Seed-Mediated Gene Flow Promotes Genetic Diversity of Weedy Rice within Populations: Implications for Weed Management

Increased infestation of weedy rice—a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (Oryza sativa) worldwide. Knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. To generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from Sri Lanka based on 23 selected microsatellite (SSR) loci. Results indicated an exceptionally high level of within-population genetic diversity (H_e = 0.62) and limited among-population differentiation (F_st = 0.17) for this predominantly self-pollinating weed. UPGMA analysis showed a loose genetic affinity of the weedy rice populations in relation to their geographical locations, and no obvious genetic structure among populations across the country. This phenomenon was associated with the considerable amount of gene flow between populations. Limited admixture from STRUCTURE analyses suggested a very low level of hybridization (pollen-mediated gene flow) between populations. The abundant within-population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seed-mediated gene flow of weedy rice along with the long-distance exchange of farmer-saved rice seeds between weedy-rice contaminated regions in Sri Lanka. In addition to other effective weed management strategies, promoting the application of certified rice seeds with no weedy rice contamination should be the immediate action to significantly reduce the proliferation and infestation of this weed in rice ecosystems in countries with similar rice farming styles as in Sri Lanka.     

Focus on Weed Control: Herbicides as Weed Control Agents: State of the Art: I. Weed Control Research and Safener Technology: The Path to Modern Agriculture

The purpose of modern industrial herbicides is to control weeds. The species of weeds that plague crops today are a consequence of the historical past, being related to the history of the evolution of crops and farming practices. Chemical weed control began over a century ago with inorganic compounds and transitioned to the age of organic herbicides. Targeted herbicide research has created a steady stream of successful products. However, safeners have proven to be more difficult to find. Once found, the mode of action of the safener must be determined, partly to help in the discovery of further compounds within the same class. However, mounting regulatory and economic pressure has changed the industry completely, making it harder to find a successful herbicide. Herbicide resistance has also become a major problem, increasing the difficulty of controlling weeds. As a result, the development of new molecules has become a rare event today.Modern industrial herbicide research begins with the analysis and definition of research objectives. A major part of this lies in the definition of economically important weeds in major arable crops (Kraehmer, 2012). Weed associations change slowly over time. It is important, therefore, to foresee such changes. Today’s weed associations result from events in the distant past. They are associated with the history of crops and the evolution of farm management. In Europe and the Americas, some large-acre crops such as winter oilseed rape and spring oilseed rape (canola), both derived from Brassica spp., and soybean (Glycine max) have attained their current importance only within the last 100 years. Other Old World crops, such as cereals, have expanded over a very long time span and were already rather widespread in Neolithic times (Zohary et al., 2012). The dominance of crop species in agricultural habitats only left room for weed species that could adapt to cultivation technologies. Changes in crop management and the global weed infestation have happened in waves. A major early factor in Europe was presumably the grain trade in the Roman period (Erdkamp, 2005). The Romans spread their preferred crops and, unintentionally, associated weed seeds throughout Europe, Asia, and Africa. A second wave of global vegetation change started in the 16th century after the discovery of the Americas. Crops and weeds were distributed globally by agronomists and botanists. Alien species started to spread on all continents. A third phase can be seen in the 19th century with the industrialization of agriculture and the breeding of competitive crop varieties. The analysis of weed spectra in arable fields grew from this historical background. Weeds are plants interfering with the interests of people (Kraehmer and Baur, 2013), which is why they have been controlled by farmers for millennia.Chemical weed control began just about a century ago with a few inorganic compounds, such as sulfuric acid, copper salts, and sodium chlorate (Cremlyn, 1991). The herbicidal activity of 2,4-dichlorophenoxyacetic acid was detected in the 1940s (Troyer, 2001). Büchel et al. (1977) and Cremlyn (1991), Worthington and Hance (1991). Targeted herbicide research began in the 1950s. In the early days, herbicide candidates progressed from screens purely on the basis of their having biology that would satisfy farmers’ requirements. Mode of action (MoA) studies did not play a major role in the chemical industry prior to the 1970s. Analytical tools were developed and the rapid elucidation of plant pathways and in vitro-based screen assays were used from the 1980s onward. However, in the 1990s and beyond, ever-increasing regulatory and economic pressures have changed the situation of the industry completely, and to satisfy the new requirements, selection criteria beyond biological activity have needed to be applied. Herbicide resistance in weeds has developed into a more serious problem that now constrains the application of certain types of herbicides in some markets. Finally, the introduction of crops resistant to cheap herbicides and of glyphosate-resistant soybean, in particular, took value out of the market and resulted in an enormous economic pressure on the herbicide-producing industry. As a result of this changing and more difficult landscape, the development of new molecules is now a rare event.

