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)。     

杂草稻叶绿体籼粳分化的多重PCR分析

通过分析籼稻93-11和粳稻培矮64S的叶绿体全基因组,优化和构建了籼粳分化的叶绿体分子标记ORF100和ORF29-TrnC^GCA的多重PCR。应用这个多重PCR对200余份世界各地杂草稻和其它水稻材料进行分析。结果表明:杂草稻中有明显的叶绿体籼粳分化,表现出明显的地域性,且与传统的中国栽培稻的南籼北粳能较好的对应。推测粳型杂草稻可能是栽培稻突变或粳型水稻(作母本)与其它类型水稻材料杂交而形成的。     

杂草稻落粒粳的抗逆境特性研究

杂草稻落粒粳（Oryza sativa）发生在我国辽宁丹东.落粒粳植株明显高于当地大多数栽培品种,颖果呈中长型,成熟后容易掉粒;果壳稻草色或黄间黑灰色,小穗无芒或有芒,芒长4～12 cm;颖果千粒重235 g,种皮桔红色.落粒粳种子在13～38 ℃条件下的发芽率均大于88%,水层2.5～10 cm处理,落粒粳植株干重减少50%～69%.在幼苗期,落粒粳对无芒稗的各项影响因子均明显大于化感潜力品种I-kung-pao,表明落粒粳无化感作用.落粒粳可以忍耐0.5%的盐碱.     

籼粳稻杂交后代的剑叶气孔性状与亚种特性的关系

水稻品种‘秋光’和‘七山占’的杂交后代F9群体,用TM1000台式扫描电镜观察水稻剑叶气孔各种性状的结果表明：籼粳杂交后代剑叶的气孔性状间变化规律不同,背部气孔密度大于腹部,背部气孔长度小于腹部,而气孔宽度则是背部大于腹部。杂交后代按照程氏指数分为籼稻、偏籼稻、偏粳稻、粳稻4种类型,它们的叶片背部气孔密度大小依次为粳型〉偏籼型〉偏粳型〉籼型;腹部和背部气孔密度的变化规律相一致。背部气孔长度依次为偏粳型〉偏籼型〉籼型〉粳型;腹部气孔长度变化为籼型〉偏粳型〉偏籼型〉粳型;背部气孔宽度变化为粳型〉偏粳型〉偏籼型〉籼型;腹部气孔宽度变化为偏粳型〉偏籼型〉粳型〉籼型。     

普通野生稻和亚洲栽培稻线粒体DNA的RFPL分析

通过７个探针、１７种内切酶探针组合对１１８份普通野生稻和７６份亚洲栽培稻的线粒体ＤＮＡ（ｍｔＤＮＡ）ＲＦＬＰ分析表明,籼粳分化是亚洲栽培稻线粒体基因组分的主流,７６个栽培稻中,３６个品种ｍｔＤＮＡ为籼型,４０个品种ｍｔＤＮＡ为粳型。普通野生稻ｍｔＤＮＡ以籼型为主（８６份）,粳型较少（７份）,１份类型难以确定,还有２４份没有籼粳分化。     

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。     

普通野生稻和亚洲栽培稻线粒体DNA的RFLP分析

通过７个探针、１７种内切酶探针组合对１１８份普通野生稻和７６份亚洲栽培稻的线粒体ＤＮＡ（ｍｔＤＮＡ）ＲＦＬＰ分析表明,籼粳分化是亚洲栽培稻线粒体基因组分化的主流,７６个栽培稻中,３６个品种ｍｔＤＮＡ为籼型,４０个品种ｍｔＤＮＡ为粳型。普通野生稻ｍｔＤＮＡ以籼型为主（８６份）,粳型较少（７份）,１份类型难以确定,还有２４份没有籼粳分化。     

