Application of resequencing to rice genomics,functional genomics and evolutionary analysis

Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing rice genomes. Based on the reference genome in rice, next-generation sequencing (NGS) using the high-throughput sequencing system can efficiently accomplish whole genome resequencing of various genetic populations and diverse germplasm resources. Resequencing technology has been effectively utilized in evolutionary analysis, rice genomics and functional genomics studies. This technique is beneficial for both bridging the knowledge gap between genotype and phenotype and facilitating molecular breeding via gene design in rice. Here, we also discuss the limitation, application and future prospects of rice resequencing.     

茶树基因组与测序技术的研究进展

茶树具有高度杂合、基因组庞大及高度重复等特点,这导致茶树基因组的前期研究进展缓慢。基因组测序技术的迅速发展有力推动茶树基因组的解析与完善。综述了基因组测序技术的发展,将近年来茶树基因组的组装与研究进展按照草图水平、染色体水平和单体型水平进行分类,探讨茶树基因组未来的应用与发展方向,为茶树功能基因组学研究和精确分子育种提供参考。     

干旱胁迫下马铃薯幼苗DNA甲基化研究

马铃薯（Solanum tuberosumL）是我国重要的粮食作物,性喜阴湿冷凉的环境,干旱严重影响着马铃薯的品质产量的稳定。试验采用PEG-6000模拟干旱胁迫处理3个品种的马铃薯幼苗,并对其基因组DNA进行甲基化敏感扩增多态性（Methvlation-sensitiveamplifiedpolymorphism,MSAP）分析,在20％的PEG胁迫下,‘大西洋’的基因组DNA甲基化程度随着时间的增长而有所增大。‘中薯3号’在20％的PEG胁迫下,随着时间的增长,甲基化基本趋势是减弱的。‘中薯5号’和‘中薯3号’情况类似,其甲基化趋势基本上也是随着时间增长而降低的。将特异带回收测序和B1ast比对,结果表明其中几条带跟与萜类化合物合成等功能基因具有一定的同源性。     

小麦的基因源

作物的基因源是指系统发育中与作物遗传关系较近、通过遗传操作可以向作物转移基因的一群植物及其基因所编码的遗传信息。研究了散作物的基因源,不仅能通晓作物种质资源的全貌,开阔育种取材的思路,而且有助于正确选择育种途径。不同作物基因源的范围大小不同。小麦的基因源包括整个小麦族,可分为三级：凡含有ＡＢＤ三个基因组的品种、品系和原始种都是普通小麦的一级基因源;含有ＡＢＤ这三个基因组中一个或两个基因组的物种是普     

The impact of climate change on global food supply and demand, food prices, and land use

Climate change induced crop yield change affects food production of countries to varying degrees, depending on the location of the farming activities. Differentiated yield changes of crops may lead to reallocation of agricultural land among uses. Key food exporters may reshuffle due to diverse climate change impact on crop farming among countries. We use a multi-region, multi-sector computable general equilibrium (CGE) model, which considers crop suitability of land in the optimal reallocation decision of land between uses, to simulate the impact on global food production, prices, and land use of crop yield change due to climate change as projected under the IPCC SRES scenario A2. Our findings show that developing countries are more adversely affected by climate change than developed countries. Developed countries are mostly located in higher latitudes, and climate change benefits the crop yield of these areas. In contrast, developing countries of the lower latitudes suffer from the reduction in crop yield being induced by climate change. Considering the fast growing population in the developing world, developed countries are expected to serve as the world’s key food exporters by 2020 should the climate change occurs as scenario A2 indicates.     

Rice production in China in the early 21st Century

Rice is the staple food crop in China. In the second half of the 20th century, rice has played an important role in feeding a large number of people. In the 21st century, rice will still be a main food crop in China and make great contribution to Chinese people's life.     

