Short Arm Of Rice Chromosome Research Articles

Identification and characterization of tsyl1, a thermosensitive chlorophyll-deficient mutant in rice (Oryza sativa)

Chloroplast development and chlorophyll biosynthesis are affected by temperature. However, the underlying molecular mechanism of this phenomenon remains elusive. Here, we isolated and characterized a thermosensitive yellow-green leaf mutant named tsyl1 (thermosensitive yellow leaf 1) from an ethylmethylsulfone (EMS)-mutagenized pool of rice. The mutant exhibits a yellow-green leaf phenotype and decreased leaf chlorophyll contents throughout development. At the mature stage of the tsyl1 mutant, the plant height, tiller number, number of spikelets per panicle and 1000 seed weight were decreased significantly compared to those of wild-type plants, but the seed setting rate and panicle length were not. The mutant phenotype was controlled by a single recessive nuclear gene on the short arm of rice chromosome 11. Map-based cloning of TSYL1, followed by a complementation experiment, showed a G base deletion at the coding region of LOC_Os11g05552, leading to the yellow-green phenotype. The TSYL1 gene encodes a signal recognition particle 54 kDa (SRP54) protein that is conserved in all organisms. The expression of tsyl1 was induced by high temperature. Furthermore, the expression of chlorophyll biosynthesis- and chloroplast development-related genes was influenced in tsyl1 at different temperatures. These results indicated that the TSYL1 gene plays a key role in chlorophyll biosynthesis and is affected by temperature at the transcriptional level.

Development of InDel markers of Bph3 and pyramiding of four brown planthopper resistance genes into an elite rice variety

Brown planthopper (BPH) is one of the most destructive pests in rice. Breeding resistant cultivars is the most effective strategy to control BPH. Bph3 is a broad-spectrum and durable BPH resistance locus spanning ~ 50 kb on the short arm of rice chromosome 4. Using the genomic variation data of 4726 rice varieties from public database, we developed 8 InDel markers within the Bph3 locus. By analyzing 563 rice varieties, we demonstrated that these markers could effectively identify Bph3-carriers, with an accuracy rate near to 90%. Through marker-assisted backcross breeding (MABC), we introduced four BPH resistance genes (Bph3/14/18/32) into an elite rice variety, Guang 8B. The results showed that Bph3 had the biggest effect, followed by Bph14 and Bph32, and Bph18 had the smallest effect. In addition, the level of BPH resistance increased with the number of genes pyramided. However, in the case of only two genes being pyramided, the resistance increase was not significant in comparison with the larger effect of the two genes. This suggests that the resistance effects are not simply additive, but epistasis may be involved. The InDel markers and pyramiding lines developed in this study will facilitate Bph3-carrier identification and BPH resistance breeding in rice.

Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identification of a novel resistance locus gm12 in rice cultivar MN62M.

The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes significant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most effective and economical approach for maintaining yield stability by controlling RGM. Identification of resistance genes will help in marker-assisted selection (MAS) to pyramid the resistance genes and develop a durable resistance variety against RGM in areas with frequent outbreaks. In this study, a mitochondrial cytochrome oxidase subunit I (mtCOI) was used to analyze the genetic diversity among Thai RGM populations. The phylogenetic tree indicated that the Thai RGM populations were homogeneously distributed throughout the country. The reactions of the resistant rice varieties carrying different resistance genes revealed different RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identified a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identified using linkage analysis in 144 F2 plants derived from a cross between susceptible cultivar KDML105 and RGM-resistant cultivar MN62M with single nucleotide polymorphism (SNP) markers and F2:3 phenotype. The locus was mapped between two flanking markers, S2_76222 and S2_419160. In conclusion, we identified a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This finding yielded DNA markers that can be used in MAS to develop cultivars with broad-spectrum resistance to RGM. Moreover, the new resistance gene provides essential information for the identification of RGM biotypes in Thailand and Southeast Asia.

Fine Mapping and Candidate Gene Analysis of the Tiller Suppression Gene ts1 in Rice.