基于叶绿体基因多样性的中国水稻起源进化研究

针对目前亚洲栽培稻起源地和进化途径学说众多、分歧巨大的现状,本研究选择原产中国的98份亚洲栽培稻和125份普通野生稻为材料,对叶绿体中atpA序列、rps16内含子序列、trnP-rpl33间隔区、trnG-trnfM序列、trnT-trnL间隔区序列的五段高突变序列进行测序,利用生物信息学方法进行比对分析,绘制Network网络图,构建系统发育树。结果表明,普通野生稻的Indel和SNP数目均比亚洲栽培稻多,序列多样性丰富;基于单倍型的Network网络图和系统发育树可将所有参试材料归为3个类群,类群I主要为粳稻与普通野生稻,类群II主要为籼稻,类群III主要为普通野生稻,而类群II和类群III亲缘关系较近,提示粳、籼两个亚种可能由偏粳、偏籼的普通野生稻分别进化而来,支持二次起源学说;所有与亚洲栽培稻亲缘关系较近的普通野生稻均来源于华南地区,支持华南地区为我国亚洲栽培稻起源中心的论点。     

水稻亚种间杂种基因效应和性状间相关性分析

以6份籼型型不育系和6份粳型或偏粳型广亲和系配制成不完全双列杂交,将杂种F1及其亲本在三个播期（5／20,6／10,6／30）试验,应用加性、显性与环境互作摸型,分析籼粳交杂种八个主要农艺性状的遗传方差组成、杂种优势的表现以及性状间的相关性等．结果表明：1）参试性状不仅加性方差和显性方差极显著,并且加性×环境或显性×环境互作方差也显著存在;但控制不同性状的基因效应稳定性尚有明显的差异．2）基因型×环境互作效应的结果,使杂种在多数性状上其群体平均优势和群体超亲优势均随播种推迟而呈下降的趋势;F1性状的平均基因型预测值显示了早播常出现植株偏高、剑叶较披和生育期相对延长,而迟播导致主穗总粒数减少3）性状间的加性和显性相关是决定遗传相关的主要因素;在株高、抽穗天数、剑叶长、主穗长和主穗总粒数等五个性状间,杂种的表型相关和遗传相关与遗传相关的四种分量间方向相同,均为显著正相关,所以要选育大穗高产的杂交组合及其配组材料,都应保证适宜的株高、生育期和剑叶长.     

漳浦野生稻表型遗传多样性分析及稻瘟病抗性评价

本研究对45份漳浦野生稻的43个表型性状进行遗传多样性、相关性和聚类分析,并采用田间病区诱发和室内接种鉴定两种方法进行苗期稻瘟病抗性鉴定评价。结果表明:(1)漳浦野生稻具有丰富的遗传多样性。31个质量性状中有22个性状出现不同程度的遗传分化,其遗传多样性指数范围为0.24～1.43,其中叶色的遗传多样性指数最高;12个数量性状的遗传多样性指数范围为1.83～2.09,其中花药长度的遗传多样性指数最高,表明该性状遗传多样性最丰富,可作为特异性资源利用。(2)12个数量性状间的相关性分析表明穗长与剑叶叶舌长、倒二叶叶舌长、剑叶长、剑叶宽、芒长呈极显著正相关;百粒重与芒长、谷粒长呈极显著和显著正相关。(3)45份漳浦野生稻可聚类为5个类群,其中第Ⅲ类群和第Ⅴ类群均仅有1份材料,分别是M2005和M1001。(4)通过2年的苗期稻瘟病抗性的鉴定,田间病区诱发鉴定筛选出抗的材料3份,中抗的材料5份;室内接种鉴定筛选出中抗的材料仅1份;其中材料M1030在田间病区诱发和室内接种的初鉴和复鉴中均表现为中抗。     

Microsatellite markers reveal multiple origins for Italian weedy rice

Weedy rice (Oryza sativa L.) is one of the major issues of rice cultivation worldwide. In Italy, it infests about 70% of the total rice area. Different Weedy Rice populations can be distinguished based on variable morphological and physiological traits; however, little is known about genetic differentiation and origin of Italian weedy rice populations. The objective of this study was to genetically and morphologically characterize and compare different Italian weedy rice populations selected on the basis of different phenotypes. The main Italian rice territory was divided into 10 geographical areas in which 40 weedy rice populations were collected and grouped according to the awn traits. All the individuals of the populations were morphologically characterized according to plant and seed traits. Genetic characterization was performed using 19 SSR markers on all the collected accessions, and several rice cultivars, including some very old (late 19th century), nowadays are no longer cultivated. ANOVA showed that morphological plant and seed traits were significantly affected by the collection area and awnedness group. The importance of the awn morphology was also reflected in the Bayesian clustering where, despite a relatively low genetic diversity, the clusters displayed different awn types. An UPGMA dendrogram confirmed the clusters detected in STRUCTURE analysis and also revealed a grouping of certain old cultivars with the weedy rice, suggesting a common origin.     

