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Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several minor genes. Its complexity and the mutable characteristic of rice blast isolates both hinder the development of the blast resistance research. The article here tried to explore the resistance gene distribution on rice chromosomes and the way of function. Totally 124 QTLs have been identified against 20 isolates using Cartographer software with a ZYQ8/JX17 DH population, which separately are at 100 loci of 72 marker intervals on 12 rice chromosomes. Of them, 16 QTLs were determined by the isolate HB-97-36-1. 82 QTLs (66.13%) are from the resistant parent alleles, ZYQ8, while 42 QTLs (33.87%) are from the susceptible parent alleles, JX17. In comparison of their positions on chromosome, most QTLs are clustered together and distributed nearby the major genes especially the regions on chromosomes 1, 2, 8, 10 and 12. Each QTL could account for the resistance variation between 3.52%–68.64%. And, a positional QTL might display the resistance to several different isolates with different contributions.

Ricexa5 gene provides recessive, race-specific resistance to bacterial blight disease caused by the pathogenXanthomonas oryzae pv.oryzae and has great value for research and breeding. In an effort to clonexa5, an F2 population of 4892 individuals was developed from thexa5 near isogenic lines, IR24 and IRBB5. A fine mapping procedure was conducted and tightly linked RFLP markers were used to screen a BAC library of IRBB56, a resistant rice line containing thexa5 gene. A 213 kb contig covering thexa5 locus was constructed. According to the sequences from the International Rice Genome Sequening Project (IRGSP), the Chinese Superhybrid Rice Genome Project (SRGP) and some sub-clones of the contig, twelve SSLP and CAPS markers were developed for fine mapping. Thexa5 gene was mapped to a 0.3 cM interval between markers K5 and T4, which spanned an interval of approximately 24 kb, co-segregating with marker T2. Sequence analysis of the 24 kb region revealed that an ABC transporter and a basal transcription factor (TFIIa) were potential candidates for thexa5 resistance gene product. The molecular mechanism by which thexa5 gene provides recessive, race-specific resistance to bacterial blight will be elucidated by the functional tests of the 24 kb DNA and the candidate genes.

A double haploid population derived from anther culture of ZYQ8/JX17, a typical indica and japonica hybrid, was used in this study. The inhibited effect of water-soluble extract of 123 DH pure lines leaves on the lettuce roots growth was investigated, and the QTLs analysis of rice allelopathy was carried out. Totally, four QTLs related to rice allelopathy were detected, and they were on chromosomes 3, 9, 10 and 12, respectively. The LOD scores were 3.40, 2.68. 2.75 and 3.08, respectively. Among them, additive effects of the QTLs on chromosomes 3 and 10 were 1.65 and 1.43, on chromosomes 9 and 12 were −1.44 and −1.58, respectively. Allelopathy characteristics of another three common rice varieties were also studied.

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have produced a draft rice genome sequence of Oryza sativa ssp. indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from both indica and japanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

A double haploid population, derived from anther culture of F1 hybrid between a typicalindica and ajaponica (ZYQ8/JX17), has been used to investigate the low temperature germinability (LTG) at 15°C. The low temperature germinability of two parents was significantly different. In 6–11 d, the germination percentage of ZYQ8 was higher than that of JX17. In 12–16 d, the germination percentage of JX17 was higher than that of ZYQ8. The quantitative trait loci (QTLs) of every day for low temperature germinability have been mapped based on a molecular linkage map constructed from this population. In 8–11 d, qLTG-9 was identified in C397B-RZ617B on chromosome 9, the additive effect was positive, showing that the allele from JX17 could increase low temperature germinability. In 12–16 d, qLTG-4 was mapped between RG908 and CT563 on chromosome 4, the additive effect was negative, showing that the allele from ZYQ8 could increase low temperature germinability. These two QTLs were detected at different stages, showing the complexity of the mechanism of low temperature germinability.

Wild rice species is an important source of useful genes for cultivated rice improvement. Some accessions ofOryza eichingeri (2n = 24, CC) from Africa confer strong resistance to brown planthopper (BPH), whitebacked planthopper (WBPH) and bacterial blight (BB). In the present study, restriction fragments length polymorphism (RFLP) and simple sequence repeats (SSR) analysis were performed on disomic backcross plants betweenOryza sativa (2n = 24, AA) andO. eichingeri in order to identify the presence ofO. eichingeri segments and further to localize BPH-resistant gene. In the introgression lines, 1–6O. eichingeri segments were detected on rice chromosomes 1, 2, 6, or/and 10. The dominant BPH resistant gene, tentatively named Bph13(t), was mapped to chromosome 2, being 6.1 and 5.5 cM away from two microsatellite markers RM240 and RM250, respectively. The transfer and localization of this gene fromO. eichingeri will contribute to the improvement of BPH resistance in cultivated rice.

