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Tree crops are explored for food sources and raw materials for industrial sectors. However, breeding tree species to meet current economic demands amid forecasts of agricultural resource scarcity and climate instability is a challenging task. This is especially true due to their long juvenile phase, often difficulties related to reproductive biology, and scarcity of genetic resources, which largely delays phenotyping and selection of segregating populations. On the other hand, genome sequence and transcriptomic data are becoming increasingly available for perennial crops, along with optimized protocols for genetic transformation and in vitro regeneration. Due to the development of these fields altogether and the advances in gene editing technologies, it is now possible to glimpse the design of tree crops with optimized traits for cultivation. We review the status of genome projects and the application of CRISPR-Cas-based systems in tree crops, alongside an exploration of gene editing technologies to develop perennial crop ideotypes. Herein, we seek to raise attention to the capabilities and potential of crop designing applied to tree species and to the opportunity that we have, as a society, to create stepwise strategies to tailor the breeding of perennial crops in the context of the current environmental challenges and increasing population demands. [ABSTRACT FROM AUTHOR]

The world is currently facing a novel viral pandemic (SARS-CoV-2), and large-scale testing is central to decision-making for the design of effective policies and control strategies to minimize its impact on the global population. However, testing for the presence of the virus is a major bottleneck in tracking the spreading of the disease. Given its adaptability regarding the nucleotide sequence of target regions, RT-qPCR is a strong ally to reveal the rapid geographical spreading of novel viruses. We assessed PCR variations in the SARS-CoV-2 diagnosis taking into account public genome sequences and diagnosis kits used by different countries. We analyzed 226 SARS-CoV-2 genome sequences from samples collected by March 22, 2020. Our work utilizes a phylogenetic approach that reveals the early evolution of the virus sequence as it spreads around the globe and informs the design of RT-qPCR primers and probes. The quick expansion of testing capabilities of a country during a pandemic is largely impaired by the availability of adequately trained personnel on RNA isolation and PCR analysis, as well as the availability of hardware (thermocyclers). We propose that rapid capacity development can circumvent these bottlenecks by training medical and non-medical personnel with some laboratory experience, such as biology-related graduate students. Furthermore, the use of thermocyclers available in academic and commercial labs can be promptly calibrated and certified to properly conduct testing during a pandemic. A decentralized, fast-acting training and testing certification pipeline will better prepare us to manage future pandemics. [ABSTRACT FROM AUTHOR]

In many legume species, somatic embryogenesis is a limiting step of in vitro regeneration, with profound implications to genetic engineering and plant breeding. In Arabidopsis thaliana, the small AFL subfamily of B3-type transcriptional factors is composed by LEC2 (LEAFY COTYLEDON 2), FUSCA (FUSCA3), and ABI3 (ABSCISIC ACID INSENSITIVE 3), which are directly involved in both zygotic and somatic embryogenesis. This study aimed to identify and analyze the expression profile of AFL subfamily genes during in vitro induction of the somatic embryogenesis in the model legume Medicago using near-isogenic genotypes contrasting for their capability of regenerating in vitro. Three AFL genes were identified in the Medicago truncatula genome: MtLEC2, MtFUSCA3 and MtABI3. RT-qPCR was used to compare the expression of these genes during the induction of somatic embryogenesis in the embryogenic genotype M9-10a and the non-embryogenic genotype M9. The AFL genes identified were highly expressed 10 days after introducing leaflet explants in vitro in the embryogenic genotype (M9-10a), whereas absence or low expression was observed in explants of the non-embryogenic genotype (M9). During zygotic embryogenesis, the Medicago Gene Atlas revealed that expression of MtFUSCA3 and MtABI3 occurred specifically during seed development, starting at 10 days after pollination. This study allowed for the identification and transcriptional characterization of MtLEC2, MtFUSCA3, and MtABI3. The expression pattern of these genes in the M9-10a genotype suggests they are involved in the Medicago truncatula somatic embryogenesis. The transcriptional profile of AFL transcription factors highlights the evolutionary conservation of this developmental pathway between the Arabidopsis and Medicago lineages and opens avenues to improve the efficiency of in vitro embryogenesis in legume crops. Key message: Expression of MtLEC2, MtFUSCA3, and MtABI3 genes was induced during somatic embryogenesis and these genes to be used as in vitro regeneration biomarkers as well as to improving somatic embryogenic rates in legumes and other crops recalcitrant to in vitro regeneration. [ABSTRACT FROM AUTHOR]