Early Embryo Exposure to Assisted Reproductive Manipulation Induced Subtle Changes in Liver Epigenetics with No Apparent Negative Health Consequences in Rabbit

[EN] Embryo manipulation is a requisite step in assisted reproductive technology (ART). Therefore, it is of great necessity to appraise the safety of ART and investigate the long-term effect, including lipid metabolism, on ART-conceived offspring. Augmenting our ART rabbit model to investigate lipid metabolic outcomes in offspring longitudinally, we detected variations in hepatic DNA methylation ART offspring in the F3 generation for embryonic exposure (multiple ovulation, vitrification and embryo transfer). Through adult liver metabolomics and proteomics, we identified changes mainly related to lipid metabolism (e.g., polyunsaturated fatty acids, steroids, steroid hormone). We also found that DNA methylation analysis was linked to changes in lipid metabolism and apoptosis genes. Nevertheless, these differences did not apparently alter the general health status. Thus, our findings suggest that ART is likely to be a player in embryo epigenetic events related to hepatic homeostasis alteration in adulthood.This research was funded by the Spanish Ministry of Economy and Competitiveness (MINECO), Spain, grant number AGL2014-53405-C2-1-P and by Conselleria d'Educacio, Investigacio, Cultura i Esport, Spain, grant number Prometeo II 2014/036. Ximo Garcia-Dominguez was supported by a research grant from the Ministry of Economy, Industry and Competitiveness of Spain (BES-2015-072429).García-Domínguez, X.; Diretto, G.; Peñaranda, D.; Frusciante, S.; García-Carpintero, V.; Cañizares Sales, J.; Vicente Antón, JS.... (2021). Early Embryo Exposure to Assisted Reproductive Manipulation Induced Subtle Changes in Liver Epigenetics with No Apparent Negative Health Consequences in Rabbit. International Journal of Molecular Sciences. 22(18):1-17. https://doi.org/10.3390/ijms22189716S117221

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

[EN] Background: K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results: As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion: K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.This work was supported by the University Polytechnic of Valencia, Grant Number 20180051 "Desarrollo de herramientas para la identificacion de genes y loci de interes en la mejora genetica del tomate y otras horticolas".Ziarsolo, P.; Hasing, T.; Hilario, R.; García-Carpintero, V.; Blanca Postigo, JM.; Bombarely, A.; Cañizares Sales, J. (2021). K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology. Plant Methods. 17(1):1-11. https://doi.org/10.1186/s13007-021-00733-6S11117

Long-term and transgenerational phenotypic, transcriptional and metabolic effects in rabbit males born following vitrified embryo transfer

[EN] The advent of assisted reproductive technologies (ART) in mammals involved an extraordinary change in the environment where the beginning of a new organism takes place. Under in vitro conditions, in which ART is currently being performed, it likely fails to mimic optimal in vivo conditions. This suboptimal environment could mediate in the natural developmental trajectory of the embryo, inducing lasting effects until later life stages that may be inherited by subsequent generations (transgenerational effects). Therefore, we evaluated the potential transgenerational effects of embryo exposure to the cryopreservation-transfer procedure in a rabbit model on the offspring phenotype, molecular physiology of the liver (transcriptome and metabolome) and reproductive performance during three generations (F1, F2 and F3). The results showed that, compared to naturally-conceived animals (NC group), progeny generated after embryo exposure to the cryopreservation-transfer procedure (VT group) exhibited lower body growth, which incurred lower adult body weight in the F1 (direct effects), F2 (intergenerational effects) and F3 (transgenerational effects) generations. Furthermore, VT animals showed intergenerational effects on heart weight and transgenerational effects on liver weight. The RNA-seq data of liver tissue revealed 642 differentially expressed transcripts (DETs) in VT animals from the F1 generation. Of those, 133 were inherited from the F2 and 120 from the F3 generation. Accordingly, 151, 190 and 159 differentially accumulated metabolites (DAMs) were detected from the F1, F2 and F3, respectively. Moreover, targeted metabolomics analysis demonstrated that transgenerational effects were mostly presented in the non-polar fraction. Functional analysis of molecular data suggests weakened zinc and fatty acid metabolism across the generations, associated with alterations in a complex molecular network affecting global hepatic metabolism that could be associated with the phenotype of VT animals. However, these VT animals showed proper reproductive performance, which verified a functional health status. In conclusion, our results establish the long-term transgenerational effects following a vitrified embryo transfer procedure. We showed that the VT phenotype could be the result of the manifestation of embryonic developmental plasticity in response to the stressful conditions during ART procedures.Funding from the Ministry of Economy, Industry and Competitiveness (Research project: AGL2014-53405-C2-1-P) and Generalitat Valenciana (Research project: Prometeo II 2014/036) is acknowledged. X.G.D. was supported by a research grant from the Ministry of Economy, Industry and Competitiveness (BES-2015-072429). 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Flower induction and development in saffron: Timing and hormone signalling pathways

