Population structure of rice (Oryza sativa) landraces from high altitude area of Indian Himalayas

This study examined the genetic diversity in 20 rice landrace populations from parts of traditional farming areas of the Indian Himalayas using 11 mapped simple sequence repeats (SSR) loci. Twenty‐four individuals sampled from each of the 20 landraces (480 individuals), which were collected from farmers from Northwest to Northeast Himalaya, showed that all landraces showed within population variation and none were homogeneous. The number of polymorphic loci in a landrace population ranged from 5 to 11. A total of 71 alleles were recorded of which 58 were common and 13 were rare. Of the 71 alleles, 46 were common to both Northwest and Northeast regions, whereas 9 were unique to the former and 16 were unique to the latter. The mean number of alleles per locus was 6.45 and for landrace populations from Northwest and Northeast regions were 5.0 and 5.64, respectively. Population differentiation, as shown by a high F_ST value (0.61), was greater for Northeast populations. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram classified the populations into three major clusters: cluster I comprised seven populations from the Northwest region, cluster II comprised seven populations from the Northeast region and cluster III comprised populations from both regions. Investigating the population genetic structure can help monitor change in diversity over time and space, and also help devise a rational plan for management of crop landraces on‐farm under farmer management.     

Population structure of rice (Oryza sativa) landraces under farmer management

Greater insight into the dynamics of genetic resources of crop plants is needed in order to pinpoint detrimental evolutionary patterns and draw up conservation priorities. The present study demonstrated farmer management of crop population structure and temporal evolution of rice genetic diversity in traditional production systems. The 16 STMS primers analysed for 11 rice landrace populations indicated enough polymorphism to fully differentiate the inter- and intrapopulation diversity. A total number of 98 alleles were recorded, of which 91 were common and seven were rare. The mean number of alleles per locus was 6.13 and for different groups of rice landrace populations, namely five populations of upland common landrace Jaulia, three populations of irrigated common landrace Thapachini and one population each of three distinct rare landraces were 4.37, 2.75 and 4.37, respectively. The study also compared genebank-conserved ( ex situ ) populations and on-farm-managed ( in situ ) landrace populations of same named landraces Jaulia and Thapachini, and revealed greater number of alleles per locus for on-farm-managed populations as compared to the populations under static management. A substantial number of alleles specific to populations under dynamic management could also be recorded. Further, the rare landrace populations included in the present study were more diverse than the common landrace populations. The rare landraces were distinct genetic entities largely representing locally common alleles. Investigating the population genetic structure is therefore helpful in monitoring change in diversity over time and space, and also for devising a rational plan for management of farmer landraces on-farm.     

广西地方稻种资源核心种质构建和遗传多样性分析

以丁颖分类体系分组原则与组内逐层聚类取样方法,对8609份广西地方栽培稻资源表型数据信息进行分析,通过对表型保留比例等评价指标的多重比较确定核心种质总体取样比例,构建出占总体样本5%(414份)的广西地方栽培稻资源初级核心种质。初级核心种质能代表总体遗传变异的89%。用34对SSR分子标记对初级核心种质进行遗传多样性分析,结果表明:广西地方栽培稻资源有较高的遗传多样性(等位基因数A为4.91,Nei’s多样性指数为0.574)。就Nei’s遗传多样性指数而言,粳稻高于籼稻,晚稻高于早稻,水稻高于陆稻,糯稻高于粘稻;来自桂中的稻种资源具有最高的遗传多样性。研究最终利用SSR数据,把414份初级核心种质压缩50%后形成209份核心种质,核心种质基因保留比例达到98%以上,有效代表了广西地方栽培稻资源多样性水平。     

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.     

OsMOGS is required for N‐glycan formation and auxin‐mediated root development in rice (Oryza sativa L.)

