Towards molecular breeding and improvement of rice in China

China is the largest producer and consumer of rice in the world and a pioneer in applying hybrid rice technology. Although hybrid rice has contributed greatly to Chinese agriculture in the past decades, its potential to improve grain quality further is being questioned. However, to meet the challenges posed by severe crop damage by pests and diseases, the extensive use of pesticides and chemical fertilizers, and a shortage of water and energy, more elite rice cultivars are needed. In recent years, China has seen continued improvements in rice genetics, powered by functional genomics as a way forward to safeguard its rice production. Here, we briefly review the current status of rice breeding in China through strategies integrating hybrid rice technology, molecular marker-assisted breeding, functional genomics and genetically modified rice.     

The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL)

The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, The Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the ‘International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation’. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae—and beyond—achieves a context that will facilitate a systems biology approach.     

Correcting common errors in identifying cancer-specific serum peptide signatures

"Molecular signatures" are the qualitative and quantitative patterns of groups of biomolecules (e.g., mRNA, proteins, peptides, or metabolites) in a cell, tissue, biological fluid, or an entire organism. To apply this concept to biomarker discovery, the measurements should ideally be noninvasive and performed in a single read-out. We have therefore developed a peptidomics platform that couples magnetics-based, automated solid-phase extraction of small peptides with a high-resolution MALDI-TOF mass spectrometric readout (Villanueva, J.; Philip, J.; Entenberg, D.; Chaparro, C. A.; Tanwar, M. K.; Holland, E. C.; Tempst, P. Anal. Chem. 2004, 76, 1560-1570). Since hundreds of peptides can be detected in microliter volumes of serum, it allows to search for disease signatures, for instance in the presence of cancer. We have now evaluated, optimized, and standardized a number of clinical and analytical chemistry variables that are major sources of bias; ranging from blood collection and clotting, to serum storage and handling, automated peptide extraction, crystallization, spectral acquisition, and signal processing. In addition, proper alignment of spectra and user-friendly visualization tools are essential for meaningful, certifiable data mining. We introduce a minimal entropy algorithm, "Entropycal", that simplifies alignment and subsequent statistical analysis and increases the percentage of the highly distinguishing spectral information being retained after feature selection of the datasets. Using the improved analytical platform and tools, and a commercial statistics program, we found that sera from thyroid cancer patients can be distinguished from healthy controls based on an array of 98 discriminant peptides. With adequate technological and computational methods in place, and using rigorously standardized conditions, potential sources of patient related bias (e.g., gender, age, genetics, environmental, dietary, and other factors) may now be addressed.     

Inhibitory activities against rice pathogens of 8-hydroxy-2,4,6-octatriynamide from <Emphasis Type="Italic">Agrocybe</Emphasis> sp.

8-Hydroxy-2,4,6-octatriynamide, a natural polyacetylene with inhibitory activities against rice pathogens, was isolated from the liquid fermentation broth of strain Agrocybe sp. YB2005 during screening for new natural chemical agents to control rice pathogens. 8-hydroxy-2,4,6-octatriynamide was purified by consecutive chromatography over a Cl8 reversed phase silica gel, sephadex LH-20 and silica gel. The chemical structure of 8-hydroxy-2,4,6-octatriynamide was elucidated through spectroscopic analyses, including 1D- and 2D-NMR, ESI mass spectrometry and X-ray single crystal diffraction. Bioassays showed that 8-hydroxy-2,4,6-octatriynamide could significantly inhibit growth of Xanthomonas oryzae with an MIC of 53.1 μM in a 96-well plate and the growth of Rhizoctonia solani at 1.02 mM in a 24-well plate. When rice leaves were inoculated with Magnaporthe grisea and cultured in artificial nutrition liquid containing 0.34 mM 8-hydroxy-2,4,6-octatriynamide, no rice blast was observed. The present study implied that 8-hydroxy-2,4,6-octatriynamide could be a candidate agent against rice pathogens.     

Genomic Epidemiology of SARS-CoV-2 in Pakistan

COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1, 2020. We identified a total of 347 mutated positions, 31 of which were over-represented in Pakistan. Meanwhile, we found over 1000 intra-host single-nucleotide variants (iSNVs). Several of them occurred concurrently, indicating possible interactions among them or coevolution. Some of the high-frequency iSNVs in Pakistan were not observed in the global population, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab) of this cluster. Furthermore, 28 putative international introductions were identified, several of which are consistent with the epidemiological investigations. In all, this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan, which could aid ongoing and future viral surveillance and COVID-19 control.     

