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The Subtelomere of oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice

Molecular Plant 2008年第5期1卷 839-850页

作者： Chuanzhu Fana Yong Zhang Yeisoo Yu Steve Rounsley Manyuan Long Rod A. Wing Arizona Genomics Institute Department of Plant Sciences University of Arizona Tucson AZ 85721 USA Department of Ecology and Evolution University of Chicago Chicago IL 60637 USA BIO5 Institute for Collaborative Research University of Arizona Tucson AZ 85721 USA

Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago （MYA）. For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.

关键词： comparative genomics gene duplication oryza sativa subtelomere new genes.

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Crossability Barriers in the Interspecific Hybridization between oryza sativa and ***

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Journal of Integrative Plant Biology 2009年第1期51卷 21-28页

作者： Xue-Lin Fu Yong-Gen Lu Xiang-Dong Liu Jin-Quan Li Guangdong Provincial Key Laboratory of Plant Molecular Breeding South China Agricultural University Guangzhou 510642 China

oryza meyeriana Baill （GG genome） is a precious germplasm in the tertiary gene pool of cultivated rice （AA genome）, and possesses important traits such as resistance and tolerance to biotic and abiotic stress. However, interspeciflc crossability barrier, a critical bottleneck restricting genes transfer from O. meyeriana to cultivars has led to no hybrids through conventional reproduction. Therefore, the reasons underlying incrossability were investigated in the present report. The results showed that：（i） at 3-7 d after pollination （DAP）, many hybrid embryos degenerated at the earlier globular-shaped stage, and could not develop into the later pear-shaped stage. Meanwhile, free endosperm nuclei started to degenerate at 1 DAP, and cellular endosperm could not form at 3 DAP, leading to nutrition starvation for young embryo development; （ii） at 11-13 DAP, almost all hybrid ovaries aborted. Even though 72.22% of hybrid young embryos were produced in the interspecific hybridization between O. sativa and O. meyeriana, young embryos were not able to further develop into hybrid plantlets via culturing in vitro. The main reason for the incrossability was hybrid embryo inviability, presenting as embryo development stagnation and degeneration since 3 DAP. Some possible approaches to overcome the crossability barriers in the interspecific hybridization between O. sativa and O. meyeriana are discussed.

关键词： crossability embryo development interspecific hybridization oryza sativa O. meyeriana.

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Transcriptome-wide profiling of RNA N^(4)-cytidine acetylation in Arabidopsis thaliana and oryza sativa

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Molecular Plant 2023年第6期16卷 1082-1098页

作者： Bin Li Donghao Li Linjun Cai Qiting Zhou Cong Liu Jianzhong Lin Yixing Li Xiaoying Zhao Li Li Xuanming Liu Chongsheng He College of Biology Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan Engineering and Technology Research Center of Hybrid RapeseedHunan UniversityChangsha410082 Hunan 410082China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina

Acetylation of N^(4)-cytidine(ac^(4)C)has recently been discovered as a novel modification of *** ac^(4)C modification has been shown to be a key regulator of RNA stability,RNA translation,and the thermal stress ***,its existence in eukaryotic mRNAs is still *** plants,the existence,distribution pattern,and potential function of RNA ac^(4)C modification are largely *** we report the presence of ac^(4)C in the mRNAs of both Arabidopsis thaliana and rice(oryza sativa).By comparing two ac^(4)C sequencing methods,we found that RNA immunoprecipitation and sequencing(acRIP-seq),but not ac^(4)C sequencing,was suitable for plant RNA ac^(4)C *** present transcriptome-wide atlases of RNA ac^(4)C modification in *** and rice mRNAs obtained by *** of the distribution of RNA ac^(4)C modifications showed that ac^(4)C is enriched near translation start sites in rice mRNAs and near translation start sites and translation end sites in Arabidopsis *** RNA ac^(4)C modification level is positively correlated with RNA half-life and the number of splicing *** to that in mammals,the translation efficiency of ac^(4)C target genes is significantly higher than that of other *** in vitro translation results confirmed that RNA ac^(4)C modification enhances translation *** also found that RNA ac^(4)C modification is negatively correlated with RNA *** results suggest that ac^(4)C is a conserved mRNA modification in plants that contributes to RNA stability,splicing,translation,and secondary structure formation.

