sensitivity and resolution compared to previous Spitzer MIR data. We identify numerous NIR and MIR nebular emission lines from iron-group elements as well as lines from the intermediate-mass element argon. The argon lines extend to higher velocities than the iron-group elements, suggesting stratified ejecta that are a hallmark of delayed-detonation or double-detonation SN Ia models. We present fits to simple geometric line profiles to features beyond 1.2 μm and find that most lines are consistent with Gaussian or spherical emission distributions, while the [Ar iii] 8.99 μm line has a distinctively flat-topped profile indicating a thick spherical shell of emission. Using our line profile fits, we investigate the emissivity structure of SN 2021aefx and measure kinematic properties. Continued observations of SN 2021aefx and other SNe Ia with JWST will be transformative to the study of SN Ia composition, ionization structure, density, and temperature, and will provide important constraints on SN Ia progenitor and explosion models

Variation in neurosurgical management of traumatic brain injury

Background: Neurosurgical management of traumatic brain injury (TBI) is challenging, with only low-quality evidence. We aimed to explore differences in neurosurgical strategies for TBI across Europe. Methods: A survey was sent to 68 centers participating in the Collaborative European Neurotrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. The questionnaire contained 21 questions, including the decision when to operate (or not) on traumatic acute subdural hematoma (ASDH) and intracerebral hematoma (ICH), and when to perform a decompressive craniectomy (DC) in raised intracranial pressure (ICP). Results: The survey was completed by 68 centers (100%). On average, 10 neurosurgeons work in each trauma center. In all centers, a neurosurgeon was available within 30 min. Forty percent of responders reported a thickness or volume threshold for evacuation of an ASDH. Most responders (78%) decide on a primary DC in evacuating an ASDH during the operation, when swelling is present. For ICH, 3% would perform an evacuation directly to prevent secondary deterioration and 66% only in case of clinical deterioration. Most respondents (91%) reported to consider a DC for refractory high ICP. The reported cut-off ICP for DC in refractory high ICP, however, differed: 60% uses 25 mmHg, 18% 30 mmHg, and 17% 20 mmHg. Treatment strategies varied substantially between regions, specifically for the threshold for ASDH surgery and DC for refractory raised ICP. Also within center variation was present: 31% reported variation within the hospital for inserting an ICP monitor and 43% for evacuating mass lesions. Conclusion: Despite a homogeneous organization, considerable practice variation exists of neurosurgical strategies for TBI in Europe. These results provide an incentive for comparative effectiveness research to determine elements of effective neurosurgical care

Prediction of components of the sporopollenin synthesis pathway in peach by genomic and expression analyses

Background: The outer cell wall of the pollen grain (exine) is an extremely resistant structure containing sporopollenin, a mixed polymer made up of fatty acids and phenolic compounds. The synthesis of sporopollenin in the tapetal cells and its proper deposition on the pollen surface are essential for the development of viable pollen. The beginning of microsporogenesis and pollen maturation in perennial plants from temperate climates, such as peach, is conditioned by the duration of flower bud dormancy. In order to identify putative genes involved in these processes, we analyzed the results of previous genomic experiments studying the dormancy-dependent gene expression in different peach cultivars.Results: The expression of 50 genes induced in flower buds after the endodormancy period (flower-bud late genes) was compared in ten cultivars of peach with different dormancy behaviour. We found two co-expression clusters enriched in putative orthologs of sporopollenin synthesis and deposition factors in Arabidopsis. Flower-bud late genes were transiently expressed in anthers coincidently with microsporogenesis and pollen maturation processes. We postulated the participation of some flower-bud late genes in the sporopollenin synthesis pathway and the transcriptional regulation of late anther development in peach.Conclusions: Peach and the model plant Arabidopsis thaliana show multiple elements in common within the essential sporopollenin synthesis pathway and gene expression regulatory mechanisms affecting anther development. The transcriptomic analysis of dormancy-released flower buds proved to be an efficient procedure for the identification of anther and pollen development genes in perennial plants showing seasonal dormancy. \ua9 2013 R\uedos et al.; licensee BioMed Central Ltd