SEED-DREAM Lab info

"Rose with prickles” is a symbol of adversity and sacrifice but the molecular bases patterning prickle remains poorly explored. Here we generated a high-quality reference genome assembly for prickleless Rosa wichuraiana ‘Basye’s Thornless’ (BT), and identified genetic elements relating to stem prickle patterning. BT genome harbors a significant high proportion of Copia-type LTR (62.74% of LTRs) and diverges remarkably from that of R. chinensis Old Blush’, a founder genotype for rose domestication. Three negatively selected and fixed QTL were identified underlying BT prickleless. Differentially expressed genes in QTL were enriched for water-use-related genes, suggesting that prickleless might hitchhike the adaptation to moisture environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, expression variation of key candidate genes associated well with prickle-patterning divergence in roses. Our efforts provide fundamental resources and insights for Rosaceae genome evolution and molecular basis of key traits, thus should benefit rose improvement.

Seed longevity (i.e., the inherent lifespan of a seed) is a polygenic feature that demands the coordination of multiple biological processes, and that shapes the persistence of seeds in the soil and the time they can be stored ex situ. Recent studies on this trait highlight the role of the antioxidant and biomolecule repair systems and the formation of the seed coat. However, the genetic basis behind their contribution has not yet been fully described or corroborated. Here, Renard et al. perform a Genome-Wide Association Study (GWAS) to identify the genes responsible for the differences in the seed longevity of 270 ecotypes of Arabidopsis thaliana. Seeds were exposed to high humidity, high temperature or elevated oxygen pressure conditions (or a combination of these) in order to accelerate the loss of their viability. The results of these assays were correlated with the genomic data available on public databases. After this, 20 candidate genes were validated through a mutant analysis, and 12 had a significant effect in longevity. Most genes were related to enzymes that participate in the metabolism of reactive oxygen species, such as NADPH oxidases (RBOHs) and dehydroascorbate reductases (DHAR1). A cytochrome hydroxylase (CYP86A8) and several transcription factors related to seed coat development also promoted longevity. This paper provides a promising starting point for future research about the mechanisms behind seed longevity.  (Summary by Carlos A. Ordóñez-Parra @caordonezparra) Plant Cell Environ. 10.1111/pce.13822

Il est temps pour les chercheurs de tracer le chemin qui permettra d’atteindre le monde sobre et soutenable de demain, de multiplier les initiatives ambitieuses à même de répondre aux enjeux socio-écologiques, comme celles de transformer des innovations high-tech en low-tech.

The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case the, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the , the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.

By Erik StokstadMay. 18, 2020 , 11:25 AM

A major change to U.S. regulation of biotech will exempt some gene-edited plants from government oversight. The new policy, published in the Federal Register today, also calls for automatic approval of variations of established kinds of genetically modified (GM) crops, easing their path to market.

Industry groups are welcoming the new rule, whereas opponents are decrying the reduction of government oversight.

“The main good thing is that it will allow certain aspects of gene editing to move forward,” says Kent Bradford, a plant geneticist at the University of California, Davis. If researchers use gene editing to design a plant that could have been bred conventionally, the new plant will be exempt from regulation. But anything else—such as moving a gene between species or rewiring metabolism—will still require a regulatory review.

doi:10.1126/science.abc8305

The process by which plant cells expand and gain shape has presented a challenge for researchers. Current models propose that these processes are driven by turgor pressure acting on the cell wall. Using nanoimaging, we show that the cell wall contains pectin nanofilaments that possess an intrinsic expansion capacity. Additionally, we use growth models containing such structures to show that a complex plant cell shape can derive from chemically induced local and polarized expansion of the pectin nanofilaments without turgor-driven growth. Thus, the plant cell wall, outside of the cell itself, is an active participant in shaping plant cells. Extracellular matrix function may similarly guide cell shape in other kingdoms, including Animalia.

TRIBUNE. Plus de 700 directrices et directeurs de laboratoires de recherche contestent, dans une tribune au « Monde », les critères qui président à l’élaboration de la loi de programmation pluriannuelle de la recherche. Ils préconisent de « renforcer les collectifs » plutôt que de promouvoir « une infime élite œuvrant au profit d’une infime partie des savoirs »

Tribune. Faute de tenir les engagements budgétaires pris par l’Etat à l’occasion de l’agenda de Lisbonne (2000), le service public de recherche et d’enseignement supérieur décroche. Son indépendance et sa stabilité sont ébranlées par des pratiques d’évaluation, de management et de gestion empruntées au secteur privé. Les politiques publiques favorisent ainsi les contrats courts et précaires au détriment des emplois pérennes, elles promeuvent la compétition contre la coopération et enjoignent de trouver des résultats rentables aux dépens de la liberté de chercher et de son incertitude radicale.

