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 ...     

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.     

Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers.

We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars 'Nipponbare' and 'Koshihikari' can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice.     

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.     

Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.)

 Ninety-four newly developed microsatellite markers were integrated into existing RFLP framework maps of four rice populations, including two doubled haploid, a recombinant inbred, and an interspecific backcross population. These simple sequence repeats (SSR) were predominantly poly(GA) motifs, targetted because of their abundance in rice. They were isolated from a previously described sheared library and a newly constructed enzyme-digested library. Differences in the average length of poly(GA) tracts were observed for clones isolated from the two libraries. The length of GA motifs averaged 21 repeat units for clones isolated from the Tsp-509-digested library, while motifs averaged 17 units for clones from the sheared library. There was no evidence of clustering of microsatellite markers near centromeres or telomeres. Mapping of the 94 newly developed markers as well as of 27 previously reported microsatellites provided genome-wide coverage of the 12 chromosomes, with an average distance of 1 SSLP (simple sequence repeat polymorphism) per 16–20 cM. Received: 13 February 1997/Accepted: 28 February 1997     

Heredity, physiology and mapping of a chlorophyll content gene of rice (Oryza sativa L.)

A single dominant gene Gc controls the trait of high chlorophyll (Chl) content in rice (cultivar (cv.) Zhenshan 97B). The contents of Chl b and total Chl increased 100% and 25%, respectively, when Gc was introduced. In addition, photosynthetic rate, biomass and grain yield also increased by 20%, 17% and 16%, respectively. Three simple sequence repeats (SSR) markers (rm462, rm6340 and rm6464) that are linked to Gc were identified by amplification of DNA samples from near-isogenic lines using two hundred pairs of primers. The genetic distances on the short arm of rice chromosome 1 between Gc and rm6464, rm6340 and rm462 were 0, 0.588 and 1.18 cM, respectively.     

水稻长穗颈基因eui紧密连锁SSR标记获得

02428h是从半矮秆材料02428体细胞培养后代中发现的隐性高秆突变体, 其株高性状由1对长穗颈基因eui和1对半矮秆基因sd-1共同控制。以02428h与半矮秆材料南京11杂交的F₂为作图群体, 利用Gramene公布的SSR标记和根据NCBI中的BAC序列自己新开发的SSR标记, 将eui基因定位在第5染色体上的RM3673和RM0012之间, 两侧遗传距离分别为0.3 cM和1.0 cM, 为该基因的分子标记辅助选择奠定了基础。     

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。     

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。     

水稻砷污染及其对砷的吸收和代谢机制

水稻是当今世界大部分地区(尤其是东南亚)的主要的粮食作物之一,同时也是砷(As)进入食物链的主要途径之一。日益严重的水稻田As污染,不但影响了稻米的产量和品质,而且通过食物链威胁着人体健康。如何减少水稻地上部(尤其是米粒)As的含量和降低其毒性,及提高水稻As耐性是亟需解决的世界食品安全问题。深入了解水稻对As的吸收、积累和代谢的生理及分子生物学机制是解决水稻As污染的关键途径。综述国内外研究,对今后深入研究提出建议。     

RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.)

 Complementary recessive genes hwd1 and hwd2 controlling hybrid breakdown (weakness of F₂ and later generations) were mapped in rice using RFLP markers. These genes produce a plant that is shorter and has fewer tillers than normal plants when the two loci have only one or no dominant allele at both loci. A cultivar with two dominant alleles at the hwd1 locus and a cultivar with two dominant alleles at the hwd2 locus were crossed with a double recessive tester line. Linkage analysis was carried out for each gene independently in two F₂ populations derived from these crosses. hwd1 was mapped on the distal region of rice genetic linkage map for chromosome 10, flanked by RFLP markers C701 and R2309 at a distance of 0.9 centiMorgans (cM) and 0.6 cM, respectively. hwd2 was mapped in the central region of rice genetic linkage map for chromosome 7, tightly linked with 4 RFLP markers without detectable recombination. The usefulness of RFLP mapping and map information for the genes controlling reproductive barriers are discussed in the context of breeding using diverse rice germplasm, especially gene introduction by marker-aided selection.     

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…     

SEMI-ROLLED LEAF 10 stabilizes catalase isozyme B to regulate leaf morphology and thermotolerance in rice (Oryza sativa L.)