[EN] The demand for saffron is expected to rise in the coming years due to its nutraceutical and medicinal properties. To cope with this, it will be necessary to develop a mechanised production of saffron. Upgrading the production methods requires accurate control of the flowering time in this species. Nevertheless, little is known about the control of flowering time in Crocus sativus L. The aim of this study is to gain insight into the floral induction regulatory networks operating in this species. A transcriptomic analysis was performed from saffron main buds in different stages of development. The identification of putative integrators of flowering time signals, like FT, as well as meristem identity genes, such as LFY and TFL1, permitted the definition of the time of flowering induction of the buds, being able to use them as molecular markers. The identification of the transcripts encoded by a DROOPING LEAF-like (DL) gene is of particular relevance because this gene might be a novel factor for carpel specification in saffron. To elucidate the hormonal signalling networks working during flower induction, transcriptomic data were used, and the content of IAA, ABA and gibberellins was determined in competent and non-competent buds to flower, during the saffron life cycle. Our results suggested that ABA might be negatively regulating corm dormancy release, but its involvement in flower induction cannot be ruled out. ABI5 and the mediator of ABA regulated dormancy gene MARD1, could be key players of this pathway. In addition, a drop in GA4 levels may also be a necessary, but insufficient, condition for floral induction and development. DELLA, TFL1 and PIF3 genes might be involved in the gibberellin pathway. Notably, IAA seems to be a positive regulator of the process, involving MP/ARF5 and ANT genes in the pathway. Taken together, these results pave the way to the unveiling of the regulatory networks controlling the vegetative-to-reproductive phase change in saffron.The activities of this study have been supported by a project funded by the "Ministerio de Ciencia, Innovacion y Universidades de Espana" [AGL2016-77078-R].Renau-Morata, B.; Nebauer, SG.; García-Carpintero, V.; Cañizares Sales, J.; Minguet, E.; De Los Mozos, M.; Molina Romero, RV. (2021). Flower induction and development in saffron: Timing and hormone signalling pathways. Industrial Crops and Products. 164:1-19. https://doi.org/10.1016/j.indcrop.2021.113370S11916

Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening

BACKGROUND. A near-isogenic line (NIL) of melon (SC10-2) with introgression in linkage group X was studied from harvest (at firm-ripe stage of maturity) until day 18 of postharvest storage at 20.5 °C together with its parental control (‘Piel de Sapo’, PS). RESULTS. SC10-2 showed higher flesh firmness and whole fruit hardness but lower juiciness than its parental. SC10-2 showed a decrease in respiration rate accompanied by a decrease in ethylene production during ripening, both of which fell to a greater extent than in PS. The introgression affected 11 volatile organic compounds (VOCs), the levels of which during ripening were generally higher in SC10-2 than in PS. Transcriptomic analysis from RNA-Seq revealed differentially expressed genes (DEGs) associated with the effects studied. For example, 909 DEGs were exclusive to the introgression, and only 23 DEGs were exclusive to postharvest ripening time. Major functions of the DEGs associated with introgression or ripening time were identified by cluster analysis. About 37 genes directly and/or indirectly affected the delay in ripening of SC10-2 compared with PS in general and, more particularly, the physiological and quality traits measured and, probably, the differential non-climacteric response. Of the former genes, we studied in more detail at least five that mapped in the introgression in linkage group (LG) X, and 32 outside it. CONCLUSION. There is an apparent control of textural changes, VOCs and fruit ripening by an expression quantitative trait locus located in LG X together with a direct control on them due to genes presented in the introgression (CmTrpD, CmNADH1, CmTCP15, CmGDSL esterase/lipase, and CmHK4-like) and CmNAC18.This work was funded by grants 11784/PI/09 (Seneca Foundation, Region of Murcia) and Ministry of Economy and Innovation (AGL2010-20858)

