中国普通野生稻核糖体RNA基因限制性片段长度多态性

对９８份普通野生稻、亚洲栽培稻及稻进行了核糖体ＲＮＡ基因间间隔区的限制性片段长度多态性分析。共发现３０种长度变异类型,组成４５种表现型。广西普通野生稻的ｒＤＮＡ间隔序列长度多样性最丰富,２４份材料中长度变异类型,     

中国大麦叶绿体DNA和核糖体RNA基因限制性片段长度多型性

本文报道了我们对我国不同大麦区80份大麦品种叶绿体DNA和核糖体RNA基因限制性片段长度多型性的研究。结果表明:rDNA间隔序列长度存在丰富的多样性,80份材料中出现了8种长度变异炎型共组成8种表现型。长度变异类型及其表现型在地理分布上存在着明显的区域性。推测这种分布上的地区性与植物对环境的适应性有关。所用的两个叶绿体DNA克隆片段未检测到限制性片段长度多型性,说明栽培大麦叶绿体DNA变异程度低。     

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。     

基于线粒体基因片段核苷酸多态性的亚洲栽培稻起源进化研究

亚洲栽培稻的祖先是普通野生稻,已成为世界公认的观点,然而亚洲栽培稻的2个亚种:粳稻和籼稻是一次起源还是二次起源仍存在很大争议,其起源地是国内还是国外依然是国际学者间争论的焦点。本文通过对184份亚洲栽培稻和203份普通野生稻3段基因序列cox3、cox1、orf 224和2段基因间序列ssv-39/178、rps2-trnfM的多样性研究,验证了以下观点:1)粳稻起源于中国,籼稻起源于中国和国外;2)亚洲栽培稻的起源为二次起源,即普通野生稻存在偏籼和偏粳2种类型,亚洲栽培稻的2个亚种籼稻和粳稻在进化过程中分别由偏籼型的普通野生稻和偏粳型的普通野生稻进化而来。     

野生稻基因组随机扩增多态性DNA(RAPD)分析

用18个随机引物对2份栽培稻、12份包含有六个基因组型的野生稻DNA进行了扩增,共获得147个多态性DNA片断,把这些多态性DNA片断作为遗传位点用UPGMA法计算出各材料间的遗传相似性系数,并作了聚类分析．主要结果如下：1普通野生稻同栽培稻的亲缘关系很近,其中江永普通野生稻更接近于粳稻．2．CCDD组的Oryzalatifolia和EE组的O．australiensis遗传多态性相似。3．B、C、D、E组的遗传多态性相似,组成一个复合体,此复合体与A组的遗传多态性也相似,而F组则相距较远．4．O．mcyeriana和Rhynchofyzasabulata尚未确定组型,RAPD测定结果表明,前者与其它组型的种亲缘关系较远,后者则与AC复合体的种较近．     

稻属某些种及栽培品种对茎尖培养的反应

本文通过稻属51份材料的茎尖培养,探讨了不同来源的材料对茎尖培养的反应。发现野生稻成苗 率较高;栽培稻成苗率较低;杂种成苗率介于野生稻与栽培稻之间;栽培稻中釉稻成苗率高于粳稻。杂 种成苗率受父母本成苗率的影响,父母本成苗率越高,则杂种成苗率越高。     

江永普通野生稻遗传多样性和籼粳基因频率监测分析

以栽培稻的8个籼-粳测验种为对照,采用39对SSR引物检测了江永野生稻居群在1982年、2008年、2017年的遗传多样性,采用38对In Del引物检测了江永野生稻居群在1982年、2008年、2017年的籼-粳基因频率。结果表明:在1982年取样保存在异位圃的40份样本的遗传多样性稍高于2008年、2017年原位保护区样本的遗传多样性;2008年取的样本数虽然比2017年多,但两次取的样本之间遗传多样性几乎没差异。不同年份取的样本之间的遗传分化系数Fst都很小,基因流Nm都较大,分化不明显。通过聚类分析和主坐标分析(PCo A),发现野生稻居群与4份栽培粳稻聚为一类,4份栽培籼稻单独聚成一类,显示江永野生稻与粳稻的血缘近于籼稻;籼-粳基因频率的分析表明,野生稻样本多属粳稻型,少数属偏粳稻型,原位保护区的偏粳稻类型单株数占取样单株总数的比例,2008年比1982年的增加了10.0%,2017年比2008年的增加了1.6%,显示江永野生稻原位保护区生境条件有利野生稻从粳稻型向偏粳稻型变异,随着野生稻产生环境适应性变异,籼型基因频率在提高。     