Table I.

History of chemical weed control innovationsPost, Postemergence application; Pre, preemergence application, based on data from Cremlyn (1991), Worthington and Hance (1991), Büchel et al. (1977), Herbicide Resistance Action Committee (www.hracglobal.com), and others.

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

Focus on Weed Control: Natural Compounds as Next-Generation Herbicides

Herbicides with new modes of action (MOAs) are badly needed due to the rapidly evolving resistance to commercial herbicides, but a new MOA has not been introduced in over 20 years. The greatest pest management challenge for organic agriculture is the lack of effective natural product herbicides. The structural diversity and evolved biological activity of natural phytotoxins offer opportunities for the development of both directly used natural compounds and synthetic herbicides with new target sites based on the structures of natural phytotoxins. Natural phytotoxins are also a source for the discovery of new herbicide target sites that can serve as the focus of traditional herbicide discovery efforts. There are many examples of strong natural phytotoxins with MOAs other than those used by commercial herbicides, which indicates that there are molecular targets of herbicides that can be added to the current repertoire of commercial herbicide MOAs.The evolutionary forces driving the survival of species include chemical interactions between organisms, which function in positive interactions such as mutualistic and symbiotic relationships and negative interactions such as competitive and parasitic relationships. These processes have led to the emergence of novel secondary metabolic pathways (often through gene duplication), producing a vast array of structurally diverse and biologically active molecules (Moore and Purugganan, 2005; Ober, 2005; Flagel and Wendel, 2009; Jiang et al., 2013). This evolutionary process is similar to a high-throughput screen. However, unlike conventional in vitro screens, which test many compounds on a single biochemical target over a very short period of time, this natural high-throughput process selects molecules based on their whole-organism activities, involving numerous chemical interactions between countless organisms and target sites over millions of years. To date, approximately 200,000 secondary metabolites have been identified (Tulp and Bohlin, 2005), with many more expected to be discovered. Few of these compounds have been examined for phytotoxicity, and the modes or mechanisms of action (MOAs) of even fewer known phytotoxins have been elucidated.The negative chemical interactions between organisms are often characterized using anthropomorphic language, such as chemical warfare, referring to the production of phytotoxins used by plant pathogens to invade their host plants (Maor and Shirasu, 2005), and the novel weapons hypothesis, which is associated with the chemical-based advantage of some invasive plant species over native plant populations (Callaway and Aschehoug, 2000; Callaway and Ridenour, 2004; Callaway and Maron, 2006; Cappuccino and Arnason, 2006; Callaway et al., 2008). While simplistic, this terminology illustrates how these toxin-based interactions exploit biochemical weaknesses between an organism and its host or enemy/competitor to enhance its own survival (Verhoeven et al., 2009). In fact, these interactions can even be multitrophic, such as when exotic plants enhance their invasiveness by promoting the growth of certain native soil pathogens noxious to native plants (Mangla et al., 2008; Barto et al., 2011).As humans evolved from a nomadic hunter-gatherer subsistence existence to an agricultural lifestyle, they learned to utilize certain biologically active secondary metabolites to manage agricultural pests. Indeed, the concept that nature is an excellent source of natural pesticides is captured in the following ancient Lithica poem (circa 400 B.C.): “All the pests that out of earth arise, the earth itself the antidote supplies” (Ibn et al., 1781). Less than a century later, Greek and Roman treatises described practices to control agricultural pests that include the use of essential oils. Similar documents are found in Chinese literature, such as a survey describing plant species used to control plant pests (Yang and Tang, 1988). The mid-20th century ushered in the use of synthetic pesticides, which have revolutionized agriculture. Like pharmaceuticals (Harvey, 1999, 2008; Newman and Cragg, 2012), many pesticides are based on natural compounds. However, natural products have not played a major role in herbicide discovery (Copping and Duke, 2007; Hüter, 2011).     

