中国野生稻及栽培稻核糖体DNA第一转录间隔区序列分析及其系统学意义

用 PCR技术从产于我国的 3种野生稻和亚洲栽培稻的 2个亚种中特异地扩增和测序了 r DNA的第一转录间隔区。普通野生稻 (Oryza rufipogon)、药用野生稻 (O.officinalis)、疣粒野生稻 (O.granu-lata)和栽培稻的两个亚种 (O.sativa ssp.indica,O.sativa ssp.japonica)的 ITS1序列为 1 93bp、1 94bp、2 1 8bp、1 94bp和 1 94bp,它们的 G/ C含量为 69.3%～ 72 .7% ,序列中位点趋异率为 1 .5%～ 1 0 .6%。序列的相似性比较和简约性分支分析的结果表明 ,普通野生稻与栽培稻的两个亚种之间的亲缘关系最为密切 ;药用野生稻与普通野生稻和与栽培稻的两个亚种的相似性都为 82 % ,说明它与 AA基因组有一定的亲缘关系 ;疣粒野生稻与普通野生稻、药用野生稻和栽培稻两个亚种的亲缘关系相对较远 ,它在稻属中可能是一个系统地位较独特的类群。以 ITS1序列构建的 3种野生稻和 2个栽培稻亚种的系统发育关系与前人用同工酶、叶绿体 DNA、线粒体 DNA和核 DNA资料重建的稻属的系统发育关系基本一致     

水稻产量相关性状驯化研究进展

水稻具有悠久的栽培历史,是重要的粮食作物,养育了1/3的世界人口。现代栽培稻(Oryza sativa)由野生稻(O.rufipogon)驯化而来,产量是驯化筛选的关键性状之一。株型、穗型和种子大小是决定水稻产量的重要性状,这些性状在水稻栽培过程中均受到了定向筛选。该文以水稻产量性状为核心,综述了株型、穗型和种子大小等性状的驯化分子机理研究进展,讨论了水稻产量驯化研究中存在的问题,展望了驯化性状和相关基因的研究前景,以期为水稻产量相关性状的驯化机理研究和水稻育种工作提供有价值的线索。     

稻属植物胚的形态结构与二(异)型子叶

长久以来植物学界认定稻(Oryza sativa L.)是单子叶植物.作者从稻胚发育的研究中确认稻胚具二型子叶,并非单子叶.稻属其他种的胚胎形态与O.sativa是否相同?是否具二型子叶?根据扫描电子显微镜的观察结果,稻属(Oryza) 22个种和亚种的胚的形态结构可以分为两种类型.O.sativa等16个种胚具腹鳞和侧鳞,属第一类型;O. meyeriana (Zoll. et Mor. ex Steud.) Baill.ssp. tuberculata W. C. Wu et Y. G. Lu, G. C. Wang等6个种(亚种)胚缺腹鳞和侧鳞,属第二类型.O.sativa和O. meyeriana ssp. tuberculata的胚胎发育过程所出现的盾片原基、胚根鞘原基、胚芽鞘原基和生长锥均来自原胚,前二者发育成胚套,是外围子叶;胚芽鞘原基发育成围在生长锥外并盖住生长锥的空心的倒锥状胚芽鞘,是顶生子叶.第一类型与第二类型稻胚都具有二型子叶.第二类型稻胚在盾片原基发育过程中并不分化出腹鳞和侧鳞,因而造成第二类型稻胚缺腹鳞与侧鳞.稻的二型子叶源于原胚的背腹极性分化.     