N‐glycosylation is a major modification of glycoproteins in eukaryotic cells. In Arabidopsis, great progress has been made in functional analysis of N‐glycan production, however there are few studies in monocotyledons. Here, we characterized a rice (Oryza sativa L.) osmogs mutant with shortened roots and isolated a gene that coded a putative mannosyl‐oligosaccharide glucosidase (OsMOGS), an ortholog of α‐glucosidase I in Arabidopsis, which trims the terminal glucosyl residue of the oligosaccharide chain of nascent peptides in the endoplasmic reticulum (ER). OsMOGS is strongly expressed in rapidly cell‐dividing tissues and OsMOGS protein is localized in the ER. Mutation of OsMOGS entirely blocked N‐glycan maturation and inhibited high‐mannose N‐glycan formation. The osmogs mutant exhibited severe defects in root cell division and elongation, resulting in a short‐root phenotype. In addition, osmogs plants had impaired root hair formation and elongation, and reduced root epidemic cell wall thickness due to decreased cellulose synthesis. Further analysis showed that auxin content and polar transport in osmogs roots were reduced due to incomplete N‐glycosylation of the B subfamily of ATP‐binding cassette transporter proteins (ABCBs). Our results demonstrate that involvement of OsMOGS in N‐glycan formation is required for auxin‐mediated root development in rice.     

A calcium- and phospholipid-dependent protein kinase from rice (Oryza sativa) leaves

Protein kinases in plants have not been examined in detail, but protein phosphorylation has been shown to be essential for regulating plant growth via the signal transduction system. A Ca²⁺- and phospholipid-dependent protein kinase, possibly involved in the intracellular signal transduction system from rice leaves, was partially purified by sequential chromatography on DE52, Phenyl Superose and Superose 12. This protein kinase phosphorylated the substrate, histone III-S, in the presence of Ca²⁺ and phosphatidylserine. The apparent molecular mass of the Ca²⁺- and phosphatidylserine-dependent protein kinase (Ca²⁺/PS PK), determined by phosphorylation in SDS-polyacrylamide gel containing histone III-S, was 50 kDa. The protein kinase differed from Ca²⁺-dependent protein kinase (CDPK) in rice leaves in that Ca²⁺/PS PK showed phospholipid dependency and the molecular mass of Ca²⁺/PS PK exceeded that of CDPK. Investigations were carried out on changes in Ca²⁺/PS PK and CDPK activity in the cytosolic and membrane fractions during germination. The maximum activity of Ca²⁺/PS PK in the cytosolic fraction was observed before imbibition and that of CDPK in the membrane fraction was noted at 6 days following imbibition. Protein kinases are likely to regulate plant growth through protein phosphorylation.     

Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome. Received: 5 May 1999 / Accepted: 16 August 1999     

水稻水溶性环氧化合物水解酶的生物信息学分析

水溶性环氧化合物水解酶（Soluble Epoxide Hydrolase,SEH）是一组催化环氧化合物水解为相应邻位二醇的酶类,在哺乳动物、植物、昆虫和微生物体内广泛存在。通过BLAST对水稻基因组的蛋白质数据库进行搜索,获得10个水溶性环氧化物水解酶（Soluble Epoxide Hydrolase SEH）sEH蛋白的同源序列。经分析发现这些基因在水稻不同胁迫处理下各个部位都有所表达,而且不同成员之间的表达模式存在较大的差异。水稻sEH蛋白主要参与角质层形成,应激反应,以及病原防御等生理过程,特别在脱毒过程中扮演着重要的角色。对蛋白质多序列联配和三级结构预测结果表明：水溶性环氧化合物水解酶的核心结构域由3个催化残基Asp、His和Asp形成三位一体的催化活性构象。这类基因的表达受抗逆环境诱导,其功能与抗逆性有关,为基因工程抗逆育种提供了参考。     

Separation and characterization of proteins in rice (Oryza sativa) suspension cultured cells