The homozygous restorer lines with a single copy of the transgeneXa21 have been obtained from the progenies of transgenic Minghui63 and Yanhui559 plants through PCR marker-assisted selection and test cross. These homozygous transgenic restorer lines can be used to breed hybrid rice with high resistance to bacterial leaf blight.

The sterility of Pingxiang male-sterile rice (Pms), possibly derided from a spontaneous mutation in Pingxiang fertile rice (Pmf), was previously reported to be controlled by a single dominant nuclear gene. It can be restored to fertility either by a dominant epistatic gene or by higher temperature treatment at the early stage of inflorescence development. In order to tag the genic male-sterile gene, Pms, Pmf and Ce 64, a cytoplasmic male-sterile restoring line without the epistatic gene for Pms, were used to construct mapping populations. Two segregation populations, “(Pms/Ce 64) F1s (sterile plant)//Pmf” F1 and “Pms//(Pmf/Ce 64) Fl” F1, were simultaneously developed. Subsequently, the genic malesterile gene was mapped between a simple sequence length polymorphism marker, RM228, and a restriction fragment length polymorphism marker, G2155, with distances of 14.9 and 2.6 cM, respectively. The tagged dominant genic male-sterile gene is temporarily designated Ms-p.

An F2 population developed from theXa-4 near isogenic lines, IR24 and IRBB4, was used for fine mapping of the rice bacterial blight resistance gene,Xa-4. Some restriction fragment length polymorphism (RFLP) markers on the high-density map constructed by Harushima et al. and the amplified DNA fragments homologous to the conserved domains of plant disease resistance (R) genes were used to construct the genetic linkage map around the geneXa-4 by scoring susceptible individuals in the population.Xa-4 was mapped between the RFLP marker G181 and the polymerase chain reaction (PCR) marker M55. The R gene homologous fragment marker RS13 was found co-segregating withXa-4 by analyzing all the plants in the population. This result opened an approach to map-based cloning of this gene, and marker RS13 can be applied to molecular marker-assisted selection ofXa-4 in rice breeding programs.

Phosphorus (P)-deficiency in rice (Oryza. Sativa. L) may cause yield reductions. This research has been conducted to map quantitative trait loci (QTLs) for tolerance to low phosphorus stress in a doubled haploid (DH) population. By using the linkage map of this population, the QTLs for relative dry weight, relative P content and relative P utilization efficiency have been located. The results indicate that one RFLP marker located on chromosome 6 is closely associated with relative root dry weight, relative shoot dry weight and relative total dry weight, which explain 24.9%, 20.5% and 25.2% of the total phenotypic variations, respectively. Two QTLs affect relative P uptake content, which account for 20.7% of the total phenotypic variations. One micro-effect QTL has been found to be associated with relative P utilization efficiency. It is suggested that the P uptake efficiency is more associated with P efficiency. Among the secondary physiological indices of P uptake efficiency, the root dry weight is more important than others.

Quantitative trait locus (QTLs) mapping for rapid visco analyser (RVA) profile parameters has been carried out by using a double haploid (DH) population derhred from a cross betweenindica variety Zhai-Ye-Qing 8 andjaponica variety Jing-Xi 17 and its genetic linkage map. The results indicate that the segregation of the RVA profiles is continually distributed among the DH lines, and some DH lines show transgressive segregation for all the parameters. A major QTL,Waxy (Wx) gene on chromosome 6 which controls the amylose synthesis, has been detected significantly for 5 traits: hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), consistency viscoslty (CSV) and setback viscoslty (SBV). Therefore, the RVA profile parameters are mainly controlled byWx gene. Other 3 and 2 QTLs have also been identified for BDV and SBV, respectively, and two of them share the same region on chromosomes 1 and 5. However, the peak viscosity (PKV) is controlled by a minor QTL on chromosome 12, qPKV-12.

This study was conducted with a clonal F2 population of rice from a cross between Jasmine 85, a resistant variety, and Lemont, a susceptible cultivar. The rice plants belonging to each F2 clone were divided into two plots, which were put in two replicates, respectively. Clonal parents were tested as controls. The plants were inoculated by short toothpicks incubated with RH-9, a virulent isolate of the pathogenic fungus,Rhizoctonia solani, which causes rice sheath blight. The extreme resistant and susceptible clonal lines were selected for construction of resistant and susceptible DNA pools, respectively. A total of 94 polymorphic markers evenly distributed on 12 rice chromosomes were used for bulked segregant analysis, three positive ones were found polymorphic between the two DNA pools, and three major QTLs for sheath blight resistance, Rh-2, Rh-3 and Rh-7, were identified. The three major QTLs were located on chromosomes 2, 3 and 7, and could explain 14.4%, 26.1% and 22.2% of the phenotypic variation.