水稻及其近亲家族

栽培稻在分类上属于禾本科(Poaceae)、稻族(Oryzeae)、稻属(Oryza)。稻属包含了两种栽培稻和20多种野生稻物种,广布于全球的热带和亚热带地区(见表)。亚洲栽培稻(O.sativa)就是我们通常食用的水稻,现已广泛地种植于全世界的热带、亚热带以及温带地区。非洲栽培稻(O.glaberrima)种植的面积很小,只在西非的某些农业生态环境中存在,它起源于非洲西部。因为它的产量很低,只有很少人食用它,但它是水稻遗传育种的重要基因资源。     

水稻CMS相关基因在稻属AA基因组中的分布及其单核苷酸多态性

水稻线粒体基因组嵌合基因orf79 和 orfH79分别被认为与BT-型和HL-型水稻CMS有关, 两者具有98%的同源性, 并且其DNA序列只存在4核苷酸的差异。对于这两个嵌合基因, 前者来源于栽培稻(Oryza. sativa L.), 而后者则来源于普通野生稻(O. rufipogon Griff.)。这意味着orf79/ orfH79可能在广泛分布于稻属AA基因组中。为了调查orf79/ orfH79在稻属物种中的分布和变异, 190份栽培稻品系[包括156份亚洲栽培稻(O. sativa var. landrace)和34份非洲栽培稻(O. glaberrima)]以及104份稻属AA基因组野生稻品系(包括O. rufipogon、O.nivara、O. glumaepatula、O. barthii、O. longistaminata和O. meridionalis 6个种), 被用于PCR扩增检测。31份具有控制粤泰A和笹锦A的特异片段的稻属AA基因组水稻品系被检测出。所有特异片段均被回收并测序, 基于DNA 序列的聚类结果显示31份水稻材料被分成了两组, 分别代表为BT-型和HL-型水稻不育细胞质组群。结果也进一步表明: HL-型水稻CMS胞质主要分布于一年生的O. nivara中; BT-型水稻CMS胞质可能来源于栽培稻变种或多年生野生稻O. rufipogon。     

水稻Pib基因及其连锁RFLP标记在栽培稻、药用野生稻和玉米中的比较物理定位

比较遗传学研究表明,禾本科不同基因组之间存在着广泛的同线性和共线性.对水稻(Oryza sativa L.)这一模式植物与其他禾本科植物的原位杂交定位可以揭示禾本科植物基因组的共同特点和进化规律,为建立禾本科遗传大体系积累资料.实验以图位克隆法分离的水稻Pib 基因(10.3 kb)和与之连锁的RFLP标记为探针, 研究了Pib及与其连锁的RFLP标记在供试种中的同源性和物理位置. Southern杂交结果表明,Pib在玉米(Zea mays L.)基因组中有同源序列.进一步利用单色和双色荧光原位杂交技术确定了Pib在栽培稻(O.sativa ssp. indica cv. Guangluai 4)、玉米和药用野生稻(O. officinalis Wall ex Watt)染色体上的物理位置.定位结果表明,Pib基因和与之连锁的RFLP标记在这3个供试种基因组中具有同线性.     

关于我国栽培稻种的起源和演变問题

水稻是世界最古老和分布最广的作物之一,种内存在着形形色色的类型和品种。栽培稻种的起源问题,很久以来就吸引着世界各国学者们的注意。稻属(Oryza)中有实际栽培价值的种只有两个,一是普通稻(Oryza sativa L.),另一是光身稻(O.glaberrima Steud.),前者原产于亚洲,后者原产于非洲。目前,除非洲栽培     

长雄野生稻有利基因的发掘与利用

人类将普通野生稻驯化为亚洲栽培稻,其农艺性状如株高、落粒性、穗型等发生了重要变化,产量也大幅提高,但许多优良性状如抗逆性等却丢失。长雄野生稻与亚洲栽培稻同属AA基因组,蕴藏了许多生物胁迫和非生物胁迫的抗性基因,被认为是亚洲栽培稻遗传改良的潜在基因库。本文总结了长雄野生稻生物及非生物胁迫抗性、地下茎性状以及其他潜在应用价值性状,包括白叶枯抗性、抗旱性、耐热性、自交不亲和性、氮高效利用以及高产等有利性状。基于长雄野生稻地下茎性状开展多年生稻育种实践的应用研究,对长雄野生稻进行从头驯化的策略进行了探讨,以期为长雄野生稻基础研究及栽培稻遗传改良提供理论参考。     