Proteins extracted from suspension cultured cells of rice were separated by two-dimensional polyacrylamide gel electrophoresis. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane and 103 electroblotted proteins were analyzed. The N-terminal amino-acid sequences of 20 out of 103 proteins were determined in this manner. N-terminal regions of the remaining proteins could not be sequenced and they were inferred to have a blocking group at the N-terminus. Internal amino-acid sequences of 32 proteins were determined by sequence analysis of peptides obtained by Cleveland peptide mapping. The amino-acid sequences determined here were compared with those of known plant and animal proteins. Furthermore, the concanavalin A-peroxidase method was used to determine which of the 103 proteins were glycosylated, and in vitro and in vivo phosphorylation was carried out to identify some of the phosphorylated proteins. Using this experimental approach, we could identify the major proteins involved in growth and development of rice cell suspension cultures and discuss on the physiological function of some of these identified proteins including the calcium binding protein, superoxide dismutase and rice ascorbate peroxidase. This revised version was published online in June 2006 with corrections to the Cover Date.     

FLOURY ENDOSPERM11‐2 encodes plastid HSP70‐2 involved with the temperature‐dependent chalkiness of rice (Oryza sativa L.) grains

The frequent occurrence of chalky rice (Oryza sativa L.) grains becomes a serious problem as a result of climate change. The molecular mechanism underlying chalkiness is largely unknown, however. In this study, the temperature‐sensitive floury endosperm11‐2 (flo11‐2) mutant was isolated from ion beam‐irradiated rice of 1116 lines. The flo11‐2 mutant showed significantly higher chalkiness than the wild type grown under a mean temperature of 28°C, but similar levels of chalkiness to the wild type grown under a mean temperature of 24°C. Whole‐exome sequencing of the flo11‐2 mutant showed three causal gene candidates, including Os12g0244100, which encodes the plastid‐localized 70‐kDa heat shock protein 2 (cpHSP70‐2). The cpHSP70‐2 of the flo11‐2 mutant has an amino acid substitution on the 259th aspartic acid with valine (D259V) in the conserved Motif 5 of the ATPase domain. Transgenic flo11‐2 mutants that express the wild‐type cpHSP70‐2 showed significantly lower chalkiness than the flo11‐2 mutant. Moreover, the accumulation level of cpHSP70‐2 was negatively correlated with the chalky ratio, indicating that cpHSP70‐2 is a causal gene for the chalkiness of the flo11‐2 mutant. The intrinsic ATPase activity of recombinant cpHSP70‐2 was lower by 23% at V_max for the flo11‐2 mutant than for the wild type. The growth of DnaK‐defective Escherichia coli cells complemented with DnaK with the D201V mutation (equivalent to the D259V mutation) was severely reduced at 37°C, but not in the wild‐type DnaK. The results indicate that the lowered cpHSP70‐2 function is involved with the chalkiness of the flo11‐2 mutant.     

Molecular cloning and structural analysis of a novel Rac gene osRACB in rice (Oryza sativa L.)

Rac is a subfamily of small GTP-binding protein family. Its molecular weight is between 20 and 30 kilodaltons. As a signal protein, Rac directly or indirectly participates in many physiological processes, such as the regulation of cytoskeleton and the transduction of stress-induced signal. So Rac is also named ?molecular switch? The switch is based on the cycle from a GTP-bound 憃n?to a GDP-bound 憃ff?state[1]. In the superfamily of GTP-binding protein, only heterotrimeric G protein, Ra…     

Genetic analysis and gene mapping of a new rolled-leaf mutant in rice (Oryza sativa L.)

To understand the development of rice leaf blades,we identified a new rolled-leaf mutant,w32,from indica cultivar IR64 through EMS mutagenesis. The mutant showed a stable rolled-leaf phenotype throughout the life cycle. Two F2 populations were developed by crossing w32 to cultivar IR24 and PA64. Genetic analysis showed that the rolled-leaf phenotype was controlled by a single recessive gene. To determine the location of the gene,bulked segregant analysis was carried out using mutant and wild-type DNA pools ...     

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.     