Better performance of germination in hyperosmotic solutions in conspecific weedy rice than cultivated rice

Weeds and crops that grow together often confront similar types of environmental stress, especially drought stress. Weedy rice (Oryza sativa f. spontanea) and cultivated rice (O. sativa L.) provide a unique pair consisting of a weed and a conspecific model crop that can be used to study the drought tolerance of plants across a large distributional range. The investigation on weedy rice's damage to paddy fields showed that it was more serious in dry direct seeding than water direct seeding. Compared with water direct seeding, the seeds of cultivated rice and weedy rice in dry direct seeding will absorb water and germinate under the condition of insufficient soil moisture. Our hypothesis is that weedy rice seeds have evolved stronger germination ability than coexisting cultivated rice under water stress, so that they can obtain more growth space in the early stage in dry direct seeding and thus obtain higher fitness. Seeds of weedy rice populations and coexisting rice cultivars were collected from 61 sites across China and were germinated with 20% polyethylene glycol‐6000 to simulate drought stress. Two drought response indices, which assessed germination rate and germination index, plus one germination stress tolerance index, indicated significantly greater drought tolerance in weedy rice populations than in coexisting rice cultivars (P < 0.01). Drought tolerance for the three indexes were indica weedy rice > indica rice cultivars, japonica weedy rice > japonica rice cultivars, and indica weedy rice > japonica rice cultivars. These results indicate that weedy rice populations show stronger drought stress tolerance than coexisting rice cultivars at various sites, specifically during the seed germination period. Furthermore, Pearson's correlation found that drought response of weedy rice populations and coexisting rice cultivars were significantly different with these environmental factors: latitude, altitude, annual mean precipitation, mean annual temperature, mean precipitation in the sowing month, mean temperature in the sowing month, and sowing methods. Weedy rice shows different patterns of drought tolerance variation across geographical (latitude and altitude) and environmental (precipitation) gradients compared to coexisting rice cultivars. This study suggests that weedy rice might have evolved new drought tolerance and could provide a useful source of genetic resources for improving drought tolerance of crop cultivars and breeding direct seeded cultivars to reduce the usage of seeds in direct seeding.     

The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice

Growth-related traits, such as greater height, greater biomass, faster growth rate and early flowering, are thought to enhance competitiveness of agricultural weeds. However, weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.), displays variation for growth traits. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Through a common garden experiment, we investigated whether growth trait divergence has occurred among U.S. weeds and their putative cultivated progenitors. We also determined polymorphism patterns in the growth candidate gene, SD1, to assess its possible role in the evolution of divergent phenotypes. We found considerable growth trait variation among weed groups, suggesting that growth trait convergence is not evident among weedy populations. Phenotypic divergence of weedy rice from cultivated ancestors is most apparent for flowering time. Introgression of a chromosomal block containing the SD1 allele from tropical japonica, the predominant U.S. rice cultivar, was detected in one weedy rice population and is associated with a change in growth patterns in this group. This study demonstrates the role of introgressive hybridization in evolutionary divergence of an important weed.     

Population genomics identifies the origin and signatures of selection of Korean weedy rice

Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population‐selective or ‐adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry inference study clearly showed that the genetic distance of Korean weedy rice was far from the wild rice and near with cultivated rice. Furthermore, 537 genes showed evidence of recent positive or divergent selection, consistent with some adaptive traits. This study indicates that Korean weedy rice originated from hybridization of modern indica/indica or japonica/japonica rather than wild rice. Moreover, weedy rice is not only a notorious weed in rice fields, but also contains many untapped valuable traits or haplotypes that may be a useful genetic resource for improving cultivated rice.     

