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[政策法规 ] Engineering Biology Metrics and Technical Standards for the Global Bioeconomy 进入全文
美国工程生物学研究联盟（EBRC）
EBRC, with partners at the U.S. National Institute of Standards and Technology (NIST), Imperial College London, and the National University of Singapore (NUS), and supported by Schmidt Futures, have published a report focused on determining the engineering biology metrics and technical standards needed to accelerate the global bioeconomy. The report summarizes the key findings that emerged from global stakeholder discussions, pulling together common themes and identified needs that arose across Europe, Asia, and the Americas. Within six key areas — data standards, metrology and metrics to quantify biological processes, scale-up and scale-out, lexicon and terminology, metrics and standardization for sustainability assessments, and standards to enable use of biomass feedstocks — opportunities are identified for focused activities to develop technical standards and metrics that will enable enhanced performance across the bioeconomy: improving reproducibility, supporting continued scale-up, and accelerating commercialization and industrial growth. A series of non-technical areas are also identified and explored, including: training and education on standards and metrics, engagement with the public and improvement of public perception and trust, regulatory clarity, and biosafety and biosecurity. As well as focusing on areas of common understanding, the report elaborates on some areas where distinct differences exist and global consensus might not be reached, highlighting these as potential focus areas for regional or national efforts going forward.
[学术文献 ] Genomic selection in plant breeding: Key factors shaping two decades of progress 进入全文
ELSEVIER
Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
[学术文献 ] A designer synthetic chromosome fragment functions in moss 进入全文
nature
Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments. By eliminating 55.8% of a 155 kb endogenous chromosomal region, we substantially simplified the genome without discernible phenotypic effects, implying that many transposable elements may minimally impact growth. We also introduced other sequence modifications, such as PCRTag incorporation, gene locus swapping and stop codon substitution. Despite these substantial changes, the complex epigenetic landscape was normally established, albeit with some three-dimensional conformation alterations. The synthesis of a partial multicellular eukaryotic chromosome arm lays the foundation for the synthetic moss genome project (SynMoss) and paves the way for genome synthesis in multicellular organisms.
[前沿资讯 ] UW–Madison researchers find persistent problems with AI-assisted genomic studies 进入全文
UW–Madison威斯康星大学
University of Wisconsin–Madison researchers are warning that artificial intelligence tools gaining popularity in the fields of genetics and medicine can lead to flawed conclusions about the connection between genes and physical characteristics, including risk factors for diseases like diabetes.
[前沿资讯 ] A chromosome-scale reference genome of grasspea (Lathyrus sativus) 进入全文
Scientific Data
Grasspea (Lathyrus sativus L.) is an underutilised but promising legume crop with tolerance to a wide range of abiotic and biotic stress factors, and potential for climate-resilient agriculture. Despite a long history and wide geographical distribution of cultivation, only limited breeding resources are available. This paper reports a 5.96 Gbp genome assembly of grasspea genotype LS007, of which 5.03 Gbp is scaffolded into 7 pseudo-chromosomes. The assembly has a BUSCO completeness score of 99.1% and is annotated with 31719 gene models and repeat elements. This represents the most contiguous and accurate assembly of the grasspea genome to date.
[学术文献 ] Efficient formation of single-copy human artificial chromosomes 进入全文
science
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
