辣椒抗烟草花叶病毒相关基因研究进展

病毒病是危害辣椒生产的主要病害之一。烟草花叶病毒(TMV)是最早被发现的病毒,它引起的烟草花叶病毒病是多种作物的重要病害,给辣椒等茄科作物的生产带来重大损失。文中综述了辣椒抗TMV防御反应中的相关基因及其研究进展,为明确辣椒抗TMV机理,挖掘抗病基因,选育抗病材料提供参考。     

Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach

Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next‐generation sequencing to allow such large‐scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large‐scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost‐effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.     

2020年中国植物科学若干领域重要研究进展

2020年中国植物科学家在国际综合性学术期刊及植物科学主流期刊发表的论文数量比上一年显著增加,在植物发育、耐逆、系统进化和作物生物学等领域取得了重要研究进展。其中,“小麦抗赤霉病基因Fhb7的克隆、机理解析及育种利用”和“提高作物品种氮肥利用效率的新机制”两项成果入选2020年度“中国生命科学十大进展”。该文总结了20...     

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Next‐generation whole‐genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence‐based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost‐efficient establishment of powerful genomic information for many species.     

Generation of chromosomal deletions in dicotyledonous plants employing a user‐friendly genome editing toolkit

Genome editing facilitated by Cas9‐based RNA‐guided nucleases (RGNs) is becoming an increasingly important and popular technique for reverse genetics in both model and non‐model species. So far, RGNs were mainly applied for the induction of point mutations, and one major challenge consists in the detection of genome‐edited individuals from a mutagenized population. Also, point mutations are not appropriate for functional dissection of non‐coding DNA. Here, the multiplexing capacity of a newly developed genome editing toolkit was exploited for the induction of inheritable chromosomal deletions at six different loci in Nicotiana benthamiana and Arabidopsis. In both species, the preferential formation of small deletions was observed, suggesting reduced efficiency with increasing deletion size. Importantly, small deletions (<100 bp) were detected at high frequencies in N. benthamiana T₀ and Arabidopsis T₂ populations. Thus, targeting of small deletions by paired nucleases represents a simple approach for the generation of mutant alleles segregating as size polymorphisms in subsequent generations. Phenotypically selected deletions of up to 120 kb occurred at low frequencies in Arabidopsis, suggesting larger population sizes for the discovery of valuable alleles from addressing gene clusters or non‐coding DNA for deletion by programmable nucleases.     

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short‐read RNA sequencing, single molecule long‐read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron‐containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non‐conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.     

Quantitative profiling and pattern analysis of triacylglycerol species in Arabidopsis seeds by electrospray ionization mass spectrometry

Plant triacylglycerols (TAGs), or vegetable oils, provide approximately 25% of dietary calories to humans and are becoming an increasingly important source of renewable bioenergy and industrial feedstocks. TAGs are assembled by multiple enzymes in the endoplasmic reticulum from building blocks that include an invariable glycerol backbone and variable fatty acyl chains. It remains a challenge to elucidate the mechanism of synthesis of hundreds of different TAG species in planta. One reason is the lack of an efficient analytical approach quantifying individual molecular species. Here we report a rapid and quantitative TAG profiling approach for Arabidopsis seeds based on electrospray ionization tandem mass spectrometry with direct infusion and multiple neutral loss scans. The levels of 93 TAG molecular species, identified by their acyl components, were determined in Arabidopsis seeds. Quantitative TAG pattern analyses revealed that the TAG assembly machinery preferentially produces TAGs with one elongated fatty acid. The importance of the selectivity in oil synthesis was consistent with an observation that an Arabidopsis mutant overexpressing a patatin‐like phospholipase had enhanced seed oil content with elongated fatty acids. This quantitative TAG profiling approach should facilitate investigations aimed at understanding the biochemical mechanisms of TAG metabolism in plants.     

LIVING TO THE BITTER END? A PERSONALIST APPROACH TO EUTHANASIA IN PERSONS WITH SEVERE DEMENTIA

The number of people suffering from dementia will rise considerably in the years to come. This will have important implications for society. People suffering from dementia have to rely on relatives and professional caregivers when their disorder progresses. Some people want to determine for themselves their moment of death, if they should become demented. They think that the decline in personality caused by severe dementia is shocking and unacceptable. In this context, some people consider euthanasia as a way to avoid total deterioration. In this article, we discuss some practical and ethical dilemmas regarding euthanasia in persons with severe dementia based on an advance euthanasia directive. We are using a personalist approach in dealing with these ethical dilemmas.     

A KOREAN PERSPECTIVE ON DEVELOPING A GLOBAL POLICY FOR ADVANCE DIRECTIVES

Despite the wide and daunting array of cross‐cultural obstacles that the formulation of a global policy on advance directives will clearly pose, the need is equally evident. Specifically, the expansion of medical services driven by medical tourism, just to name one important example, makes this issue urgently relevant. While ensuring consistency across national borders, a global policy will have the additional and perhaps even more important effect of increasing the use of advance directives in clinical settings and enhancing their effectiveness within each country, regardless of where that country's state of the law currently stands. One cross‐cultural issue that may represent a major obstacle in formulating, let alone applying, a global policy is whether patient autonomy as the underlying principle for the use of advance directives is a universal norm or a construct of western traditions that must be reconciled with alternative value systems that may place lesser significance on individual choice. A global policy, at a minimum, must emphasize respect for patient autonomy, provision of medical information, limits to the obligations for physicians, and portability. And though the development of a global policy will be no easy task, active engagement in close collaboration with the World Health Organization can make it possible.     

ADVANCE DIRECTIVES IN THE NETHERLANDS: AN EMPIRICAL CONTRIBUTION TO THE EXPLORATION OF A CROSS‐CULTURAL PERSPECTIVE ON ADVANCE DIRECTIVES

Research Objective: This study focuses on ADs in the Netherlands and introduces a cross‐cultural perspective by comparing it with other countries. Methods: A questionnaire was sent to a panel comprising 1621 people representative of the Dutch population. The response was 86%. Results: 95% of the respondents didn't have an AD, and 24% of these were not familiar with the idea of drawing up an AD. Most of those familiar with ADs knew about the Advanced Euthanasia Directive (AED, 64%). Both low education and the presence of a religious conviction that plays an important role in one's life increase the chance of not wanting to draw up an AD. Also not having experienced a request for euthanasia from someone else, and the inconceivability of asking for euthanasia yourself, increase the chance of not wanting to draw up an AD. Discussion: This study shows that the subjects of palliative care and end‐of‐life‐decision‐making were very much dominated by the issue of euthanasia in the Netherlands. The AED was the best known AD; and factors that can be linked to euthanasia play an important role in whether or not people choose to draw up an AD. This differentiates the Netherlands from other countries and, when it comes to ADs, the global differences between countries and cultures are still so large that the highest possible goals, at this moment in time, are observing and possibly learning from other cultural settings.