Plant architecture and stress tolerance play important roles in rice breeding. Specific leaf morphologies and ideal plant architecture can effectively improve both abiotic stress resistance and rice grain yield. However, the mechanism by which plants simultaneously regulate leaf morphogenesis and stress resistance remains elusive. Here, we report that SRL10, which encodes a double-stranded RNA-binding protein, regulates leaf morphology and thermotolerance in rice through alteration of microRNA biogenesis. The srl10 mutant had a semi-rolled leaf phenotype and elevated sensitivity to high temperature. SRL10 directly interacted with catalase isozyme B (CATB), and the two proteins mutually increased one other's stability to enhance hydrogen peroxide (H₂O₂) scavenging, thereby contributing to thermotolerance. The natural Hap3 (AGC) type of SRL10 allele was found to be present in the majority of aus rice accessions, and was identified as a thermotolerant allele under high temperature stress in both the field and the growth chamber. Moreover, the seed-setting rate was 3.19 times higher and grain yield per plant was 1.68 times higher in near-isogenic line (NIL) carrying Hap3 allele compared to plants carrying Hap1 allele under heat stress. Collectively, these results reveal a new locus of interest and define a novel SRL10–CATB based regulatory mechanism for developing cultivars with high temperature tolerance and stable yield. Furthermore, our findings provide a theoretical basis for simultaneous breeding for plant architecture and stress resistance.     

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.     

利用SSR定位籼稻品种Kaharamana中抗褐飞虱基因Bph9

褐飞虱是危害水稻生产最重要的害虫之一,利用寄主抗性被认为是防治褐飞虱最经济而有效的方法。斯里兰卡水稻品种Kaharamana对东亚和东南亚的褐飞虱种群均表现抗虫性,利用分子遗传学的方法对其携带的Bph9基因进行了SSR定位。所用的遗传群体为来源于Kaharamana和02428的含有180个单株的F2分离群体,每个F2单株套袋自交获得F2：3家系。利用苗期集团鉴定埘F2：3家系进行抗褐飞虱鉴定,以推测相应F2单株的基因型。连锁分析表明,Bph9位于第12染色体上的两个SSR标记RM463和RM5341之间,分别与之相距6．8cM和9．7cM。该标记有助十将Bph9用于分子标记辅助选择育种研究。     

Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.)

The growing number of rice microsatellite markers warrants a comprehensive comparison of allelic variability between the markers developed using different methods, with various sequence repeat motifs, and from coding and non-coding portions of the genome. We have performed such a comparison over a set of 323 microsatellite markers; 194 were derived from genomic library screening and 129 were derived from the analysis of rice-expressed sequence tags (ESTs) available in public DNA databases. We have evaluated the frequency of polymorphism between parental pairs of six inter- subspecific crosses and one inter-specific cross widely used for mapping in rice. Microsatellites derived from genomic libraries detected a higher level of polymorphism than those derived from ESTs contained in the GenBank database (83.8% versus 54.0%). Similarly, the other measures of genetic variability [the number of alleles per locus, polymorphism information content (PIC), and allele size ranges] were all higher in genomic library-derived microsatellites than in their EST-database counterparts. The highest overall degree of genetic diversity was seen in GA-containing microsatellites of genomic library origin, while the most conserved markers contained CCG- or CAG-trinucleotide motifs and were developed from GenBank sequences. Preferential location of specific motifs in coding versus non-coding regions of known genes was related to observed levels of microsatellite diversity. A strong positive correlation was observed between the maximum length of a microsatellite motif and the standard deviation of the molecular-weight of amplified fragments. The reliability of molecular weight standard deviation (SDmw) as an indicator of genetic variability of microsatellite loci is discussed. Received: 5 May 1999 / Accepted: 16 August 1999     

Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types

Genetic variation between samples of Oryza sativa from 19 localities in Bangladesh and Bhutan was assessed using two PCR-based molecular marker systems: RAPD (random amplification of polymorphic DNA) and ISSR-PCR (inter-simple sequence repeat polymerase chain reaction). Employing RAPD, a set of 14 decanucleotides of arbitrary sequence directed the amplification of 94 reproducible marker bands, 47 (50%) of which were polymorphic. In addition, a set of 9 ISSR primers were used to direct amplification of 71 PCR products, 40 (56%) of which were polymorphic. Multivariate analyses of the two PCR-based molecular marker data sets provided evidence that the patterns of variation correspond with the classification described by Glaszmann [9] using isozyme analysis. Subtle differences in the relationships revealed between rice groups using the two types of PCR-based marker led to investigations of their map positions using an intraspecific doubled haploid mapping population. The observation that the chromosomal locations of markers can influence diversity assessments is presented and the significance of this is discussed.