Assessment of SNP and In Del Variations Among Rice Lines of Tulaipanji x Ranjit

Genotyping by sequencing(GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms(SNPs) in crop species. Genotypic variation studies(SNPs and insertion-deletions/In Dels) were performed using four rice lines based on GBS data by aligning to the reference genome Nipponbare. Local aromatic rice landrace Tulaipanji was crossed with Ranjit, and two distinct lines were identified from the progenies: one line with awns and aroma traits and the other without awns and aroma. Total number of SNPs and In Dels identified were 52 810 and 4 327 at read depth 10, respectively. Out of the total polymorphic SNPs/In Dels, 16 490 were intergeneric, 7 812 were inside gene, and 4 435 were intronic. Phylogenetically, Tulaipanji was closer to the reference genome nipponbare. Based on recurrent parent genome analysis, out of 10 013 alleles, 92.52% was introgressed into progeny-awn from Tulaipanji and 7.48% from Ranjit, whereas progeny-awnless carried 89.19% alleles from Ranjit and only 10.81% alleles from Tulaipanji. In addition, progeny-awn was the highest heterozygous(83.88%) and progeny-awnless was the least(2.24%) at this fifth generation of recombinant inbred lines. These SNP variations may be linked to the phenotypic traits and can be utilized in crop improvement through linkage mapping. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.     

Improving Rice to Meet Food and Nutritional Needs: Biotechnological Approaches

SUMMARY

The livelihood and calorie needs of large populations based in developing countries is dependent on rice cultivation. More than three billion people consume rice as a staple food. To meet the future demands of the human population, innovative tools such as genomics are being used to improve rice yield increase, for the incorporation of stress resistance/tolerance in rice varieties, and for the improvement of the nutritional quality of rice. These new tools include: sequencing, large-scale analysis of expressed sequence tags, high throughout microarray analysis and genetic transformation. Rice now serves as a model for a science based crop design for the agronomic, nutritional, and economic benefit of farmers. This article discusses the use of biotechnology as a tool to improve the rice plant for the benefit of mankind.     

Lignin and polyphenols as allelochemicals

By the microbiological action, lignin from vegetal wastes is transformed at soil level in organic prebiotic products with physiological activity on plants development. On the other hand, some micromolecular compounds resulted from plant wastes decomposition, along with polyphenols coming from extraction of plant residues could play a role of allelochemicals. The understanding of the allelochemical action mechanisms allow us to use these compounds to enhance crop production and develop a more sustainable agriculture, including weed and pest control through crop rotations, residue management and a variety of approaches in biocontrol. Other goals are to adopt allelochemicals as herbicides, pesticides and growth stimulants, modify crop genomes to manipulate allelochemicals production and better elucidate chemical communications between the components of ecosystem. The result obtained in the utilization of lignins and polyphenols as allelochemicals are presented in this review.     

二代测序技术在水稻基因组学和转录组学研究中的应用

二代测序技术是测序技术的一次革命性突破,它具有高通量、高精度、低成本的优势,为水稻基因组学研究提供了新的研究方法和解决方案。概述了以使用合成法测序和连接法测序为原理的二代测序技术的特点和发展,并总结了其在水稻基因组学,包括结构基因组学和功能基因组学以及转录组学研究中的应用,并就当前测序技术的发展趋势作了展望。     

DNA sequencing methods contributing to new directions in cereal research

DNA sequencing allows the decoding of the genetic code, facilitating the discovery of the molecular genetic basis of biological systems. Knowledge of the sequence of genes in cereals provides a key to understanding many of their nutritional and functional properties. For many years DNA sequencing technology advanced slowly with incremental advances in the di-deoxy or Sanger method. New technologies are now greatly increasing the power of DNA sequencing. Second (next) generation sequencing has dramatically reduced the cost of DNA sequencing and increased the amount of data that can be collected. Further advances exploiting third generation sequencing promise to accelerate these developments. The DNA sequences of cereal species, genotypes or even individual seeds can now be obtained delivering a new level of capability in cereal science.     