De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages

[EN] Paralogues pairs are more frequently observed in eels (Anguilla sp.) than in other teleosts. The paralogues often show low phylogenetic distances; however, they have been assigned to the third round of whole genome duplication (WGD), shared by all teleosts (3R), due to their conserved synteny. The apparent contradiction of low phylogenetic difference and 3R conserved synteny led us to study the duplicated gene complement of the freshwater eels. With this aim, we assembled de novo transcriptomes of two highly relevant freshwater eel species: The European (Anguilla anguilla) and the Japanese eel (Anguilla japonica). The duplicated gene complement was analysed in these transcriptomes, and in the genomes and transcriptomes of other Actinopterygii species. The study included an assessment of neutral genetic divergence (4dTv), synteny, and the phylogenetic origins and relationships of the duplicated gene complements. The analyses indicated a high accumulation of duplications (1217 paralogue pairs) among freshwater eel genes, which may have originated in a WGD event after the Elopomorpha lineage diverged from the remaining teleosts, and thus not at the 3R. However, very similar results were observed in the basal Osteoglossomorpha and Clupeocephala branches, indicating that the specific genomic regions of these paralogues may still have been under tetrasomic inheritance at the split of the teleost lineages. Therefore, two potential hypotheses may explain the results: i) The freshwater eel lineage experienced an additional WGD to 3R, and ii) Some duplicated genomic regions experienced lineage specific rediploidization after 3R in the ancestor to freshwater eels. The supporting/opposing evidence for both hypotheses is discussed.This study received funding from the project REPRO-TEMP (AGL2013-41646-R) funded by the Spanish Ministry of Economy and Competitiveness, and from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 642893 (IMPRESS), which also included the predoctoral contracts of CR and JGHJ. VG has a postdoctoral grant from the Spanish Ministry of Science, Innovation and Universities (MICIU; Programa Juan de la Cierva-Incorporacion; IJCI-2017-34200). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Rozenfeld, C.; Blanca Postigo, JM.; Gallego Albiach, V.; García-Carpintero, V.; Herranz-Jusdado, JG.; Pérez Igualada, LM.; Asturiano, JF.... (2019). De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. 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The GB4.0 Platform, an All-In-One Tool for CRISPR/Cas-Based Multiplex Genome Engineering in Plants

CRISPR/Cas ability to target several loci simultaneously (multiplexing) is a game-changer in plant breeding. Multiplexing not only accelerates trait pyramiding but also can unveil traits hidden by functional redundancy. Furthermore, multiplexing enhances dCas-based programmable gene expression and enables cascade-like gene regulation. However, the design and assembly of multiplex constructs comprising tandemly arrayed guide RNAs (gRNAs) requires scarless cloning and is still troublesome due to the presence of repetitive sequences, thus hampering a more widespread use. Here we present a comprehensive extension of the software-assisted cloning platform GoldenBraid (GB), in which, on top of its multigene cloning software, we integrate new tools for the Type IIS-based easy and rapid assembly of up to six tandemly-arrayed gRNAs with both Cas9 and Cas12a, using the gRNA-tRNA-spaced and the crRNA unspaced approaches, respectively. As stress tests for the new tools, we assembled and used for Agrobacterium-mediated stable transformation a 17 Cas9-gRNAs construct targeting a subset of the Squamosa-Promoter Binding Protein-Like (SPL) gene family in Nicotiana tabacum. The 14 selected genes are targets of miR156, thus potentially playing an important role in juvenile-to-adult and vegetative-to-reproductive phase transitions. With the 17 gRNAs construct we generated a collection of Cas9-free SPL edited T plants harboring up to 9 biallelic mutations and showing leaf juvenility and more branching. The functionality of GB-assembled dCas9 and dCas12a-based CRISPR/Cas activators and repressors using single and multiplexing gRNAs was validated using a Luciferase reporter with the Solanum lycopersicum Mtb promoter or the Agrobacterium tumefaciens nopaline synthase promoter in transient expression in Nicotiana benthamiana. With the incorporation of the new web-based tools and the accompanying collection of DNA parts, the GB4.0 genome edition turns an all-in-one open platform for plant genome engineering

Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato

[EN] The development of high nitrogen use efficiency (NUE) cultivars under low N inputs is required for sustainable agriculture. To this end, in this study, we analyzed the impact of long-term suboptimal N conditions on the metabolome and transcriptome of tomato to identify specific molecular processes and regulators at the organ scale. Physiological and metabolic analysis revealed specific responses to maintain glutamate, asparagine, and sucrose synthesis in leaves for partition to sustain growth, while assimilated C surplus is stored in the roots. The transcriptomic analyses allowed us to identify root and leaf sets of genes whose expression depends on N availability. GO analyses of the identified genes revealed conserved biological functions involved in C and N metabolism and remobilization as well as other specifics such as the mitochondrial alternative respiration and chloroplastic cyclic electron flux. In addition, integrative analyses uncovered N regulated genes in root and leaf clusters, which are positively correlated with changes in the levels of different metabolites such as organic acids, amino acids, and formate. Interestingly, we identified transcription factors with high identity to TGA4, ARF8, HAT22, NF-YA5, and NLP9, which play key roles in N responses in Arabidopsis. Together, this study provides a set of nitrogen-responsive genes in tomato and new putative targets for tomato NUE and fruit quality improvement under limited N supply.This study was supported by grants from The National Institute for Agriculture and Food Research and Technology (CSIC-INIA) (RTA2015-00014-c02-00 to JMA and RTA2015-00014-c02-01 to SGN) and the Community of Madrid (AGRISOST-CM S2018/BAA-4330 to JMA). We also want to acknowledge the "Severo Ochoa Program for Centers of Excellence in R&D" from the Agencia Estatal de Investigacion of Spain (Grant SEV-2016-0672) for supporting the scientific services used in this study. J. Canales was supported by the Agencia Nacional de Investigacion y Desarrollo de Chile (ANID, FONDECYT 1190812) and ANID-Millennium Science Initiative Program (ICN17-022).Renau-Morata, B.; Molina Romero, RV.; Minguet, E.; Cebolla Cornejo, J.; Carrillo, L.; Martí-Renau, R.; García-Carpintero, V.... (2021). Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato. Agronomy. 11(7):1-26. https://doi.org/10.3390/agronomy11071320S12611

PYL1- and PYL8-like ABA Receptors of Nicotiana benthamiana Play a Key Role in ABA Response in Seed and Vegetative Tissue

19 pags., 7 figs., 3 tabs. -- This article belongs to the Special Issue Drought and Heat Stress Signalling Responses in PlantsTo face the challenges of climate change and sustainable food production, it is essential to develop crop genome editing techniques to pinpoint key genes involved in abiotic stress signaling. The identification of those prevailing abscisic acid (ABA) receptors that mediate plant-environment interactions is quite challenging in polyploid plants because of the high number of genes in the PYR/PYL/RCAR ABA receptor family. Nicotiana benthamiana is a biotechnological crop amenable to genome editing, and given the importance of ABA signaling in coping with drought stress, we initiated the analysis of its 23-member family of ABA receptors through multiplex CRISPR/Cas9-mediated editing. We generated several high-order mutants impaired in NbPYL1-like and NbPYL8-like receptors, which showed certain insensitivity to ABA for inhibition of seedling establishment, growth, and development of shoot and lateral roots as well as reduced sensitivity to the PYL1-agonist cyanabactin (CB). However, in these high-order mutants, regulation of transpiration was not affected and was responsive to ABA treatment. This reveals a robust and redundant control of transpiration in this allotetraploid plant that probably reflects its origin from the extreme habitat of central Australia.This research was supported by grant PID2020-113100RB (P.L.R.) and PID2020-119805RB (A.A.) funded by MCIN/AEI/10.13039/501100011033 and by Newcotiana H2020 760331 (D.O.).Peer reviewe

The systematicity challenge to anti-representational dynamicism

After more than twenty years of representational debate in the cognitive sciences, anti-representational dynamicism may be seen as offering a rival and radically new kind of explanation of systematicity phenomena. In this paper, I argue that, on the contrary, anti-representational dynamicism must face a version of the old systematicity challenge: either it does not explain systematicity, or else, it is just an implementation of representational theories. To show this, I present a purely behavioral and representation-free account of systematicity. I then consider a case of insect sensorimotor systematic behavior: communicating behavior in honey bees. I conclude that anti-representational dynamicism fails to capture the fundamental trait of systematic behaviors qua systematic, i.e., their involving exercises of the same behavioral capacities. I suggest, finally, a collaborative strategy in pursuit of a rich and powerful account of this central phenomenon of high cognition at all levels of explanation, including the representational level