【Mol Plant】2024年技术方法与资源类文章总结(一)

Review 2024

We developed “PanSK” (Pan-SSP k-mer) for genotype-to-phenotype prediction based on an SSP-based pangenome resource. PanSK uses 29-mer sequences that represent each SSP gene at the pangenomic level to reveal untapped diversity across landraces and modern cultivars.

Mol Plant |中国农大小麦研究中心建立小麦籽粒储藏蛋白泛基因组图谱和表型预测模型，助力加工品质遗传改良

Here, we present a novel 3D spatial–spectral data fusion approach to collect high-quality 3DMPCs of plants by integrating the next-best-view planning for adaptive data acquisition and neural reference field (NeREF) for radiometric calibration. This approach was used to acquire 3DMPCs of perilla, tomato, and rapeseed plants with diverse plant architecture and leaf morphological features evaluated by the accuracy of chlorophyll content and equivalent water thickness (EWT) estimation.

Mol Plant | 浙江大学岑海燕团队提出一种基于无人车表型平台的植物三维多光谱点云生成方法

This study optimized DNA extraction and library preparation, achieving DNA lengths exceeding 485 kb; average N50 read lengths of 80.57 kb, reaching up to 440 kb; and maximum reads of 5.83 Mb.

Mol Plant | 北大农研院李博生团队发表超长和选择性测序方法高效获得植物完整T2T基因组

We presented PDLLMs (Plant DNA Large Language Models), a group of DNA large language models based on five foundational model architectures that are tailored for analyzing and processing plant genomes. These models utilize distinct architectural approaches to better accommodate the unique characteristics of plant genomic data. Besides, we constructed 10 plant datasets and finetuned 198 models for genomic prediction tasks.

Mol Plant | 扬州大学农学院张韬教授课题组开发了一系列基于植物基因组的基础DNA大语言模型

In this study, we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana benthamiana. 

Mol Plant | 法国Alain Tissier团队通过工程化CRISPR/Cas内切核酸酶实现高效的大片段DNA定点插入

We have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F₁ populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F₁ population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that does not contribute to phenotype segregation in the F₁ population.

Mol Plant | 中国农科院蔬菜所开发异交物种基因高效定位的新算法工具OcBSA

We added an hFTO cassette under the control of the constitutive soybean M8L promoter to a previously reported pGES401 vector, which we designated pGES501. The gene-editing efficiency of pGES501 was first assayed in soybean hairy roots at 11 genomic target sites. The indel frequency in hairy roots transformed with pGES501 was higher at six of 11 sites, and the overall average editing efficiencies were 53.27% in pGES501 and 42.72% in pGES401. This indicates that co-expressing hFTO can improve gene-editing efficiency in soybean.

Mol Plant | 广州大学关跃峰课题组联合北京大学贾桂芳课题组开发一种显著提高基因编辑效率的新方法

In this study, to explore whether heterologous expression of PAR could be applied for synthetic apomixis in rice, we constructed the sgMiMe_pAtEC1.1:ToPAR vector, aiming for simultaneously mutating REC8, PAIR1, and OSD1, the components of the MiMe system, and heterologously expressing the dandelion PAR.

We developed Smart Breeding Platform (https://sbp.ibreed.cn), a user-friendly, web-based tool for the management and analysis of large-scale genetic, genomic, and phenomic data.

Mol Plant | 中国农科院作科所和阿里巴巴联合发布首个全流程智慧育种平台

We developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC–MS) runs operated in a data-dependent acquisition (DDA) mode.

Mol Plant | 中国科学院遗传与发育研究所研发一种高效的植物磷酸化蛋白质组学新技术GreenPhos

We constructed a comprehensively curated plant RLK database (https://biotec.njau.edu.cn/rlkdb), which contains valuable resources for investigating the origin and evolution of the RLK family and multiple online tools for personalized analysis.

Mol Plant | 南京农业大学窦道龙团队构建第一个植物RLK数据库

Here, we present BambooBase (https://bamboo.genobank.org/), a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.

Mol Plant | 中国科学院昆明植物研究所李德铢团队发表竹类组学和分类学信息平台

Here, we introduce WTV 2.0, which enabled the construction of a high-coverage library containing 2111 plant volatiles, and report the development of a comprehensive selective ion monitoring (cSIM) acquisition method, including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method, that can acquire the smallest but sufficient number of ions for most plant volatiles, as well as the automatic qualitative and semi-quantitative analysis of cSIM data.

Mol plant︱崖州湾国家实验室/海南大学罗杰课题组建立新一代广泛靶向植物挥发组学方法

In this study, we constructed a species-level variation atlas of genomes and metabolomes using 299 citrus accessions. A total of 19 829 significant SNPs were targeted to 653 annotated metabolites, among which multiple significant signals were identified for secondary metabolites, especially flavonoids.

Mol Plant | 浙江大学孙崇德教授团队解析柑橘群体生物活性物质分化的遗传基础

By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1.

Mol Plant|中国科学院遗传发育所肖军课题组通过多技术联合分析系统鉴定了小麦穗发育的转录调控因子

Here we present a near-complete cucumber reference genome, representing a significant advancement for this highly complex genome. To assemble the remaining fragments of the cucumber reference genome, we employed a hybrid assembly approach.

Mol Plant | 中国农科院张圣平团队建立黄瓜多组学综合数据库