Effect of iron plaque outside roots on nutrient uptake by rice (Oryza sativa L.). Zinc uptake by Fe-deficient rice

This solution culture study examined the effect of the deposition of iron plaque on zinc uptake by Fe-deficient rice plants. Different amounts of iron plaque were induced by adding Fe(OH)₃ at 0, 10, 20, 30, and 50 mg Fe/L in the nutrient solution. After 24 h of growth, the amount of iron plaque was correlated positively with the Fe(OH)₃ addition to the nutrient solution. Increasing iron plaque up to 12.1 g/kg root dry weight increased zinc concentration in shoots by 42% compared to that at 0.16 g/kg root dry weight. Increasing the amount of iron plaque further decreased zinc concentration. When the amounts of iron plaque reached 24.9 g/kg root dry weight, zinc concentration in shoots was lower than that in shoots without iron plaque, implying that the plaque became a barrier for zinc uptake. While rice plants were pre-cultured in –Fe and +Fe nutrient solution in order to produce the Fe-deficient and Fe-sufficient plants and then Fe(OH)₃ was added at 20, 30, and 50 mg Fe/L in nutrient solution, zinc concentrations in shoots of Fe-deficient plants were 54, 48, and 43 mg/kg, respectively, in contrast to 32, 35, and 40 mg/kg zinc in shoots of Fe-sufficient rice plants. Furthermore, Fe(OH)₃ addition at 20 mg Fe/L and increasing zinc concentration from 0.065 to 0.65 mg Zn/L in nutrient solution increased zinc uptake more in Fe-deficient plants than in Fe-sufficient plant. The results suggested that root exudates of Fe-deficient plants, especially phytosiderophores, could enhance zinc uptake by rice plants with iron plaque up to a particular amount of Fe.     

Genetic analysis and molecular mapping of a novel gene for zebra mutation in rice （Oryza sativa L.）

A novel zebra mutant, zebra-15, derived from the restorer line JinhuilO （Oryza sativa L. ssp. indica） treated by EMS, displayed a distinctive zebra leaf from seedling stage to jointing stage. Its chlorophyll content decreased （55.4%） and the ratio of Chla/Chlb increased （90.2%） significantly in the yellow part of the zebra-15, compared with the wild type. Net photosynthetic rate and fluorescence kinetic parameters showed that the decrease of chlorophyll content significantly influenced the photosynthetic efficiency of the mutant. Genetic analysis of F2 segregation populations derived from the cross of XinonglA and zebra-15 indicated that the zebra leaf trait is controlled by a single recessive nuclear gene. Ninety-eight out of four hundred and eighty pairs of SSR markers showed the diversity between the XinonglA and the zebra-15, their F2 population was then used for gene mapping. Zebra-15 （Z-15） gene was primarily restricted on the short arm of chromosome 5 by 150 F2 recessive individuals, 19.6 cM from marker RM3322 and 6.0 cM from marker RM6082. Thirty-six SSR markers were newly designed in the restricted location, and the Z-15 was finally located between markers nSSR516 and nSSR502 with the physical region 258 kb by using 1,054 F2 recessive individuals.     