Tiller number is one of the key factors that influences rice plant type and yield components. In this study, an EMS-induced rice tiller suppression mutant ts1 was characterized. Morphological and histological observations revealed that, in the ts1 plants, the tiller buds were abnormally formed and therefore cannot outgrow into tillers. With an F2 population derived from a cross between ts1 and an indica cultivar Wushansimiao, a major gene, tiller suppression 1 (ts1) was fine-mapped to a 108.5 kb genomic region between markers ID8378 and SSR6884 on the short arm of rice chromosome 2. Candidate gene analysis identified nineteen putative genes. Among them, ORF4 (LOC_Os02g01610) is a PPR gene which harbored a point mutation c.+733/C→T in ts1 mutant plants. A co-dominant SNP marker cd-733C/T was subsequently developed and the SNP assay demonstrated that the point mutation co-segregated with tiller suppression phenotype. Quantitative RT-PCR analysis showed that the expression level of ORF4 in ts1 plants was significantly lower than that in their wild plants, and the expression of rice tillering regulators MOC1 and HTD1 was also significantly decreased in ts1 plants. Our data indicated that ORF4 was a strong candidate gene for ts1 and ts1 might play a role in regulating rice tillering through MOC1 and HTD1 associated pathway. The results above provide a basis for further functional characterization of ts1 and will shed light on molecular mechanism of rice tillering. The informative SNP marker cd-733C/T will facilitate marker-assisted selection of ts1 in rice plant type breeding.

Map-based cloning and characterization of the novel yellow-green leaf gene ys83 in rice (Oryza sativa)

Leaf-color mutants have been extensively studied in rice, and many corresponding genes have been identified up to now. However, leaf-color mutation mechanisms are diverse and still need further research through identification of novel genes. In the present paper, we isolated a leaf-color mutant, ys83, in rice (Oryza sativa). The mutant displayed a yellow-green leaf phenotype at seedling stage, and then slowly turned into light-green leaf from late tillering stage. In its yellow leaves, photosynthetic pigment contents significantly decreased and the chloroplast development was retarded. The mutant phenotype was controlled by a recessive mutation in a nuclear gene on the short arm of rice chromosome 2. Map-based cloning and sequencing analysis suggested that the candidate gene was YS83 (LOC_Os02g05890) encoding a protein containing 165 amino acid residues. Gene YS83 was expressed in a wide range of tissues, and its encoded protein was targeted to the chloroplast. In the mutant, a T-to-A substitution occurred in coding sequence of gene YS83, which caused a premature translation of its encoded product. By introduction of the wild-type gene, the ys83 mutant recovered to normal green-leaf phenotype. Taken together, we successfully identified a novel yellow-green leaf gene YS83. In addition, number of productive panicles per plant and number of spikelets per panicle only reduced by 6.7% and 7.6%, respectively, meanwhile its seed setting rate and 1000-grain weight (seed size) were not significantly affected in the mutant, so leaf-color mutant gene ys83 could be used as a trait marker gene in commercial hybrid rice production.

Fine mapping and candidate gene analysis of qHD5, a novel major QTL with pleiotropism for yield-related traits in rice (Oryza sativa L.).

A major QTL for heading date, qHD5, was fine-mapped to a 52.59-kb region on the short arm of rice chromosome 5. Heading date (HD) is one of the most important traits that enables rice to adapt to seasonal differences and specific growth conditions in diverse growing regions. In this study, a major-effect quantitative trait locus (QTL), qHD5, was resolved as a single Medelian factor that causes NIL(BG1) and NIL(XLJ) (two near-isogenic lines (NILs) used in our study) to have at a minimum of 10-day difference in HD under both long-day and short-day conditions in rice. qHD5 was initially mapped to a 309.52-kb genomic region in our previous study. Here, using an advanced BC4F3 population and map-based cloning, we further narrowed the location of qHD5 to a 52.59-kb region between the H71 and RD502 markers. Sequence analysis revealed that Os05g03040, which putatively encodes an AP2 (APETALA2) transcription factor, has six single nucleotide polymorphisms (SNPs) between NIL(BG1) and NIL(XLJ). On this basis, this gene was concluded to be the most probable candidate gene for qHD5. Our results also showed that Hd3a, RFT1, Hd1, Ehd1, and Ghd7 were differentially expressed in the two NILs. Moreover, qHD5 was found to affect yield-related traits such as flag leaf width, flag leaf length, branch number, and 1000-grain weight.