漳江口红树林沉积物可培养真菌多样性

红树林真菌由于其独特的生态特征、多样性特点和丰富的新型生物活性代谢产物而引起了广泛的关注。本文以漳江口红树林保护区4个采样点的沉积物为研究对象,采用8种筛选培养基（RBM、PDA、CDA、Martin、YM、SDA、ISP2和R2A）分离可培养真菌,根据ITS序列分析对其进行物种鉴定,并利用多样性指数分析评价不同采样点真菌群落的差异。结果共分离到274株真菌,隶属于2门12纲23目39科52属,其中优势属为枝顶孢属（Acremonium）（20.8%）和青霉属（Penicillium）（11.3%）,其次是枝孢属（Cladosporium）（7.3%）和帚枝霉属（Sarocladium）（7.3%）。8种筛选培养基中,分离出真菌种属类型最丰富的培养基是RBM,其次是PDA。根据Shannon-Wiener多样性指数（H′）、Simpson优势度指数（D）、Magalef丰富度指数（R）和Pielou均匀度指数（J）的分析结果,在属的水平上,距海洋的位置越近,真菌的群落多样性越高,真菌分布越均匀。     

空间粒度变化对景观格局分析的影响

认识空间异质性的多尺度依赖性和景观格局特征对尺度效应关系的影响是进行空间尺度推绎的基础。以2种真实景观(中国广东粤北植被景观与美国凤凰城城市景观)和SIMMAP景观中性模型产生的27种模拟景观为对象。利用景观格局分析软件FRAGSTATS对18种常用景观指数的尺度效应进行了系统的分析。根据这些指数对空间粒度变化的响应曲线和尺度效应关系,18种景观指数可分为3类。第1类指数随空间粒度的增大单调减小。具有比较明确的尺度效应关系(幂函数下降),尺度效应关系受景观空间格局特征的影响较小;这类指数包括缀块数、缀块密度、边界总长、边界密度、景观形状指数、缀块面积变异系数、面积加权平均缀块形状指数、平均缀块分维数和面积加权平均缀块分维数。第2类指数随空间粒度的增大将最终下降。但不是单调下降的;尺度效应关系比较多样,可表现为幂函数下降、直线下降或阶梯形下降。主要受缀块空间分布方式和缀块类优势度的交互影响;这类指数有5种：平均缀块形状指数、双对数回归分维数、缀块丰度、缀块丰度密度和Shannon多样性指数。第3类指数随空间粒度的变粗而增加。随缀块类优势度均等性的增加。尺度效应关系由阶梯形增加、对数函数增加、直线增加向幂函数增加过渡。尺度效应关系主要受缀块类优势度的影响;此类指数包括平均缀块面积、缀块面积标准差、最大缀块指数与聚集度。景观指数随空间粒度变化是一种1临界现象,当粒度大于或小于1临界值时,景观指数对空间粒度变化非常敏感。变化速率非常大。绝大部分情况下。真实景观粒度效应关系和曲线形状与模拟景观所得分析结果相似。说明模拟景观具有很好的代表性。文中也讨论了本研究结果与前人研究的异同。分析了造成差异的原因。景观指数的粒度效应关系与指数本身所反映的景观格局信息有一定关系,总体上来说。随粒度增加。缀块数、边界长度、缀块形状的复杂性、多样性将减小,而平均缀块面积和聚集度将增加。一系列的尺度效应图和不同景观指数的尺度效应关系可作为景观格局分析时指数选择、分析结果的解释和进行空间尺度推绎的参考。     

Electrostatic potentials of the S‐locus F‐box proteins contribute to the pollen S specificity in self‐incompatibility in Petunia hybrida

Self‐incompatibility (SI) is a self/non‐self discrimination system found widely in angiosperms and, in many species, is controlled by a single polymorphic S‐locus. In the Solanaceae, Rosaceae and Plantaginaceae, the S‐locus encodes a single S‐RNase and a cluster of S‐locus F‐box (SLF) proteins to control the pistil and pollen expression of SI, respectively. Previous studies have shown that their cytosolic interactions determine their recognition specificity, but the physical force between their interactions remains unclear. In this study, we show that the electrostatic potentials of SLF contribute to the pollen S specificity through a physical mechanism of ‘like charges repel and unlike charges attract’ between SLFs and S‐RNases in Petunia hybrida. Strikingly, the alteration of a single C‐terminal amino acid of SLF reversed its surface electrostatic potentials and subsequently the pollen S specificity. Collectively, our results reveal that the electrostatic potentials act as a major physical force between cytosolic SLFs and S‐RNases, providing a mechanistic insight into the self/non‐self discrimination between cytosolic proteins in angiosperms.     

Editorial

<正>As 2013 has been wrapped up and a prosperous year of2014 is coming,I would like to take this opportunity to express my appreciation to all editorial board members,authors reviewers and readers for their great and generous support to Journal of Genetics and Genomics(JGG)over the past years Meanwhile,I also like to share with you some of the journal’s