云南栽培稻种SSR 遗传多样性比较

采用64个SSR标记对96份云南水稻(Oryz a sativa)地方品种和选育品种的遗传多样性进行比较分析。结果发现64个标记都具有多态性, 共检测到741个等位基因, 每个多态性位点检测到的等位基因数为2-29个, 平均11.57个; Nei基因多样性指数(He)范围在0.345(RM321)-0.932(RM1)之间, 平均为0.56。水稻品种的遗传多样性并非按地理位置均匀分布, 而是在相 似系数为0.17的水平上明显分为2个不同类群, 即籼稻类群和粳稻类群, 且籼粳亚种间的SSR多样性差异不明显, 籼稻平均等位基因数(Ap)和Nei基因多样性指数(Ap=10.6, He=0.46)与粳稻品种(Ap=10.7, He=0.48)十分接近, 可能与这些品种间存在一定频率的基因交流有关。糯稻和非糯稻在籼稻群和粳稻群中都有表现, 没有特别的分布规律。云南栽培稻选育品种与地方稻亲缘关系较近, 其遗传基础可能来源于云南水稻地方品种。本研究结果表明, SSR标记能较好地区分云南栽培稻品种, 且云南水稻地方品种遗传多样性丰富, 存在大量的优质性状可供育种实践选择。     

宁夏水稻选育品种遗传多样性和亲缘关系分析

选择31份宁夏近年来育成或审定的水稻品种(系),利用分布于12条染色体的36对SSR引物进行遗传多样性和遗传距离分析.共检测到159个等位基因,品种间不同位点等位基因数目不等,平均4.4个.Nei基因多样性指数变幅为0.031 7～0.844 4,平均为0.508 8.按育成或审定年份,把31份水稻分为3组,SSR分析...     

Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice

Emerging evidence supports that cooked rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health traits. Metabolites from ten diverse varieties of cooked rice were detected using ultra performance liquid chromatography coupled to mass spectrometry. A total of 3,097 compounds were detected, of which 25% differed among the ten varieties. Multivariate analyses of the metabolite profiles showed that the chemical diversity among the varieties cluster according to their defined subspecies classifications: indica, japonica, and aus. Metabolite-specific genetic diversity in rice was investigated by analyzing a collection of single nucleotide polymorphisms (SNPs) in genes from biochemical pathways of nutritional importance. Two classes of bioactive compounds, phenolics and vitamin E, contained nonsynonymous SNPs and SNPs in the 5' and 3' untranslated regions for genes in their biosynthesis pathways. Total phenolics and tocopherol concentrations were determined to examine the effect of the genetic diversity among the ten varieties. Per gram of cooked rice, total phenolics ranged from 113.7 to 392.6 μg (gallic acid equivalents), and total tocopherols ranged between 7.2 and 20.9 μg. The variation in the cooked rice metabolome and quantities of bioactive components supports that the SNP-based genetic diversity influenced nutritional components in rice, and that this approach may guide rice improvement strategies for plant and human health.     

Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice

In Asian cultivated rice (Oryza sativa L.), aroma is one of the most valuable traits in grain quality and 2-ACP is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. Although the major locus for grain fragrance (frg gene) has been described recently in Basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different varieties is still limited. Here we report on characterisation of the frg gene in the Azucena variety, one of the few aromatic japonica cultivars. We used a RIL population from a cross between Azucena and IR64, a non-aromatic indica, the reference genomic sequence of Nipponbare (japonica) and 93-11 (indica) as well as an Azucena BAC library, to identify the major fragance gene in Azucena. We thus identified a betaine aldehyde dehydrogenase gene, badh2, as the candidate locus responsible for aroma, which presented exactly the same mutation as that identified in Basmati and Jasmine-like rices. Comparative genomic analyses showed very high sequence conservation between Azucena and Nipponbare BADH2, and a MITE was identified in the promotor region of the BADH2 allele in 93-11. The badh2 mutation and MITE were surveyed in a representative rice collection, including traditional aromatic and non-aromatic rice varieties, and strongly suggested a monophylogenetic origin of this badh2 mutation in Asian cultivated rices. Altogether these new data are discussed here in the light of current hypotheses on the origin of rice genetic diversity.     

水稻SSR标记的遗传多样性研究进展

本文从SSR标记优点和适用于研究水稻遗传多样性入手,综述了SSR标记在水稻核心种质构建与评价、遗传结构、稻种起源演化等方面的研究进展。总结了水稻遗传多样性的地带性特征（云南是中国稻种资源的最大遗传多样性中心和优异种质的富集地;西南稻区粳稻品种遗传多样性最丰富;南方稻区粳稻品种的遗传多样性高于北方粳稻遗传多样性）、遗传多样性与生态地理位置密切相关、目前水稻品种遗传基础狭窄、多样性降低等特征,分析了遗传多样性成因及影响因素,特别指出了育种行为对遗传多样性的影响,并针对当前水稻品种遗传多样性较低的问题提出了对策。     