Identification and gene mapping of a grain-filling mutant <italic>gef1</italic> in rice

Grain filling is an extremely important process in rice growth and development. This process which involves complex genetic regulatory networks and environmental interaction, is directly related to the formation of rice yield and quality. A stable inherited mutant with grain extended filling ( gef1 ) was identified from an EMS mutagenized population of Yixiang 1B. The investigation of agronomic traits, measurement of physiological and biochemical characteristics, histology observation, gene expression analysis and gene mapping were performed in this study. Compared with the wild type plants, the grain filling rate of gef1 was significantly lower than that of Yixiang 1B, resulting in the grain filling time of gef1 was about 30 days delay. Meanwhile, the 1000-grain weight of gef1 became bigger and seed setting rate decreased by 22%. During the development of caryopsis, we found that the soluble sugar content in wild type showed a single peak curve, and the content maintained at a low level throughout the grain filling stage. However, the soluble sugar content of the gef1 was significantly higher than that of the wild type, and showing a bimodal curve. It revealed that the transportation and distribution of photosynthate, and starch synthesis were inefficiency in gef1 . In addition, histocytological analysis showed that the number of big vascular bundles in the same transection parts of rachis, the first top internodes and the second top internodes were all decreased in gef1 , and indicated that the transport efficiency of photosynthate was one of the limiting factors in the rate of grain filling. The scanning electron microscope showed that the glume of gef1 had smooth surface and slender cells. Scanning of grain transection showed that gef1 had spherical amyloplasts and arranged loosely, but the wild type had unregular polygon amyloplasts and packed closely. These results suggested that the changes of grain size associated with the cell number and shape of glume, and gef1 had impact on rice quality. Additionally, by analyzing the expression of the glycometabolism-related genes in developing caryopsis, we found that all of them were keeping at a low level in gef1 compared with the wild type. By analyzing the three crosses gef1 /Yixiang 1B, gef1 /02428 and gef1 /Kitaake, we found that the F1 plants of these three crosses were all normal and indicated that the mutant trait was controlled by a recessive gene. The ratio of normal plants to mutant plants in the three F2 populations was 3:1 and indicating that the mutant trait was controlled by a single recessive nuclear gene. gef1 was preliminarily mapped on the short arm of rice chromosome 3, and was narrowed to a 198 kb region between InDel3-1 and InDel3-2. This region has 21 open reading frames and there was no homologous gene had been reported within it, and the further identification work of candidate genes is ongoing.

Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids.

Over the next decade, wheat grain production must increase to meet the demand of a fast growing human population. One strategy to meet this challenge is to raise wheat productivity by optimizing plant stature. The Reduced height 8 (Rht8) semi-dwarfing gene is one of the few, together with the Green Revolution genes, to reduce stature of wheat (Triticum aestivum L.), and improve lodging resistance, without compromising grain yield. Rht8 is widely used in dry environments such as Mediterranean countries where it increases plant adaptability. With recent climate change, its use could become increasingly important even in more northern latitudes. In the present study, the characterization of Rht8 was furthered. Morphological analyses show that the semi-dwarf phenotype of Rht8 lines is due to shorter internodal segments along the wheat culm, achieved through reduced cell elongation. Physiological experiments show that the reduced cell elongation is not due to defective gibberellin biosynthesis or signalling, but possibly to a reduced sensitivity to brassinosteroids. Using a fine-resolution mapping approach and screening 3104 F2 individuals of a newly developed mapping population, the Rht8 genetic interval was reduced from 20.5 cM to 1.29 cM. Comparative genomics with model genomes confined the Rht8 syntenic intervals to 3.3 Mb of the short arm of rice chromosome 4, and to 2 Mb of Brachypodium distachyon chromosome 5. The very high resolution potential of the plant material generated is crucial for the eventual cloning of Rht8.