Population Structure of Peronospora effusa in the Southwestern United States

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales.     

Modeling Spruce Budworm Population Revisited: Impact of Physiological Structure on Outbreak Control

Understanding the dynamics of spruce budworm population is very important for the protection of spruce and balsam fir trees of North American forests, and a full understanding of the dynamics requires careful consideration of the individual physiological structures that is essential for outbreak control. A model as a delay differential equation is derived from structured population system, and is validated by comparing simulation results with real data from the Green River area of New Brunswick (Canada) and with the periodic outbreaks widely observed. Analysis of the equilibrium stability and examination of the amplitudes and frequencies of periodic oscillations are conducted, and the effect of budworm control strategies such as mature population control, immature population control and predation by birds are assessed. Analysis and simulation results suggest that killing only budworm larvae might not be enough for the long-term control of the budworm population. Since the time required for development during the inactive stage (from egg to second instar caterpillar) causes periodic outbreak, a strategy of reducing budworms in the inactive stage, such as removing egg biomass, should also be implemented for successful control.     

Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

Plant Molecular Biology Reporter - Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant...     

东北地区杂草稻与栽培稻的遗传多样性及籼粳分化

利用88对籼粳特异性分子标记对收集于我国东北三省的35份杂草稻和36份栽培稻遗传基础及籼粳分化进行研究,结果表明上述标记能够高效地鉴别稻属资源的籼粳属性,共检测到156个等位基因,平均有效等位基因(Na)为1.773。遗传多样性分析表明,东北地区杂草稻多样性水平略高于当地栽培稻,其中杂草稻的等位基因数(Na)、杂合度(He)、基因多样性(Hsk)以及多态性信息含量(PIC)分别为1.659、0.006、0.076和0.085,而东北栽培稻分别为1.557、0.004、0.060和0.067。遗传结构和聚类分析结果表明,东北地区杂草稻与栽培稻具有较近的亲缘关系,均存在一定程度的籼粳分化。进一步对籼粳血缘进行相对量化分析发现,杂草稻的籼型基因型频率(F_i=0.050)略高于当地栽培稻(F_i=0.043)。东北三省籼型基因型频率变化趋势为:辽宁杂草稻(0.062)辽宁栽培稻(0.058)吉林栽培稻(0.048)黑龙江杂草稻(0.041)吉林杂草稻(0.024)黑龙江栽培稻(0.020)。     

Focus on Weed Control: Indaziflam Herbicidal Action: A Potent Cellulose Biosynthesis Inhibitor