云南栽培稻种SSR遗传多样性比较

采用64个SSR标记对96份云南水稻（Oryza sativa）地方品种和选育品种的遗传多样性进行比较分析。结果发现64个标记都具有多态性,共检测到741个等位基因,每个多态性位点检测到的等位基因数为2—29个,平均11．57个：Nei基因多样性指数（He）范围在0．345（RM321）-0．932（RM1）之间,平均为0．56。水稻品种的遗传多样性并非按地理位置均匀分布,而是在相似系数为0．17的水平上明显分为2个不同类群,即籼稻类群和粳稻类群,且籼粳亚种间的SSR多样性差异不明显,籼稻平均等位基因数（Ap）和Nei基因多样性指数（Ap=10．6,He=0．46）与粳稻品种（Ap=10．7,He=0．48）十分接近,可能与这些品种间存在一定频率的基因交流有关。糯稻和非糯稻在籼稻群和粳稻群中都有表现,没有特别的分布规律。云南栽培稻选育品种与地方稻亲缘关系较近,其遗传基础可能来源于云南水稻地方品种。本研究结果表明,SSR标记能较好地区分云南栽培稻品种,且云南水稻地方品种遗传多样性丰富,存在大量的优质性状可供育种实践选择。     

辽宁省近15年的部分水稻主栽品种的简单重复序列(SSR)多态性分析

应用简单重复序列(SSR)标记方法对辽宁省近15年的14个大面积种植的水稻品种进行遗传多样性分析的结果表明,17对引物共产生43个位点,其中多态性位点17个,平均每对SSR引物检测到2.53个,占位点总数的39.53%。用Nei’s公式计算水稻品种间的遗传距离,并以算术平均非加权聚类(UPGMA)法进行聚类分析并结合系谱分析结果表明,辽宁省近15年的水稻主栽品种遗传多样性不够丰富,多数品种间的亲缘关系较近,欲进一步提高产量还需拓宽遗传基础。     

Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses

Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5' nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3' NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3' NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.     

Identification of determinants involved in initiation of hepatitis C virus RNA synthesis by using intergenotypic replicase chimeras

The 5' nontranslated region (NTR) and the X tail in the 3' NTR are the least variable parts of the hepatitis C virus (HCV) genome and play an important role in the initiation of RNA synthesis. By using subgenomic replicons of the HCV isolates Con1 (genotype 1) and JFH1 (genotype 2), we characterized the genotype specificities of the replication signals contained in the NTRs. The replacement of the JFH1 5' NTR and X tail with the corresponding Con1 sequence resulted in a significant decrease in replication efficiency. Exchange of the X tail specifically reduced negative-strand synthesis, whereas substitution of the 5' NTR impaired the generation of progeny positive strands. In search for the proteins involved in the recognition of genotype-specific initiation signals, we analyzed recombinant nonstructural protein 5B (NS5B) RNA polymerases of both isolates and found some genotype-specific template preference for the 3' end of positive-strand RNA in vitro. To further address genotype specificity, we constructed a series of intergenotypic replicon chimeras. When combining NS3 to NS5A of Con1 with NS5B of JFH1, we observed more-efficient replication with the genotype 2a X tail, indicating that NS5B recognizes genotype-specific signals in this region. In contrast, a combination of the NS3 helicase with NS5A and NS5B was required to confer genotype specificity to the 5' NTR. These results present the first genetic evidence for an interaction between helicase, NS5A, and NS5B required for the initiation of RNA synthesis and provide a system for the specific analysis of HCV positive- and negative-strand syntheses.     

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

RAPD analysis of jasmine rice-specific genomic structure.

Total genomic DNA was extracted from 29 samples of rice seed, including jasmine rice Oryza sativa L. subsp indica 'KDML105', 'KDML105'-derived varieties, nonaromatic Thailand rice, and japonica rice. Polymorphism in RAPD profiles was analyzed to explore the genomic structure specific to jasmine rice. The degree of band sharing was used to evaluate genetic distance between varieties and to construct a phylogenetic tree. RD15, CNTLR85033, and CNT87040 were found to be closest to 'KDML105', which was consistent with the true relation among them. Four RAPD fragments that cooperatively distinguished jasmine rice from others were cloned and sequenced. PCR amplification using pairs of primers designed specifically further confirmed the credibility of the RAPD result. Comparison through Genbank revealed that a 454 bp RAPD band was similar to the first intron of a putative Cf2/Cf5 disease resistance gene and a 1,107 bp RAPD band similar to a wall-associated kinase (wak) gene sequence.     

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.     