Sequence Composition and Gene Content of the Short Arm of Rye (Secale cereale) Chromosome 1

BackgroundThe purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide.Methodology/Principal FindingsMultiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice.ConclusionsThe present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.

Fine mapping of a major quantitative trait locus, qFLL6.2, controlling flag leaf length and yield traits in rice (Oryza sativa L.)

Fine mapping of a quantitative trait locus, qFLL6.2, controlling flag leaf length (FLL) and yield traits in rice was conducted using four sets of near isogenic lines (NILs) that were developed from a common residual heterozygote at F7 generation of the indica rice cross Zhenshan 97/Milyang 46. Each of the NIL sets consisted of 40 lines that are S1 progenies of ten maternal homozygotes, ten paternal homozygotes, and 20 heterozygotes differing in a portion of the 1.19-Mb interval RM3414–RM6917 on the short arm of rice chromosome 6. Analysis of phenotypic differences among the three genotypic groups in each NIL set delimited qFLL6.2 to a 62.1-kb region flanked by simple sequence repeat marker RM3414 and sequence-tagged site marker Si2944. This QTL explained 52.73% of the phenotypic variance, and the Zhenshan 97 allele increased FLL by 2.40 cm. Based on data collected from homozygous lines of three of the NIL sets, qFLL6.2 was shown to have major effects on all the three yield traits analyzed, including the number of spikelets per panicle, the number of filled grains per panicle, and grain weight per panicle. A comparison of the different groups revealed that the effect of qFLL6.2 was highly consistent across different genetic backgrounds and environments, providing a good candidate for map-based cloning and investigating the source–sink relationship in rice.

Validation and dissection of quantitative trait loci for leaf traits in interval RM4923-RM402 on the short arm of rice chromosome 6

Validation and dissection of a QTL region for leaf traits in rice which has been reported in a number of independent studies were conducted. Three sets of near isogenic lines (NILs) were originated from a residual heterozygous line derived the indica cross Zhenshan 97B/Milyang 46. They were overlapping and totally covered a 4.2-Mb heterogenous region extending from RM4923 to RM402 on the short arm of rice chromosome 6. Each NIL set consisted of 10 maternal lines and 10 paternal lines. They were measured for the length, width, perimeter and area of the top three leaves and the number of spikelets per panicle, number of grains per panicle and grain weight per panicle. In NIL sets 6-4 and 6-7, differing in intervals RM4923-RM225 and RM19410-RM6119, respectively, significant variations with the enhancing alleles from the female parent ZS97 were shown for the length, perimeter and area except for the area of the third leaf from top in 6-4, but the effects were lower in 6-4 than in 6-7. No significant effects were detected for the three traits in the remaining NIL set. It was shown that flag leaf length (FLL) is the primary target of the QTLs detected. Two QTLs for FLL linked in repulsion phase were resolved, of which qFLL6.2 located in the 1.19-Mb interval RM3414-RM6917 had a major effect with the enhancing allele from Zhenshan 97B, and qFLL6.1 located in the 946.8-kb interval RM19350-RM19410 had a smaller effect with the enhancing allele from Milyang 46. The two QTLs also exerted pleiotropic effects on the yield traits.

Flanking Microsatellite Markers for Breeding Varieties Against Asian Rice Gall Midge

The Asian rice gall midge, Orseolia oryzae Wood-Mason (Cecidomyiidae: Diptera) is a serious pest of wet season rice in South and Southeast Asia. Due to internal feeding habit and presence of biotypes of the pest, the most feasible way to control is breeding varieties resistant against multiple biotypes through marker-assisted breeding (MAB). But very few versatile co-dominant markers linked to the gall midge resistance genes are available. We used a set of F9 recombinant inbred lines (RILs) of the cross TN1/PTB10 and identified microsatellite markers for the gall midge resistance gene in cv. PTB10 on short arm of rice chromosome 8. Markers RM22550 and RM547 flank the gene at a distance of 0.9 and 1.9 cM, respectively. Amplification of the markers in gall midge resistant and susceptible cultivars showed that these markers can be successfully used in MAB for development of gall midge resistant varieties.