Cellulose biosynthesis is a common feature of land plants. Therefore, cellulose biosynthesis inhibitors (CBIs) have a potentially broad-acting herbicidal mode of action and are also useful tools in decoding fundamental aspects of cellulose biosynthesis. Here, we characterize the herbicide indaziflam as a CBI and provide insight into its inhibitory mechanism. Indaziflam-treated seedlings exhibited the CBI-like symptomologies of radial swelling and ectopic lignification. Furthermore, indaziflam inhibited the production of cellulose within <1 h of treatment and in a dose-dependent manner. Unlike the CBI isoxaben, indaziflam had strong CBI activity in both a monocotylonous plant (Poa annua) and a dicotyledonous plant (Arabidopsis [Arabidopsis thaliana]). Arabidopsis mutants resistant to known CBIs isoxaben or quinoxyphen were not cross resistant to indaziflam, suggesting a different molecular target for indaziflam. To explore this further, we monitored the distribution and mobility of fluorescently labeled CELLULOSE SYNTHASE A (CESA) proteins in living cells of Arabidopsis during indaziflam exposure. Indaziflam caused a reduction in the velocity of YELLOW FLUORESCENT PROTEIN:CESA6 particles at the plasma membrane focal plane compared with controls. Microtubule morphology and motility were not altered after indaziflam treatment. In the hypocotyl expansion zone, indaziflam caused an atypical increase in the density of plasma membrane-localized CESA particles. Interestingly, this was accompanied by a cellulose synthase interacting1-independent reduction in the normal coincidence rate between microtubules and CESA particles. As a CBI, for which there is little evidence of evolved weed resistance, indaziflam represents an important addition to the action mechanisms available for weed management.Cellulose is a composite polymer of β-1,4-linked glucan chains and is the main load-bearing structure of plant cell walls (Jarvis, 2013). Although cellulose is a relatively simple polysaccharide molecule, its synthesis is quite complex. The principle catalytic unit is a plasma membrane (PM)-localized protein complex referred to as the cellulose synthase complex (CSC; Davis, 2012). In plants, the CSC, visualized with freeze fracture microscopy, is a solitary, hexagonal rosette-shaped complex (Herth and Weber, 1984; Delmer, 1999) and at least three of the catalytic CELLULOSE SYNTHASE A (CESA) proteins are required in each CSC for the production of cellulose (Desprez et al., 2007; Persson et al., 2007). In addition to CESAs, several accessory proteins have been discovered to be necessary for the production and deposition of cellulose, such as KORRIGAN (Lane et al., 2001), COBRA (Roudier et al., 2005) and CELLULOSE SYNTHASE INTERACTING1 (CSI1; Gu et al., 2010), as well as several others that are yet to be identified. The loss of function in any of the aforementioned proteins causes complete or partial loss of anisotropic growth in cells undergoing expansion, resulting in radial swelling. Severe radial swelling in rapidly expanding tissue is also a common symptomology observed in seedlings treated with cellulose biosynthesis inhibitors (CBIs). Therefore, numerous potential herbicidal targets exist (mechanisms of action) for the broad group of known CBIs.Classification of an herbicide to the CBI designation was traditionally achieved by short-term [¹⁴C]radioisotope tracer studies focused on the incorporation of Glc into cellulose (Heim et al., 1990; Sabba and Vaughn, 1999). More recently, time-lapse confocal microscopy of reporter-tagged CESA proteins (Paredez et al., 2006) has been used to further classify CBIs. CBIs can be classified into at least three primary groups based on how treatment disrupts the normal tracking and localization of fluorescently labeled CESAs (for review, see Brabham and DeBolt, 2012). The disruption is, it can be assumed, the result of the inhibitory mechanism of the CBI. In the first group, isoxaben and numerous other compounds cause YELLOW FLUORESCENT PROTEIN YFP):CESAs to be depleted from the PM and concomitantly accumulate in cytosolic vesicles (called small CESA compartments or microtubule-associated cellulose synthase compartments; Paredez et al., 2006; Crowell et al., 2009; Gutierrez et al., 2009) The second group, consisting only of dichlobenil (DCB), causes YFP:CESAs to become immobilized and hyperaccumulated at distinct foci in the PM (Herth, 1987; DeBolt et al., 2007b). The third group influences CSC-microtubule (MT)-associated functions resulting in errant movement and localization of YFP:CESAs (DeBolt et al., 2007a; Yoneda et al., 2007). These different disruption processes suggest that each CBI group targets a different aspect of the complex cellulose biosynthetic process.A lack of evolved weed resistance in the field suggests that CBIs are potentially underutilized tools for weed control (Sabba and Vaughn, 1999; Heap, 2014). CBIs have also been useful research tools in decoding fundamental aspects of cellulose biosynthesis. An exogenous application of a CBI provides spatial and temporal inhibition of cellulose. Resistance screens to CBIs have uncovered key genes in cellulose biosynthesis (Scheible et al., 2001; Desprez et al., 2002). Furthermore, CBIs such as isoxaben have also been effective in linking accessory proteins with CESAs in the CSC (Robert et al., 2005; Gu et al., 2010). Therefore, it is important to extend our range of CBI compounds. Indaziflam (Fig. 1A), an herbicide introduced by Bayer Crop Science, was recently proposed to be a CBI and was reported to have a photosystem II inhibition value of 9.4 (Meyer et al., 2009; Dietrich and Laber, 2012). Indaziflam is labeled for use in turf, for perennial crops, and for nonagricultural situations for preemergent control of grasses and broadleaf weeds (Meyer et al., 2009; Brosnan et al., 2011). The aim herein was to investigate indaziflam as a CBI and to characterize its inhibitory effect on cellulose biosynthesis.Open in a separate windowFigure 1.Indaziflam is a fluoroalkytriazine-containing compound that inhibits elongation in seedlings of P. annua and Arabidopsis. A, Chemical structure of indaziflam. B to D, Images of 7-d-old seedlings treated with increasing concentrations of indaziflam. B shows light-grown P. annua seedlings (indaziflam concentrations from left to right are 0, 100, 250, 500, 1,000, 5,000, and 10,000 pm). C and D show light-grown and dark-grown Arabidopsis seedlings, respectively (indaziflam concentrations from left to right are 0, 100, 250, 500, 1,000, and 2,500 pm). Indaziflam treatment induced swollen cells. E, Representative images of the primary root of P. annua grown in plates for 4 d with and without 10 nm indaziflam. F, Transgenic Arabidopsis seedlings expressing GFP:PIP2 were examined by laser scanning confocal microscopy and images represent visualization of the primary root grown vertically for 7-d plates without and with 250 pm indaziflam. PIP2, Plasma membrane intrinsic protein2. Bar = 10 mm in B, 5 mm in C and D, 2 mm in E, and 50 μm in F.     