Genetic analysis of sequences in the 3' nontranslated region of hepatitis C virus that are important for RNA replication

The genome of the hepatitis C virus (HCV) is a plus-strand RNA molecule that carries a single long open reading frame. It is flanked at either end by highly conserved nontranslated regions (NTRs) that mediate crucial steps in the viral life cycle. The 3' NTR of HCV has a tripartite structure composed of an about 40-nucleotide variable region, a poly(U/UC) tract that has a heterogeneous length, and a highly conserved 98-nucleotide 3'-terminal sequence designated the X tail or 3'X. Conflicting data as to the role the sequences in the 3' NTR play in RNA replication have been reported. By using the HCV replicon system, which is based on the self-replication of subgenomic HCV RNAs in human hepatoma cell line Huh-7, we mapped in this study the sequences in the 3' NTR required for RNA replication. We found that a mutant with a complete deletion of the variable region is viable but that replication is reduced significantly. Only replicons in which the poly(U/UC) tract was replaced by a homouridine stretch of at least 26 nucleotides were able to replicate, whereas RNAs with homopolymeric guanine, adenine, or cytosine sequences were inactive. Deletions of individual or all stem-loop structures in 3'X were not tolerated, demonstrating that this region is most crucial for efficient RNA replication. Finally, we found that none of these deletions or substitutions within the 3' NTR affected RNA stability or translation, demonstrating that the primary effect of the mutations was on RNA replication. These data represent the first detailed mapping of sequences in the 3' NTR assumed to act as a promoter for initiation of minus-strand RNA synthesis.     

Genetic Diversity of Global Aromatic Rice Varieties

Genetic diversity of 434 rice accessions collected from 16 countries, including 345 fragrance rice varieties and 89 non fragrance rice varieties, have been analyzed. A total of 573 alleles were detected by using 77 simple sequence repeats (SSR) primer pairs covering all rice 12 chromosomes. The value of allelic polymorphism information content (PIC) ranged from 0090 to 0845, with an average of 0516 per locus; Gene diversity (GD) varied from 0091 to 0859, with an average of 0573; The mean value of major allele frequencies (MAF) was 0540, covering from 0251 to 0953. In addition, 434 rice accessions are divided into three sub populations by cluster and population structure analysis, and FST between sub populations showed a mean of -0116, ranging from -0623 to 0494; The score of genetic distance calculated by Nei′s method appeared from 0207 to 0355. Major allele frequencies within each sub population distributed from 0408 to 0746, and gene diversity level from 0354 to 0699, while PIC from 0320 to 0658. Sequencing 6 mitochondrion genes in 18 rice varieties exhibited no different in 5 genes, whereas Mit4 contains a 3 SNPs in the gene body, which acts as an important marker to understanding the relationship between Indica/Japonica differentiation and the evolution of fragrant gene. Finally, genetic diversity and mitochondrion gene sequencing would help to know about the origin of fragrant resource and benefit rice breeding.     

The Puzzle of Italian Rice Origin and Evolution: Determining Genetic Divergence and Affinity of Rice Germplasm from Italy and Asia

The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H _e = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.     

不同国家水稻品种的遗传多样性分析

探讨世界不同国家水稻品种的遗传多样性,旨在为各国品种资源的有效利用提供理论依据。本研究利用63对引物对36份来源于不同国家的水稻品种进行遗传多样性分析。共检测到269个等位基因,每个位点的等位基因数(Na)平均为4.54个,有效等位基因数(Ne)平均为3.22,基因多样性指数(H)平均为0.64,Shannon’s信息指数(I)平均为1.21,引物RM206、RM257、RM410、RM235、RM266的等位基因数较多在7条以上。所处纬度相近的国家或地区的水稻品种之间的遗传距离较近,被聚为同一类群,而所处纬度较远的国家或地区的水稻品种被分到了不同类群。结果表明,水稻品种之间的遗传差异与纬度和地理距离有很大的关系。     

Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

BACKGROUND AND AIMS: Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. METHODS: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). KEY RESULTS: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. CONCLUSIONS: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.     

SSR标记揭示的云南地方稻品种遗传多样性及其保育意义

为了探索水稻(Oryza sativa L.)地方品种的遗传多样性及其有效保育方法,对采自云南省17个村寨的82个水稻地方品种和3个国际常用的典型籼稻和粳稻品种进行了微卫星(SSR)分子标记的分析.利用19对SSR引物在85个水稻品种中共扩增出了83个基因型,其分子量变异在100～500 bp之间.基于各品种SSR基因型遗传相似系数聚类分析而获得的UPGMA树状图表明各水稻品种之间存在较大的遗传多样性,其相似系数变异在0.15～0.90之间.但这些地方品种的遗传多样性并非呈均等的地理分布.这85个水稻品种在相似系数为0.52之处分为二组,其中一组包括几乎所有的籼稻品种,而另一组包括全部的粳稻品种,表明SSR标记能很好揭示水稻籼-粳分化.同时,有些来自不同采集地的同名品种表现出一定的遗传差异,说明同名异物的现象存在.云南水稻地方品种具有丰富的遗传多样性,对其有效保育十分重要和迫切,但只有根据遗传多样性的水平和分布特点,采用正确的保育对策和取样方法才能确保对云南水稻地方品种的有效保育.结果进一步表明,选用适当的微卫星引物,可以为准确鉴定籼稻和粳稻品种及研究其进化规律提供有效的分子标记方法,并有利于有目标的水稻遗传资源保育和育种创新.