Genetic Analysis and Gene Mapping of a Novel Yellow-Green Leaf Mutant in Rice

An inherited stably yellow-green leaf mutant D83 was isolated by chemistry mutagenesis.Its whole plant exhibited yellow-green trait at the seedling stage,and gradually changed into pea green from the tillering stage.Compared with its wild-type parent 10079,at the seedling stage,the contents of chlorophyll a,chlorophyll b,and carotenoid decreased by 45.03%,53.93%,and 39.56%,at the maturation period,the number of spikelets per panicle reduced by 9.45%,the 1000-grain weight decreased by 10.76%,respectively.Genetic analysis of F1 and F2 generations of D83 crossed with green rice varieties showed that the yellow-green leaf trait was controlled by one pair of recessive nuclear genes.Genetic mapping of the mutant gene was conducted by using molecular marker and F2 mapping population of D83/Zhefu802.The results suggested that the mutant gene of D83 was mapped on the short arm of rice chromosome 2,nearby SSR marker RM110,between InDel markers Ch2-27 and Ch2-32.The genetic distances from the target gene to two InDel markers were 1.2 cM and 2.3 cM,respectively.The mutant gene of D83 was considered to be a new yellow-green leaf gene in rice and designated tentatively as chl13(t).

Quantitative Trait Loci for Panicle Size and Grain Yield Detected in Interval RM111-RM19 784 on the Short Arm of Rice Chromosome 6

A rice residual heterozygous line (RHL) carrying a heterozygous segment extending from RM111 to RM19784 on the short arm of rice chromosome 6 was selected from a RHL-derived population used previously. The resultant F 2:3 population was used to detect quantitative trait loci (QTLs) for three yield traits, the number of spikelets per panicle (NSP), the number of grains per panicle (NGP) and grain yield per plant (GY). Two QTLs for NSP, one QTL for NGP and one QTL for GY were detected, all of which were partially dominant and had the enhancing alleles from the maternal line Zhenshan 97B. Analysis based on the genotypic groups of the markers closely linked to the two QTLs for NSP indicated that they did not interact with each other. Two F 2 populations and two near isogenic line (NIL) sets segregating in two sub-regions of interval RM111-RM19784 were developed. The two QTLs for NSP were validated, of which one had major effect and was co-segregated with heading date gene Hd1, and the other had smaller effect and was located in an upper region linked to Hd1. The two regions also showed significant effects on the number of filled grain and grain yield, although the effect on the number of filled grain was less consistent.

Dissection of QTLs for Hull Silicon Content on the Short Arm of Rice Chromosome 6

The QTL qHUS6 for hull silicon content in rice was previously located on the short arm of rice chromosome 6. By using an F 2:3 population segregating in the RM587–RM19784 region harboring qHUS6 in an isogenic background, two QTLs for hull silicon content were detected, of which qHUS6-1 was located in the distal region and qHUS6-2 in the region proximal to the centromere. Three rice plants carrying small heterozygous segments in the target region were selected, of which two covered the qHUS6-1 region and the other covered the qHUS6-2 region. Three F 2:3 populations were derived from the selfed seeds of the three plants, respectively. QTL mapping was performed using the two populations segregating in the qHUS6-1 region, and qHUS6-1 was delimited to a 147.0-kb region flanked by the markers RM510 and RM19417. Five groups of F 3 lines with different genotypic compositions in the qHUS6-2 region were selected from the other F 2:3 population. Two QTLs were separated with two-way ANOVA, of which qHUS6-2a was located in the interval defined by RM19706–RM19795 and qHUS6-2b in the interval RM314–RM19665.