野生稻保护：严峻的现状

水稻是世界上最重要的粮食作物之一,为全球一半以上的人口提供了食物来源。野生稻是水稻近缘野生种的总称,包括水稻所在稻属(Oryza)22个野生种以及稻属11个近缘属的野生种,广泛分布于亚洲、非洲、拉丁美洲以及澳大利亚的热带和亚热带地区。由于野生稻是长期自然选择的结果,蕴藏着丰富的物种和遗传多样性,具有大量栽培稻所没有的遗传变异,是     

亚洲栽培稻起源、演化中两个重要稻种类型的研究

分布子云南及南亚的光稃稻和镰刀谷在研究亚洲栽培稻(O.sativa L.)的起源、演化及稻作育种上有重要意义。它们在分类上的地位往往被误分,进而影响这些类型的开发利用。研究表明,光稃稻是普通野生稻被引上亚洲的热带与亚热带山区在旱地上首先被人类驯化成的原始粳型陆稻,当其进一步被引向高海拔和高纬度时则演化成普通粳稻。镰刀谷迄今多被划为籼稻,我们的初步研究表明,镶刀谷大部分属粳稻,其中也包括一部分籼稻。它的起源及其分类上的地位尚待研究。     

Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites

The origins of the Asian cultivated rice Oryza sativa from its wild ancestor O. rufipogon have been debated for decades. The question mainly concerns whether it originated monophyletically or polyphyletically. To shed light on the origins and demographic history of rice domestication, we genotyped a total of 92 individual plants from the two O. sativa subspecies and O. rufipogon for 60 microsatellites. An approximate Bayesian method was applied to estimate demographic parameters for O. rufipogon vs. O. sativa ssp. indica and O. rufipogon vs. O. sativa ssp. japonica. We showed that the japonica subspecies suffered a more severe bottleneck than the indica subspecies and thus a greater loss of genetic variation during its domestication. Across microsatellite loci there is a significant positive correlation in the reduction of genetic diversity between the two subspecies. The results suggest that completely independent domestication of indica and japonica subspecies may not explain our data and that there is at least partial sharing of their ancestral populations and/or recent gene flow between them.     

Independent domestication of Asian rice followed by gene flow from japonica to indica

Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.     

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.     

Genome-wide intraspecific DNA-sequence variations in rice

Genome-wide comparative analysis of the DNA sequences of two major cultivated rice subspecies, Oryza sativa L. ssp indica and Oryza sativa L. ssp japonica, have revealed their extensive microcolinearity in gene order and content. However, deviations from colinearity are frequent owing to insertions or deletions. Intraspecific sequence polymorphisms commonly occur in both coding and non-coding regions. These variations often affect gene structures and may contribute to intraspecific phenotypic adaptations.     

Genetic control of a transition from black to straw-white seed hull in rice domestication

The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.     

Evolutionary Genomics of Weedy Rice in the USA

Red rice is an interfertiie, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the cropin the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America andthe weed has been proposed to have evolved through multiple mechanisms, including "de-domestication" of UScrop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedyOryza strains. The phenotype of US red rice ranges from "crop mimics", which share some domestication traitswith the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity haveindicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, whichhave never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show geneticsimilarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known aboutthe evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to furthercharacterize the evolutionary genomics of this aggressive weed.     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice （Oryza rufipogon L.） in relation to the domestication of cultivated rice （O. sativa L.）

It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice （O. sativa）. However, how the two subspecies of O. sativa （indica and japonica） were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism （SSILP） markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups： one group （Group I） comprises all the O. rufipogon accesions from tropical （South and Southeast） Asia as well as the standard indica rice; the other group （Group II） comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. ruffpogon might occur after its speciation from other AA-genome species.     

Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice

Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill-Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species.     

The extent of linkage disequilibrium in rice (Oryza sativa L.)

Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably >500 kb), followed by tropical japonica (approximately 150 kb) and indica (approximately 75 kb). LD extends over a shorter distance in O. rufipogon (<40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.