低钾胁迫对水稻(Oryza sativa L.)化感潜力变化的影响

研究以国际公认的化感水稻P1312777和非化感水稻Lemont为供体,稗草（Echinochloa cru-galli L.）为受体,采用稻／稗共培体系,研究低钾胁迫对水稻化感潜力变化的影响及其机制。受体稗草的形态指标分析结果表明,低钾胁迫促使化感水稻P1312777对共培稗草的根长、株高和干重的抑制率均升高,增幅远大于非化感水稻Lemont。受体稗草生理生化指标分析结果表明,低钾胁迫下化感与非化感水稻对受体稗草保护酶系（SOD、POD、CAT）及根系活力的抑制作用增强,但化感水稻P1312777比非化感水稻Lemont的抑制程度大,且达极显著差异。实时荧光定量PCR分析结果表明,低钾胁迫下,化感水稻P1312777根部与叶部中酚类代谢的关键酶——苯丙氨酸解氨酶、肉桂酸-4-羟化酶、羟化酶、O-甲基转移酶的基因均上调表达,而非化感水稻根部相应酶均下调表达,叶部除苯丙氨酸解氨酶上调,其余酶也下调表达。而萜类代谢途径关键酶——HMG—CoA还原酶、角鲨烯合酶、单萜烯环化酶、倍半萜烯环化酶、二萜烯环化酶的基因,在两种水稻根部中呈现出相同或相似的表达方式（上调或下调）,即HMG—CoA还原酶上调表达,角鲨烯合酶、单萜烯环化酶、倍半萜烯环化酶、二萜烯环化酶下调表达;而在水稻叶部,非化感水稻Lmont相应酶基因表达方式仍然不变,化感水稻P1312777除了角鲨烯合酶下调表达,其余4个酶均上调表达。水稻根系分泌物中酚类物质的HPLC分析结果表明,低钾胁迫下,化感水稻P1312777根系分泌物中,所检出的酚酸类物质总量是正常营养条件下的2．30倍,而非化感水稻Lemont则是正常营养条件下的0．91倍。综合分析认为低钾胁迫下,化感水稻P1312777抑草能力增强主要是由于酚类代谢途径关键酶基因表达上调,导致酚类代谢途径旺盛,分泌出更多的酚类物质,进而破坏受体稗草保护酶系统,抑制了稗草的正常生长。     

Polyamines in various rice (Oryza sativa) genotypes with respect to sodium chloride salinity

Physiological responses of various rice genotypes were studied in relation to salt (NaCl) stress. Cultivars CSR-1 and Dular germinated well in different NaCl regimes compared to cvs Rupsail, Assam Getu and M-1–48. At 100 m M NaCl, the lowest germination was observed in cv. M-1–48. Cvs CSR-1 and Dular were relatively effective in maintaining high concentrations of polyamines as well as arginine decarboxylase (EC 4.1.1.19) activity in coleoptiles and roots in a non-stressed condition. The activities of two biodegradative enzymes, diamine oxidase (EC 1.4.3.6) and polyamine oxidase (EC 1.4.3.4), were lowest in cv. CSR-1. The polyamine content was not significantly altered when seedlings of cv. CSR-1 were exposed to 100 m M NaCl. However, in cv. M-1–48 enhancement of arginine decarboxylase activity with concomitant accumulation of polyamines was observed. Leakage of metabolites and changes in the levels of Na⁺ and Cl⁻ were prominent in cv. M-1–48 under saline conditions. The results suggest a correlation between polyamine and salt stress-induced responses in rice genotypes.     

Efficient transformation of Korean rice cultivars (Oryza sativa L) mediated byAgrobacterium tumefaciens

The purpose of this study was to improve transformation efficiency for three Korean rice cultivars, Ilpum, Dasan, and Namyang. Using two different media with or without light, efficiencies of callus induction, regeneration, and transformation of the Korean cultivars were compared to Japanese cultivar, Nipponbare, as a control. Immature cv. Nipponbare seeds produced 35.5% and 16.1% regeneration efficiency on CIM and N6D media, respectively. Among the Korean cultivars, only cv. Ilpum induced on CIM in the dark was actively regenerated with efficiency of 8.2%. With LBA4404 (pTOK233), no difference for the efficiency of transformation was found between mature and immature seeds of cv. Ilpum. This result reveals that mature seeds can be substituted for this study with no difference. The anther-derived calli of cv. Namyang inoculated with either LBA4404 (pTOK233) or EHA101 (pSMABuba) showed regeneration efficiencies of 14.5% and 20.9%, respectively, even though efficiency of transformation did not differ with these two vectors. We suggest that the anther-derived calli are better-materials for transformation experiment due to their genotype-independent regeneration. In the assay of GUS, all of the calli that survived on the second selection medium were strongly stained. PCR-Southern blot analyses confirmed that T-DNA was stably transformed into all tissues selected. Cvs. Nipponbare and Namyang transformed by LBA4404 (pTOK233) showed positive color in the NPTII ELISA.