海南黎族聚居区山栏稻的起源演化研究

以14份海南黎族聚居区的山栏稻为研究材料、以原产于中国的69份亚洲栽培稻和110份普通野生稻为对照组,分别对核中SSⅡ基因、ITS基因和Ehd1基因、叶绿体中ndhC-trnV基因以及线粒体中cox3基因等5段序列进行测序,分析基因序列多样性和单倍型,并揭示海南黎族聚居区山栏稻的起源地和驯化过程。结果表明,黎族聚居区山栏稻的基因多样性低于亚洲栽培稻,而亚洲栽培稻的基因多样性低于普通野生稻;85%左右的山栏稻为偏粳型;山栏稻与广东和湖南的普通野生稻亲缘关系较近,而与海南的普通野生稻的亲缘关系较远,推测黎族的山栏稻可能起源于广东和湖南的普通野生稻。     

来自中国云南野生稻的抗稻瘟病遗传资源

与Pi-ta^＋等位基因相比,含有Pi-ta^＋等位基因的栽培稻具有抗稻瘟病特性。本研究用基因序列分析的方法检测了来自云南的不同栽培稻品种以及不同类型和来源的普通野生稻种和非洲长雄蕊野生稻种中的Pi-ta^＋基因,发现Pi-ta地基因在稻属植物中高度保守,但Pi-ta^＋等位基因的存在极其稀有。在所检测的栽培稻和野生稻中仅有来源于云南景洪的直立型普通野生稻中含有Pi-ta^＋等位基因。而与Pi-ta基因相比,另一个水稻抗稻瘟病基因Pib,经部分同源序列克隆及测序发现该基因在不同野生稻中的变异较大。在所克隆的不同野生稻Pib基因同源序列中,也只有来源于直立型普通野生稻的序列能按该基因的开放阅读框进行正常翻译。对不同类型普通野生稻的抗稻瘟病能力的初步鉴定结果表明,直立型普通野生稻对供试的本地稻瘟病生理小种具有较强抗性,其抗性可能源于所含的Pi=ta^＋等位基因及可能有功能的Pib基因。由于普通野生稻与栽培稻同属AA基因组型,因此,云南直立型普通野生稻可通过杂交育种或基因工程途径用于栽培稻的抗稻瘟病性能改良。     

广东特殊生境的普通野生稻(Oryza rufipogon Griff)遗传变异研究

选择来自广东佛冈县地处山林区远离稻田的一个普通野生稻生境中的25份野生稻样本,以国外多年生、一年生普通野生稻7份样本和广东地方栽培稻8个品种为对照进行种植观察,调查了21个形态生物学性状,对调查数据作方差分析表明,有20个性状表现极显著差异,1个性状表现显著差异.通过模糊聚类分析,可将25份样本分为4类,各类与对照材料之间表现不同的遗传差异,说明该生境野生稻存在较丰富的遗传变异,但从形态生物学和生育期观察,从中尚未发现一年生型、栽培型、粳型等变异类型的分化.     

Extraordinarily polymorphic ribosomal DNA in wild and cultivated rice.

A collection of 481 rice accessions was surveyed for ribosomal DNA (rDNA) intergenic spacer length polymorphism to assess the extent of genetic diversity in Chinese and Asian rice germplasm. The materials included 83 accessions of common wild rice, Oryza rufipogon, 75 of which were from China; 348 entries of cultivated rice (Oryza sativa), representing almost all the rice growing areas in China; and 50 cultivars from South and East Asia. A total of 42 spacer length variants (SLVs) were detected. The size differences between adjacent SLVs in the series were very heterogeneous, ranging from ca. 21 to 311 bp. The 42 SLVs formed 80 different rDNA phenotypic combinations. Wild rice displayed a much greater number of rDNA SLVs than cultivated rice, while cultivated rice showed a larger number of rDNA phenotypes. Indica and japonica groups of O. sativa contained about equal numbers of SLVs, but the SLV distribution was significantly differentiated: indica rice was preferentially associated with longer SLVs and japonica rice with shorter ones. The results may have significant implications regarding the origin and evolution of cultivated rice, as well as the inheritance and molecular evolution of rDNA intergenic spacers in rice. Key words : rDNA, Oryza rufipogon, Oryza sativa, germplasm diversity, evolution.     

Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter.

Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the intergenic spacer was used as an indicator of length variation of rDNA repeat units. rDNA repeat units in E. tef ranged in size from 8.4 to 11.07 kbp. Considerable size variation of rDNA repeats was present among accessions, between individual plants within some accessions, and within single plants. A total of 19 spacer length (sl) phenotypes was observed in 16 accessions in which 11-42 plants were analyzed. A single restriction site polymorphism was detected in PI442115 that was also distinguished by having a single sl variant. Variation in the rRNA genes is a useful indicator of genetic diversity in E. tef germplasm.     

Variability of chloroplast DNA and nuclear ribosomal DNA in cassava (Manihot esculenta Crantz) and its wild relatives

Chloroplast DNA (cp) and nuclear ribosomal DNA (rDNA) variation was investigated in 45 accessions of cultivated and wild Manihot species. Ten independent mutations, 8 point mutations and 2 length mutations were identified, using eight restriction enzymes and 12 heterologous cpDNA probes from mungbean. Restriction fragment length polymorphism analysis defined nine distinct chloroplast types, three of which were found among the cultivated accessions and six among the wild species. Cladistic analysis of the cpDNA data using parsimony yielded a hypothetical phylogeny of lineages among the cpDNAs of cassava and its wild relatives that is congruent with morphological evolutionary differentiation in the genus. The results of our survey of cpDNA, together with rDNA restriction site change at the intergenic spacer region and rDNA repeat unit length variation (using rDNA cloned fragments from taro as probe), suggest that cassava might have arisen from the domestication of wild tuberous accessions of some Manihot species, followed by intensive selection. M. esculenta subspp flabellifolia is probably a wild progenitor. Introgressive hybridization with wild forms and pressures to adapt to the widely varying climates and topography in which cassava is found might have enhanced the crop's present day variability.     

Genetic differentiation of wild relatives of rice as assessed by RFLP analysis

To study genetic diversity and relationships of wild relatives of rice, 58 accessions of Oryza rufipogon, Oryza nivara, Oryza sativa f. spontanea and the cultivated Oryza sativa, representing a wide range of their distribution, were analyzed using the restriction fragment length polymorphism (RFLP) technique. All 30-used RFLP probes detected polymorphisms among the Oryza accessions, with an average of 3.8 polymorphic fragments per probe. Considerable genetic diversity was scored among the Oryza accessions with a similarity coefficient ranging from 0.28 to 0.93; but the cluster analysis of the accessions did not show an apparent grouping based on the species classification, instead they were scattered randomly in different groups. Noticeably, the Oryza accessions from the same geographic region, or near-by geographic regions, tended to be clustered in the same groups. The indica rice varieties showed relatively high genetic diversity and were scattered in different groups of their wild relatives, but the japonica varieties showed a relatively low variation and formed an independent group. It is concluded from the molecular analytical result that: (1) the four Oryza taxa have a remarkably close relationship and their independent species status need to be carefully reviewed; (2) geographic isolation has played a significant role in the differentiation of the Oryza accessions; therefore, a wide geographic range needs to be covered in collecting wild rice germplasm for ex situ conservation; and (3) the conventional conclusion of indica rice being directly domesticated from its ancestral wild species, and japonica rice being derived from indica, gains support from our data.     

Molecular and cytological characterization of 5S rDNA in Oryza species: genomic organization and phylogenetic implications.