Le 1er février, confirmant le projet d’élaboration d’une loi de programmation pluriannuelle de la recherche, le premier ministre déclarait : « Gouverner, c’est choisir, et choisir, c’est renoncer ; nous devons donc faire des choix et décider ce qui est le plus important. »On comprend qu’il ne faudra garder que les « meilleurs » d’entre nous. Mais selon quels critères ? Ceux qui obtiennent des prix internationaux ou des labellisations d’« excellence », déposent des brevets, obtiennent de très gros financements européens et font des recherches à haut « facteur d’impact » ?

Soumettant la recherche à une pensée utilitariste et comptable, le management public mesure aujourd’hui la performance à court terme et ne considère le fruit du travail scientifique que par les seuls travaux à haute visibilité et à rentabilité immédiate. Pourtant chacun sait que la recherche ne peut être que le fait d’une vaste communauté, « stars » comprises : aucun « génie » n’existe sans un collectif stable, compétent et à l’abri de la précarité.

Des postes précaires de compensation de plus en plus nombreux

L’application généralisée et systématique des critères de la « performance », dont on connaît pourtant bien les défauts et les travers, constitue un danger majeur qui met notamment en péril notre indépendance vis-à-vis des financements privés et internationaux. Que se passera-t-il quand les chercheuses et les chercheurs travaillant dans les domaines de l’énergie, de l’économie,de l’agriculture ou de la pharmacie ne seront plus financés que par le secteur privé ou des intérêts sectoriels ? Les sciences où les brevets sont rares, qui ne nécessitent pas de gros équipements et dont les travaux profitent davantage à l’intelligence collective et au progrès social sont-elles amenées à disparaître ?

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• As abscisic acid (ABA) receptors, PYR1/PYL/RCAR (PYLs) play important roles in ABA‐mediated seed germination, but the regulation of PYLs in this process, especially at the transcriptional level, remains unclear.
• In this study, we found that expression of 11 of 14 PYL s changes significantly during seed germination and is affected by exogenous ABA. Two PYLs, PYL11 and PYL12, both of which are expressed specifically in mature seeds, positively modulate ABA‐mediated seed germination.
• However, ABI5 was found to modulate the PYL11‐ and PYL12‐mediated ABA response. In the abi5‐7 mutant, ABA hypersensitivity caused by PYL11 and PYL12 overexpression was totally or partially blocked. By contrast, ABI5 regulates the expression of PYL11 and PYL12 by directly binding to their promoters. Moreover, the expression of eight other PYL s is also affected during the germination of abi5 mutants. Promoter analysis revealed that an ABI5‐binding region is present next to the TATA box or initiator box.
• Together, our data demonstrate the role of PYL11 and PYL12 in seed germination. In addition, the identification of PYL s as targets of ABI5 reveals a role of ABI5 in the feedback regulation of ABA‐mediated seed germination.

Genome editing by site‐directed nucleases (SDNs) such as TALEN or Cas9 is a versatile tool that generates variations in the recipient genome at specific target sites. SDNs produce a sequence‐specific DNA break that is repaired by the plant's natural DNA repair mechanisms; as the repair is inherently imperfect, it results in target‐site variants. Depending on the type of approach, we can distinguish between three types of alterations. SDN‐1 introduces base‐pair changes or small insertions/deletions without addition of foreign DNA. The exact change cannot be predetermined and is quasi random at the target site. SDN‐2 uses a small DNA template to generate a specific change by homologous recombination. SDN‐3 inserts larger DNA elements of foreign origin using a similar approach as SDN‐2 (ref. 1); the introduction of larger pieces of DNA is typically considered as transgenic. Many countries have now adapted their biosafety legislation based on this classification of SDN‐induced variants (Fig 1).

Functional divergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum(wheat) and Secale cereale (rye) accumulate delphinidin‐derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleruone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue‐coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co‐evolved together. We also identified a Pooideae‐specific flavonoid 3′,5′‐hydroxylase (F3′5′H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3′5′Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional divergence for plant diversity and environmental adaptation.