宁夏杂草稻的遗传多样性及其亲缘关系分析

以宁夏杂草稻、选育品种、地方品种共143份水稻种质为试验材料,进行主要农艺性状的的表型鉴定评价,并利用24对SSR引物进行不同类型水稻种质的遗传多样性比较、遗传相似性和聚类分析。表型评价表明,宁夏杂草稻表现为矮秆和早熟,表型变异范围较大;多数杂草稻种皮呈红色,颖壳呈秆黄色,均落粒。SSR标记分析结果,共检测到141个等位基因,每个位点等位基因数目变异在3~11个,平均为5.8333个;Nei's基因多样性指数变幅为0.2241~0.8065,平均为0.5219。杂草稻种质的等位基因数、有效等位基因数、Shannon指数均高于选育品种和地方品种。在不同来源杂草稻群体中,来自吴忠和永宁东河的杂草稻Nei's基因多样性指数最高,分别为0.4912和0.4814,而来自青铜峡的杂草稻Nei's基因多样性指数最低,为0.2802。相似性分析表明,杂草稻与地方品种高度相似,相似系数高达0.9585,而杂草稻与选育品种的相似性较低,其相似系数为0.4584;选育品种与地方品种的相似系数只有0.3560。聚类分析表明,参试材料分为3个类群,其中选育品种单独聚类于第Ⅰ类群,其遗传背景明显区别于杂草稻和地方品种;第Ⅱ类包括大部分杂草稻和地方品种,不同来源杂草稻及地方品种间分布比较均匀;第Ⅲ类是由小部分杂草稻和地方品种组成。宁夏杂草稻的分布没有明显的区域性,宁夏杂草稻与地方品种高度融合且遗传相似性很高。     

基于分型测序技术的粒用高粱遗传多样性和群体结构分析

了解粒用高粱的遗传多样性和群体结构,能有效提高粒用高粱新品种的选育效率。本研究利用基因分型测序技术(GBS,genotyping by sequencing)对120份粒用高粱材料开展了全基因组基因分型,共获得了3456个多态性的SNP标记,其多态性信息含量指数(PIC,polymorphism information content)介于0.013～0.574之间,平均值为0.381。根据SNP标记在120份高粱材料中的基因分型数据,计算了材料间的遗传距离,其变异范围为0.084～0.613,平均遗传距离为0.365。群体进化树分析和主成分分析都将120份高粱材料划分为3个类群,类群1主要由包括美国材料MN-3609在内的亲缘关系较远的高粱材料组成,类群2主要由中国北方的高粱材料组成,类群3主要由中国南方的高粱材料组成。群体结构分析表明,当K=3时,ΔK取得最大值,说明120份高粱材料可以划分为3个类群,其划分结果与群体进化树分析和主成分分析基本一致。本研究从基因型多样性水平上阐释了粒用高粱的遗传背景和群体结构,为中国粒用高粱新品种的选育提供了理论依据。     