Genetic variation and possible origins of weedy rice found in California

Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene‐specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.     

Assessment of gene flow from a herbicide-resistant indica rice (Oryza sativa L.) to the Costa Rican weedy rice (Oryza sativa) in Tropical America: factors affecting hybridization rates and characterization of F1 hybrids

Herbicide-resistant rice cultivars allow selective weed control. A glufosinate indica rice has been developed locally. However, there is concern about weedy rice becoming herbicide resistant through gene flow. Therefore, assessment of gene flow from indica rice cultivars to weedy rice is crucial in Tropical America. A field trial mimicking crop–weed growing patterns was established to assess the rate of hybridization between a Costa Rican glufosinate-resistant rice line (PPT-R) and 58 weedy rice accessions belonging to six weedy rice morphotypes. The effects of overlapping anthesis, morphotype, weedy accession/PPT-R percentage, and the particular weedy accession on hybridization rates were evaluated. Weedy rice accessions with short overlapping anthesis (4–9 days) had lower average hybridization rates (0.1%) than long anthesis overlapping (10–14 days) accessions (0.3%). Hybridization also varied according to weedy rice morphotype and accession. Sativa-like morphotypes (WM-020, WM-120) hybridized more readily than intermediate (WM-023, WM-073, WM-121) and rufipogon-like (WM-329) morphotypes. No hybrids were identified in 11 of the 58 accessions analyzed, 21 accessions had hybridization rates from 0.01% to 0.09%, 21 had rates from 0.1% to 0.9%, and 5 had frequencies from 1% to 2.3%. Another field trial was established to compare the weedy rice-PPT-R F₁ hybrids with their parental lines under noncompetitive conditions. F₁ hybrids had a greater phenotypic variation. They had positive heterosis for vegetative trait and reproductive potential (number of spikelets and panicle length) traits, but negative heterosis for seed set. This study demonstrated the complexity of factors affecting hybridization rates in Tropical America and suggested that the phenotype of F₁ hybrids facilitate their identification in the rice fields.     

Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives

BACKGROUND AND AIMS: Transgene escape through gene flow from genetically modified (GM) crops to their wild relative species may potentially cause environmental biosafety problems. The aim of this study was to assess the extent of gene flow between cultivated rice and two of its close relatives under field conditions. METHODS: Experiments were conducted at two sites in Korea and China to determine gene flow from cultivated rice (Oryza sativa L.) to weedy rice (O. sativa f. spontanea) and common wild rice (O. rufipogon Griff.), respectively, under special field conditions mimicking the natural occurrence of the wild relatives in Asia. Herbicide resistance (bar) and SSR molecular finger printing were used as markers to accurately determine gene flow frequencies from cultivated rice varieties to their wild relatives. KEY RESULTS: Gene flow frequency from cultivated rice was detected as between approx. 0.011 and 0.046 % to weedy rice and between approx. 1.21 and 2.19 % to wild rice under the field conditions. CONCLUSIONS: Gene flow occurs with a noticeable frequency from cultivated rice to its weedy and wild relatives, and this might cause potential ecological consequences. It is recommended that isolation zones should be established with sufficient distances between GM rice varieties and wild rice populations to avoid potential outcrosses. Also, GM rice should not be released when it has inserted genes that can significantly enhance the ecological fitness of weedy rice in regions where weedy rice is already abundant and causing great problems.     

A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits

Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.     

杂草稻种质资源的综合评价

从韩国引入34份杂草稻种质资源,在云南生态条件下进行田间农艺性状、抗病性及品质的综合鉴定,从中筛选出6份综合性状优良或具有某种优异性状的种质,可供育种利用。     

杂草稻的研究现状与展望

杂草稻属于野生稻与栽培稻中间类型.一方面,由于杂草稻与栽培稻之间的前期形态、生理生化特性相似,很难化学控制其在稻田发生,影响水稻产量与品质;另一方面,杂草稻长期自然生长繁衍,其抗病、虫、寒、旱、盐碱等特性优于栽培稻,而且与栽培稻的亲缘关系相对接近,是一种改良栽培稻抗逆性的天然基因库.