Quantitative trait loci (QTLs) controlling salt-tolerance at the seedling stage in rice (Oryza sativa L.) were identified by interval mapping (SIM) and composite interval mapping (CIM) using a doubled haploid population ZJDH and its high resolution genetic linkage map. The population was derived from an inter-subspecific cross between anindica variety Zhaiyeqing8 (ZYQ8) and ajaponica variety Jingxil7 (JX17). Analysis of survival days of seedlings treated with 0.7% NaCl revealed that a major salt-tolerance quantitative trait locus (QTL), Std, was present between markers RG612 and C131 on chromosome 1 when using both MAPMAKER/QTL 1.1 and PLABQTL 1.0 (SIM). Its allele which contributes to salt-tolerance was from ZYQ8. In addition, seven more QTLs which give additive effect on salt-tolerance are identified when using PLABQTL (CIM), and most of them were from JX17.

The rice aneuploids with telochromosomes are ideal genetic stocks for chromosome arm identification and microdissection. A rice telo-tetrasomic line with two extra short arms of chromosome 5 (5S) was used in the present study. The amrs of 5S were microdissected from the prometaphase cells in mitosis and amplified with linker adaptor PCR (LA-PCR). The amplified fmgments, ranging from 200–3000 bp, were confirmed to be from the rice chromosome arm 5S by the rice STS and miamatellite markers.

Genetic mapping of microsatellite markers was carried out in a rice DH population derived from across between Zaiyeqing 8 (indica) and Jingxi 17 (japonica). A total of 89 microsatellite markers, including 84 (GA)n, 2(TCT)n, 2(ATT)n, and, l(ATC)n motifs, were integrated relatively evenly into the established genetic map of the DH population. This will facilitate the utilization of microsatillite markers in rice gene mapping and marker aided breeding.

A spontaneous white panicle mutant was found from the F6 progenies of an indica/japonica cross. The mutant exhibits white stripes on its basal leaves while the panicles, rachis and pedicel are milky white colored at flowering stage. Genetic analysis in an F2 population from the cross of Zhi7/white panicle mutant indicates that the white panicle phenotype is controlled by a single recessive nuclear gene, tentatively termed aswp(t). Using microsatellite markers, thewp(t) gene was anchored between the markers of SSR101 and SSR63.9 with a map distance of 2.3 and 0.8 cM, respectively, and co-segregated with the marker of SSR17 on rice chromosome 1.

AFLP analysis of near-isogenic lines of the stripe rust resistance geneYr10 was carried out with 6Pst I-primers and 10Taq I -primers with the donor parent ofYr10 gene as the check. A total of about 4200 distinguishable bands were amplified, of which 5 were stable. The genetic linkage of the 5 polymorphic DNA fragments with the target gene were tested preliminarily on a segregating F2 population derived from a cross between the gene donor parent “More” and susceptible cultivar “Mingxian 169”. The DNA fragment PT0502 was found closely linked to theYr10 gene and cloned and sequenced. Based on the sequence specific primers for PCR were designed and synthesized. Genetic linkage analysis with 195 segregating F2 plants indicated that the genetic distance was 0.5 cM between the main product SC200 fragment produced by PCR with the primers and theYr10 gene. The primers can be used to detect theYr10 gene quickly, effectively and exactly.

We have analyzed a lax mutant that exhibits altered panicle architecture in rice. The primary and secondary rachis-branches are normally initiated and each branch ends in a terminal spikelet, but all the lateral spikelets are absent and the terminal spikelet displays variegated structures in the mutant. An F2 population from the cross between the lax mutant and a japonica variety, W11, was constructed and analyzed. Using microsatellite and CAPS markers, the lax locus was mapped on the long arm of chromosome 1, co-segregated with a CAPS marker, LZ1, within an interval of 0.28 cM between a CAPS marker, HB2, and a microsatellite marker, MRG4389. RT-PCR analysis revealed that the expressions of the rice B-function MADS-box genes OsMADS2, OsMADS4, OsMADS16 and OsMADS3 were significantly reduced, whereas the expression of the rice A-function gene RAP1A was not altered.

A method of constructing restriction map by optical mapping and single molecule fluorescent microscopy is described. DNA molecules were aligned and adsorbed on a glass coverslip surface by a modified “molecular combing” technique, and then the surface-immobilized DNAs were cleaved in situ with a restriction endonuclease. Individual DNA molecules digested by the endonuclease EcoR I were observable with fluorescent microscopy. Using optical mapping, a physical map of a rice bacterial artificial chromosome clone was constructed. This method will facilitate genomic mapping and tracing the dynamic process in real time at a single molecule level with fluorescence microscopy.