We investigated the molecular characteristics and chromosomal organization of 5S rDNA in the genus Oryza, including diploid and tetraploid species. A phylogenetic tree of Oryza species was constructed based on the non-transcribed spacer sequences of 5S rDNA, and some novel relationships were discovered. Specifically, comparative sequence analysis of 5S rDNA in several wild rice species showed unique characteristics inconsistent with the model of concerted evolution: (1) multiple distinct 5S rDNA types were detected within a species, leading to intraspecific divergence of 5S rDNA; (2) multiple identical 5S rDNA types were shared among species, resulting in interspecies clustering of 5S rDNA types; and (3) intraspecific nucleotide diversity was detected within a 5S rDNA class. Our results obtained by fluorescence in situ hybridization revealed that each rice species studied contained only one 5S rDNA locus with two hybridization sites, which were located on either chromosome 7 or chromosome 11. These results suggest that different 5S rDNA classes within the rice genome were arranged together and that one pair of 5S rDNA loci from a diploid progenitor of the tetraploid species might have been lost during evolution. Taken together, our data show that 5S rDNA in rice species is more informative at the gene level than at the chromosome level.     

Ribosomal gene spacer length variability in cultivated and wild rice species

Summary Restriction fragment length polymorphism of the rDNA spacer was studied in the genus Oryza using a cloned rice rDNA probe. One-hundred-five accessions, including 58 cultivated rice and 47 wild species with various genome types, were analysed. Seven size classes differing from one another by an increment of ca. 300 bp were observed amongst the Asiatic cultivated rice of the species O. sativa. A general tendency from a smaller spacer in the Japonica subtypes to longer ones in Indica is observed. Classification as Japonica or Indica on the basis of rDNA pattern generally agrees with classification based on isozyme patterns. In contrast, African rice of the species O. glaberrima does not display any rDNA size variation. When wild species are considered, extensive variation is observed, but the fragment sizes do not fall into regularly increasing size classes except for O. rufipogon and O. longistaminata. The variation is greater in these species than in the cultivated ones.     

Length and sequence heterogeneity in 5S rDNA of Populus deltoides.

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.     

普遍野生稻和亚洲栽培稻遗传多样性的研究

用 ４４个 ＲＦＬＰ标记对来自中国、印度、泰国等亚洲 １０个国家的普通野生稻（简称普野,下同）和来自多个国家的７５个栽培稻品种,从多态位点的比率、等位基因数、基因型数、平均杂合度及平均基因多样性等多个方面,比较了不同国家和不同地区的普通野生稻、栽培稻籼粳亚种及栽培稻与普野之间遗传多样性的差异。结果表明：中国普野的遗传多样性最大;其次是印度普野;南亚普野的平均基因多样性大于东南亚普野,而多态位点的比率、等位基因数及基因型数等却低于东南亚普野;栽培稻的遗传多样性明显小于普通野生稻。在所检测的４４个位点中,栽培稻的多态位点数仅为野生稻的３／４,等位基因数约为野生稻的６０％,基因型种类约为野生稻的１／２。栽培稻中籼稻的遗传多样性高于粳稻。在平均每个位点的实际杂合度上,以中国普野杂合度最高,普通野生稻是栽培稻的２倍。说明从野生稻演化成栽培稻的过程中,经过自然选择和人工选择,杂合度降低,等位基因减少,基因多样性下降。     

Polymorphism at rDNA loci in barley and its relation with climatic variables

The variation in length of the intergenic spacer (IGS) region of the ribosomal DNA repeat unit was examined in 63 accessions of wild barley, Hordeum spontaneum, and seven accessions of cultivated barley, Hordeum vulgare. The accessions of wild barley were collected from ecologically diverse climatic and edaphic microsites in Israel, and the barley cultivars were those grown in India. Sixteen spacer-length variants (slvs) observed in the present study presumably belonged to two known rDNA loci (Rrn1 and Rrn2). Each accession had one or more variants, which together represented the rDNA phenotype. The rDNA phenotypes of wild barley accessions were widely diverse and differed substantially from those of cultivated barley. The slv phenotypes and the corresponding alleles were shown to be largely correlated with different climatic, edaphic and ecogeographical microsites and niches (the ”Evolution Canyon” at Lower Nahal Oren, Mount Carmel; and Tabigha, Eastern Upper Galilee Mountains), so that a particular rDNA phenotype of an accession could be used to predict the climate and soil to which the accession belonged. This sharp microsite ecogeographic variation in ribosomal DNA appears adaptive in nature, and is presumably driven by climatic and edaphic natural selection. Received: 1 March 2001 / Accepted: 21 May 2001