Focus on Weed Control: A Novel Rice Cytochrome P450 Gene,CYP72A31, Confers Tolerance to Acetolactate Synthase-Inhibiting Herbicides in Rice and Arabidopsis

Target-site and non-target-site herbicide tolerance are caused by the prevention of herbicide binding to the target enzyme and the reduction to a nonlethal dose of herbicide reaching the target enzyme, respectively. There is little information on the molecular mechanisms involved in non-target-site herbicide tolerance, although it poses the greater threat in the evolution of herbicide-resistant weeds and could potentially be useful for the production of herbicide-tolerant crops because it is often involved in tolerance to multiherbicides. Bispyribac sodium (BS) is an herbicide that inhibits the activity of acetolactate synthase. Rice (Oryza sativa) of the indica variety show BS tolerance, while japonica rice varieties are BS sensitive. Map-based cloning and complementation tests revealed that a novel cytochrome P450 monooxygenase, CYP72A31, is involved in BS tolerance. Interestingly, BS tolerance was correlated with CYP72A31 messenger RNA levels in transgenic plants of rice and Arabidopsis (Arabidopsis thaliana). Moreover, Arabidopsis overexpressing CYP72A31 showed tolerance to bensulfuron-methyl (BSM), which belongs to a different class of acetolactate synthase-inhibiting herbicides, suggesting that CYP72A31 can metabolize BS and BSM to a compound with reduced phytotoxicity. On the other hand, we showed that the cytochrome P450 monooxygenase CYP81A6, which has been reported to confer BSM tolerance, is barely involved, if at all, in BS tolerance, suggesting that the CYP72A31 enzyme has different herbicide specificities compared with CYP81A6. Thus, the CYP72A31 gene is a potentially useful genetic resource in the fields of weed control, herbicide development, and molecular breeding in a broad range of crop species.The mechanism of herbicide tolerance can be classified roughly into two groups: target-site and non-target-site herbicide tolerance (Powles and Yu, 2010). Target-site herbicide tolerance is caused by the prevention of herbicide binding to the target enzyme, caused by point mutations occurring in the latter. It is relatively easy to elucidate the molecular mechanisms of target-site herbicide tolerance, because it is regulated mostly by a single gene encoding a target enzyme harboring point mutations. On the other hand, non-target-site herbicide tolerance is caused by reduction to a nonlethal dose of herbicide reaching the target enzyme, caused by mechanisms such as activation of herbicide detoxification, decrease of herbicide penetration, and herbicide compartmentation in plant cells (Yuan et al., 2007). Among these mechanisms, the oxidization of herbicides by endogenous cytochrome P450 monooxygenase is thought to be a major pathway in plants (Werck-Reichhart et al., 2000; Siminszky, 2006; Powles and Yu, 2010). From the point of view of weed control, non-target-site herbicide tolerance is a greater threat to crop production and in the evolution of herbicide-resistant weeds, because it is often involved in resistance to multiherbicides that inhibit different target proteins, including never-used and potential plant growth regulators (Yuan et al., 2007; Powles and Yu, 2010). Conversely, it is expected that multiherbicide-tolerant crops could be produced easily by the application of non-target-site herbicide tolerance. Moreover, information gained from study of the molecular mechanisms of non-target-site herbicide tolerance can be applied to the research and development of novel herbicides and plant growth regulators.Acetolactate synthase (ALS; also known as acetohydroxy acid synthase) plays a key role in the biosynthesis of branched-chain amino acids such as Val, Leu, and Ile in many organisms. ALS is the primary target site for at least four classes of herbicides: sulfonylurea, imidazolinone, pyrimidinyl carboxylates, and triazolopyrimidine herbicides (Shimizu et al., 2002, 2005). These herbicides can inhibit ALS activity, resulting in plant death caused by a deficiency of branched-chain amino acids. ALS-inhibiting herbicides control many weed species in addition to exhibiting high selectivity in major crops and low toxicity to mammals, which lack the branched-chain amino acid biosynthetic pathway. However, various mutations in ALS that confer ALS-inhibiting herbicide tolerance have been found in many weeds (Shimizu et al., 2005; Powles and Yu, 2010). Similar mutations in ALS have also been reported in crops (Shimizu et al., 2005). To date, crops that show tolerance to ALS-inhibiting herbicides have been produced by various approaches, such as conventional mutation breeding, conventional transformation, and pinpoint mutagenesis via gene targeting based on information obtained from analyses of ALS mutants (Shimizu et al., 2005; Endo and Toki, 2013). On the other hand, weeds that show tolerance to ALS-inhibiting herbicides by cytochrome P450-mediated detoxification have also been reported (Powles and Yu, 2010). However, compared with target-site herbicide tolerance, little is known of the molecular mechanism of herbicide metabolism mediated by cytochrome P450. In rice (Oryza sativa), an herbicide-sensitive mutant has been produced by γ-ray irradiation (Zhang et al., 2002). This mutant showed 60-fold higher sensitivity to bensulfuron-methyl (BSM), a sulfonylurea herbicide, compared with wild-type rice (Pan et al., 2006). Genetic mapping and complementation tests revealed that a cytochrome P450, CYP81A6, is involved in BSM tolerance (Pan et al., 2006). As far as we know, this is the only example of the isolation and characterization of a cytochrome P450 gene involved in nontarget herbicide tolerance in rice.Bispyribac sodium (BS), a pyrimidinyl carboxylate herbicide, is effective in controlling many annual and perennial weeds, with excellent selectivity on direct-seeded rice (Shimizu et al., 2002). Recently, it was reported that japonica rice varieties show higher sensitivity to BS compared with indica rice varieties at the early stages of plant growth (Ohno et al., 2008; Taniguchi et al., 2010). A mutated ALS gene confers BS tolerance in plants including rice (Shimizu et al., 2005; Endo and Toki, 2013). However, the deduced amino acid sequences were shown to be highly conserved among japonica and indica rice varieties, and ALS levels of sensitivity to BS were similar in japonica and indica rice varieties (Taniguchi et al., 2010). These results suggest the possibility that indica rice varieties might show higher tolerance to BS due to the acquisition of nontarget herbicide tolerance.In this study, we isolated and characterized a novel cytochrome P450 gene, CYP72A31, involved in BS tolerance in rice. We also demonstrated that overexpression of CYP72A31 confers tolerance to ALS-inhibiting herbicides, including BS and BSM, in Arabidopsis (Arabidopsis thaliana).     