Overexpression of IbPAL1 promotes chlorogenic acid biosynthesis in sweetpotato

Sweetpotato[Ipomoea batatas(L.)Lam.],a food crop with both nutritional and medicinal uses,plays essential roles in food security and health-promoting.Chlorogenic acid(CGA),a polyphenol displaying several bioactivities,is distributed in all edible parts of sweetpotato.However,little is known about the specific metabolism of CGA in sweetpotato.In this study,IbPAL1,which encodes an endoplasmic reticulum-localized phenylalanine ammonia lyase(PAL),was isolated and characterized in sweetpotato.CGA accumulation was positively associated with the expression pattern of IbPAL1 in a tissue-specific manner,as further demonstrated by overexpression of IbPAL1.Overexpression of IbPAL1 promoted CGA accumulation and biosynthetic pathway genes expression in leaves,stimulated secondary xylem cell expansion in stems,and inhibited storage root formation.Our results support a potential role for IbPAL1 in sweetpotato CGA biosynthesis and establish a theoretical foundation for detailed mechanism research and nutrient improvement in sweetpotato breeding programs.     

Large scale identification of SSR marker in perilla by next generation sequencing

Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiquitous and widely used in eukaryotic genomes. EST-SSRs identification of perilla was performed in 116,387 reads generated by Illumina paired-end sequencing technology. In total 25,449 unigenes containing SSR and 33,867 SSR loci were identified, and 19,400 primer pairs were designed. Polymorphism of SSR primers was conducted by searching for insertions and deletions (INDELs), and 1,567 unique SSRs were predicted. Totally, 200 SSR primer pairs were selected for polymorphic validation among 23 perilla accessions. Results showed that 175 primer pairs produced amplicons, and 30 pairs exhibited polymorphism. Polymorphic ratio was higher by using INDEL method than using conventional primers. Phylogenetic analysis showed the 2 distinct groups: P. frutescens var. frutescens and P. frutescens var. crispa. Wrinkled leaf trait and seed trait were distinct between these 2 groups. However, no clear leaf color or geographic relationship was detected. The large scale development and identification of SSR marker in this research laid a foundation for genetic analysis and marker assisted breeding of cultivated perilla.     

Molecular regulation and genetic control of rice thermal response

Global warming threatens food security. Rice (Oryza sativa L.), a vital food crop, is vulnerable to heat stress, especially at the reproductive stage. Here we s...     

Sustainable agriculture and chemical control: opponents or components of the same strategy?

Sustainability is a term which is frequently used — and even abused. Since the Rio Earth Summit, it has been recognised as encompassing three interdependent dimensions: economic impact, social needs and the environment. This paper considers the role of chemical crop protection in sustainable agriculture in Western Europe. It discusses the contribution of industry, both as a provider of products and as a responsible partner for stakeholders, such as farmers, food processors, food retailers and regulatory authorities. A conceptual and factual framework is proposed which reconciles the various elements of sustainable agriculture and chemical crop protection. It concludes that sustainable crop protection is a challenge but is feasible if all players contribute their share.     

水稻高产高效优质栽培研究的现状(英文)

近年来一些发达国家利用信息技术和先进知识大力发展精准农业 ,以达到改良作物表现和提高环境质量的目的。中国的农学家依据精准农业的原理并结合本国的实践 ,初步提出了水稻等作物在高产栽培条件下基本苗、施肥和灌溉的定量方法和关键指标 ,为构建具有中国特色的作物精准栽培技术体系奠定了基础。水稻直播省工节本 ,其应用面积在亚洲正逐年增加。杂草控制和倒伏问题是制约水稻直播产量及其应用面积扩大的两大因素。水稻地膜覆盖栽培近几年正在中国兴起。地膜覆盖可增温保墒、节约用水和减少氮肥损失。但地膜覆盖对环境带来的污染应引起重视。作物栽培已从单纯注重产量 ,转变为产量、优质、高效相统一 ,注重环境的保护 ,重视无公害食品、绿色食品、有机食品的开发。农业信息技术运用于作物栽培技术的研究 ,将促进栽培技术的现代化、标准化和智能化。     

Epidemiological assessment of cassava mosaic disease in Central African Republic reveals the importance of mixed viral infection and poor health of plant cuttings