Divinyl Chlorophyll(ide) a Can Be Converted to Monovinyl Chlorophyll(ide) a by a Divinyl Reductase in Rice

3,8-Divinyl (proto)chlorophyll(ide) a 8-vinyl reductase (DVR) catalyzes the reduction of 8-vinyl group on the tetrapyrrole to an ethyl group, which is indispensable for monovinyl chlorophyll (Chl) synthesis. So far, three 8-vinyl reductase genes (DVR, bciA, and slr1923) have been characterized from Arabidopsis (Arabidopsis thaliana), Chlorobium tepidum, and Synechocystis sp. PCC6803. However, no 8-vinyl reductase gene has yet been identified in monocotyledonous plants. In this study, we isolated a spontaneous mutant, 824ys, in rice (Oryza sativa). The mutant exhibited a yellow-green leaf phenotype, reduced Chl level, arrested chloroplast development, and retarded growth rate. The phenotype of the 824ys mutant was caused by a recessive mutation in a nuclear gene on the short arm of rice chromosome 3. Map-based cloning of this mutant resulted in the identification of a gene (Os03g22780) showing sequence similarity with the Arabidopsis DVR gene (AT5G18660). In the 824ys mutant, nine nucleotides were deleted at residues 952 to 960 in the open reading frame, resulting in a deletion of three amino acid residues in the encoded product. High-performance liquid chromatography analysis of Chls indicated the mutant accumulates only divinyl Chl a and b. A recombinant protein encoded by Os03g22780 was expressed in Escherichia coli and found to catalyze the conversion of divinyl chlorophyll(ide) a to monovinyl chlorophyll(ide) a. Therefore, it has been confirmed that Os03g22780, renamed as OsDVR, encodes a functional DVR in rice. Based upon these results, we succeeded to identify an 8-vinyl reductase gene in monocotyledonous plants and, more importantly, confirmed the DVR activity to convert divinyl Chl a to monovinyl Chl a.

Detection of a brown planthopper resistance gene bph4 at the same chromosomal position of Bph3 using two different genetic backgrounds of rice

The brown planthopper (BPH) resistance gene bph4 has previously been assigned on the short arm of rice chromosome 6. However, the map position of the gene could not be determined. To detect the bph4 locus, 15 polymorphic simple sequence repeat (SSR) markers covering genetic distance of 0.0–63.4 cM on chromosome 6 were used to survey 15 BPH resistant (R) and susceptible (S) individuals from each of the 95 and 78 F2 populations derived from crosses of TN1/Babawee and Babawee/KDML105, respectively. One SSR marker, RM586, was associated with the R and S from the F2 populations. Additional markers surrounding the RM586 locus were examined to define the location of bph4. From the genetic linkage map and QTL analysis of 95 and 78 F2 individuals, the bph4 locus was mapped at the same chromosomal region of Bph3 between two flanking markers RM589 and RM586. Markers linked to the resistance gene explained 58.8–70.1% of the phenotypic variations and can be used for marker-assisted selection in BPH-resistant breeding programs. In addition, our experiment provides evidence that a recessive gene could behave as a dominant gene under different genetic backgrounds.

Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice

A days to heading QTL (dth1.1) located on the short arm of rice chromosome 1 was sub-divided into eight sub-introgression lines (SILs) to analyze the genetic basis of transgressive variation for flowering time. Each SIL contained one or more introgression(s) from O. rufipogon in the genetic background of the elite Oryza sativa cultivar, Jefferson. Each introgression was defined at high resolution using molecular markers and those in the dth1.1 region were associated with the presence of one or more flowering time genes (GI, SOC1, FT-L8, EMF1, and PNZIP). SILs and controls were evaluated for flowering time under both short- and long-day growing conditions. Under short-day lengths, lines with introgressions carrying combinations of linked flowering time genes (GI/SOC1, SOC1/FT-L8, GI/SOC1/FT-L8 and EMF1/PNZIP) from the late parent, O. rufipogon, flowered earlier than the recurrent parent, Jefferson, while recombinant lines carrying smaller introgressions marked by the presence of GI, SOC1, EMF1 or PNZIP alone no longer flowered early. Under long-day length, lines carrying SOC1/FT-L8, SOC1 or PNZIP flowered early, while those carrying GI or EMF1 delayed flowering. Across all experiments and in the field, only SIL_SOC1/FT-L8 was consistently early. A preliminary yield evaluation indicated that the transgressive early flowering observed in several of the SILs was also associated with a measurable and positive effect on yield. These SILs represent a new source of variation that can be used in breeding programs to manipulate flowering time in rice cultivars without the reduction in yield that is often associated with early maturing phenotypes.