Population Structure and Genetic Diversity in Popular Rice Varieties of India as Evidenced from SSR Analysis

We report here on the phylogenetic analysis, population substructure, and identification of molecular tags of 25 popular rice varieties and four landraces from different ecological belts of India employing a set of 52 simple sequence repeat (SSR) markers. Genetic analysis using the SSR markers categorized the genotypes into two major clusters, distributed according to their pedigree. Population structure analysis suggested that the optimum number of subpopulations was three (K?=?3) in the popular varieties and landraces. At K?=?5 the allelic distribution was much more similar to the phylogenetic dendrogram. The molecular diversity and population structure analysis indicated that there is not much variation among the popular rice cultivars of India. The study has identified SSR markers producing unique alleles, which should aid in the precise identification, maintenance, and genetic purity analysis of rice varieties.     

稻田蜘蛛优势种对飞虱对叶蝉控制力的分析

系统调查结果表明,长沙地区早稻田中,蜘蛛优势种相对稳定,在水稻各生育期内均为拟水狼蛛和食虫沟瘤蛛,并无更替现象,采用灰色关联分析法,研究了长沙地区稻田蜘蛛优势种群对飞虱,叶蝉种群数量的控制程度,结果表明拟水狼蛛和食品沟瘤蛛对飞 虱,叶蝉种 数量影响最大,其次为锥腹肖蛸和八斑鞘腹蛛,当拟水狼蛛与飞虱之比为1：20．2,食虫沟瘤蛛与飞虱之比为1：14．5以上时,蜘蛛对飞虱显示出明显的控制力。     

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.