Cassava is a vital crop in Africa and represents the main food crop in Central African Republic (CAR). CAR has recently faced large reductions in cassava yields that have led to a surge in market prices. To better understand the causes of the reduction in yield, we identified biotic constraints to cassava production by means of a large-scale plant epidemiological survey conducted in 2007 and 2008. Standard protocols were used for the assessment of the major cassava pests and diseases. Cassava mosaic disease (CMD) was shown to be the most serious constraint to cassava in CAR, with symptoms observed at all localities surveyed. CMD is distributed throughout the country, with an average incidence of 85%. Importantly, 94% of diseased plants had cutting-derived CMD infection suggesting that farmers mostly use virus-infected cuttings for planting. PCR amplification and direct sequencing of partial fragments of the Rep ORF revealed that the causal agents of CMD in CAR are African cassava mosaic virus (ACMV) and the Uganda strain of East African cassava mosaic virus (EACMV-UG). We also demonstrated that 58% of CMD samples present mixed infections (ACMV and EACMV-UG) and that these samples had significantly higher symptom severities. Our results suggest that mixed infection and synergism between CMGs, could be an important feature in the yield reduction of cassava plants in CAR, similar to the other severe CMD epidemics reported in East Africa.     

Germplasm Enhancement and Breeding Strategies for Crop Quality in Japan

Abstract

Rice is the staple food for most Asians. Breeding efforts at the national and international levels have resulted in high-yielding varieties with resistance/tolerance to biotic and abiotic constraints. Consequently Asia has enjoyed rice self-sufficiency in recent years. Now in some countries over-production of rice has occurred, partly because of reduced rice consumption. For instance, in 1962 Japan had a per capita rice consumption of 118.3 kg and then this rapidly declined to about 60kg in 2003. Imbalances between production and consumption in rice and other crops have promoted a paradigm shift of breeding objectives oriented from producers to consumers. Germplasm enhancement (pre-breeding) and breeding strategies now focus on a broad range of crop and food qualities, which are closely associated with industrial and processing properties and human health and nutrition. In particular, physiological functions of chemical compounds involved in crop products are being studied as a part of breeding programs. Diverse plant genetic resources and advances in plant genome research have contributed to successful breeding strategies to improve and manage crop and food quality. Recent progress in germplasm enhancement and breeding strategies for quality improvement of rice, wheat, soybean and sweet potato in Japan is discussed.     

High-Quality de novo Genome Assembly of Huajingxian 74, a Receptor Parent of Single Segment Substitution Lines

Rice(Oryza sativa L.)is grown nearly worldwide and provides the staple food for more than half of the global population(Luo et al,2017).The genomes of several cultivated rice varieties including Nipponbare(NPB)(Kawahara et al,2013;Sakai et al,2013),IR64(Tanaka et al,2020),93-11(Zhang et al,2018)and R498(Du et al,2017)at chromosome level,and Minghui 63 and Zhenshan 97(Zhang et al,2016)at scaffold level have been assembled,annotated and released,among which the R498 and NPB genomes are widely used as reference genomes in rice research.However,there are thousands of rice cultivars,landraces and wild rice varieties in the world with dramatically different genetic backgrounds,and the genomes of native rice varieties in South China,which is one of the major rice production areas in China,have not been de novo assembled.Huajingxian 74(HJX74)is an indica rice variety bred in South China Agricultural University,Guangdong Province with widely environmental adaptability and high yield(www.ricedata.cn/variety/varis/602548.htm).HJX74 exhibits significant phenotypic and genetic differences from those varieties whose whole genomes have been properly sequenced and assembled(Fig.1).     

水稻镉积累影响因素与低镉稻米生产策略

镉是一种生物毒性极强且分布广泛的重金属元素.农田中的镉不仅影响作物的生长发育,而且可通过食物链进入人体内,当富集到一定程度会危害人体健康.水稻是我国重要的粮食作物之一,在保障我国粮食安全中的地位举足轻重,但水稻同时也是对镉吸收和积累最强的大宗谷类作物之一.近些年"镉大米"事件在我国频繁发生,稻米镉污染已成为一个备受社会...