Genetic and physical mapping of blast resistance gene Pi-42(t) on the short arm of rice chromosome 12

We have identified, genetically mapped and physically delimited the chromosomal location of a new blast resistance gene from a broad spectrum resistant genotype ‘DHR9’. The segregation analysis of an F2 progeny of a cross between a susceptible cv. ‘HPU741’ and the resistant genotype ‘DHR9’ suggested that the resistance was conditioned by a single dominant gene. A RAPD marker, OPA82000, linked to the resistance gene was identified by the linkage analysis of 109 F2 individuals. By chromosomal landing of the sequence of RAPD marker on the sequence of reference cv. Nipponbare, the gene was mapped onto rice chromosome 12. Further linkage analysis with two polymorphic simple sequence repeat (SSR) markers, RM2529 and RM1337 of chromosome 12, confirmed the chromosomal localization of the resistance gene. Based on linkage analysis of 521 susceptible F2 plants and comparative haplotype structure analysis of the parental genotypes with SSR and sequence tagged site (STS) markers developed from the Nipponbare PAC/BAC clones of chromosome 12, the resistance gene was delimited within a 2 cM interval defined by STS marker, STS5, on the telomeric side and SSR marker, RRS6 on the centromeric side. By aligning the sequences of linked markers on the sequence of cv. Nipponbare, a ~4.18 Mb cross-over cold region near the centromere of chromosome 12 was delineated as the region of blast resistance gene. In this region, six putatively expressed NBS-LRR genes were identified by surveying the equivalent genomic region of cv. Nipponbare in the TIGR Whole Genome Annotation Database (http://www.tigr.org). NBS-LRR locus, LOC_Os12g18374 situated in BAC clone OJ1115_G02 (Ac. No. AL772419) was short-listed as a potential candidate for the resistance gene identified from DHR9. The new gene was tentatively designated as Pi-42(t). The markers tightly linked to gene will facilitate marker-assisted gene pyramiding and cloning of the resistance gene.

A Rice Mutant Sensitive to Al Toxicity is Defective in the Specification of Root Outer Cell Layers

Outer cell layers of rice roots, which comprise epidermis, exodermis and sclerenchyma, have been proposed to protect the roots from various stresses in soil. Here, we report a mutant which is defective in the specification of outer cell layers, and examined the role of these layers in Al and other metal resistance. Morphological and histochemical observations revealed that the mutant isolated based on Al sensitivity frequently showed a disordered pattern of periclinal cell division in the epidermal layers at a region close to the root apical meristem. The lateral root caps in the mutant became difficult to peel off from the epidermis, and epidermal cells became smaller and irregular with far fewer root hairs. Furthermore, some exodermal cells were transformed into additional sclerenchyma cells. However, there was no difference in the inner cell layers between the wild-type rice and the mutant. The mutant showed similar root growth to the wild-type rice in the absence of Al, but greater inhibition of root elongation by Al was found in the mutant. Morin staining showed that Al penetrated into the inner cortical cells in the mutant. Furthermore, the mutant was also sensitive to other metals including Cd and La. Taken together, our results indicate that root outer cell layers protect the roots against the toxicity of Al and other metals by preventing metal penetration into the inner cells. Genetic analysis showed that the mutant phenotypes were controlled by a single recessive gene, which was located on the short arm of rice chromosome 2.