关键词： N^(4)-acetylcytidine epitranscriptome Arabidopsis thaliana oryza sativa

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The WRKY Gene Family in Rice （oryza sativa）

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Journal of Integrative Plant Biology 2007年第6期49卷 827-842页

作者： Christian A. Ross Yue Liu Qingxi J. Shen Bioinformatics Core School of Life Sciences University of Nevada Las Vegas Nevada 89154 USA

WRKYgenee encode transcription factors that are Involved In the regulation of various biological processes. These zinc-finger proteins, especially those members mediating stress responses, are uniquely expanded In plants. To facilitate the study of the evolutionary history and functions of this eupergene family, we performed an exhaustive search for WRKY genes using HMMER and a Hidden Markov Model that was specifically trained for rice. This work resulted In a comprehensive list of WRKYgene models In oryza sativa L. eep. indica and L. eep. Japonica. Mapping of these genes to Individual chromosomes facilitated elimination of the redundant, leading to the Identification of 98 WRKYgenee In Japonica and 102 In indica rice. These genes were further categorized according to the number and structure of their zinc-finger domains. Based on a phylogenetlc tree of the conserved WRKY domains and the graphic display of WRKY loci on corresponding indica and Japonica chromosomes, we Identified possible WRKY gene duplications within, and losses between the two closely related rice subspecies. Also reviewed are the roles of WRKY genes In disease resistance and responses to salicylic acid and Jaemonlc acid, seed development and germination mediated by glbberelllns, other developmental processes Including senescence, and responses to ablotlc stresses and abeclelc acid In rice and other plants. The signaling pathways mediating WRKY gene expreeelon are also discussed.

关键词： gene family indica japonica oryza sativa rice WRKY.

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Overexpression of OsKTN80a, a katanin P80ortholog, caused the repressed cell elongation and stalled cell division mediated by microtubule apparatus defects in primary root in oryza sativa

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Journal of Integrative Plant Biology 2014年第7期56卷 622-634页

作者： Lei Wan Xiuwen Wang Shaoqing Li Jun Hu Wenchao Huang Yingguo Zhu State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University

Katanin, a microtubule-severing enzyme, consists of two subunits：the catalytic subunit P60, and the regulatory subunit P80. In several species, P80 functions in meiotic spindle organization, the flagella biogenesis, the neuronal development, and the male gamete production. However, the P80 function in higher plants remains elusive. In this study, we found that there are three katanin P80 orthologs （OsKTN80a, OsKTN80b, and OsKTN80c） in oryza sativa L. Overexpression of OsKTN80a caused the retarded root growth of rice seedlings. Further investigation indicates that the retained root growth was caused by the repressed cell elongation in the elongation zone and the stalled cytokinesis in the division zone in the root tip. The in vivo examination suggests that OsKTN80a acts as a microtubule stabilizer. We＆amp;nbsp;prove that OsKTN80a, possibly associated with OsKTN60, is involved in root growth via regulating the cell elongation and division.

关键词： Cell division cell expansion oryza sativa OsKTN8oa rootgrowth

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Identification and cell wall analysis of interspecific hybrids between oryza sativa and oryza ridleyi

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Journal of Integrative Agriculture 2017年第8期16卷 1676-1681页

作者： YI Chuan-deng LI Wei WANG De-rong JIANG Wei HU Da-bang ZHOU Yong LIANG Guo-hua GUMing-hong Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of Ministry of EducationYangzhou UniversityYangzhou 225009P.R.China

oryza ridleyi is an allotetraploid wild species with the HHJJ genome, and oryza sativa is a diploid cultivated rice that has the AA genome. Although the wide hybrid between the two species is difficult to obtain, we overcome this difficulty by young embryo rescue. An obvious heterosis was primarily found for the plant height, tillering ability, vegetative vigor, etc. However, the hybrid panicle and culm traits were found to resemble that of the wild rice parent, O. ridleyi, for the long awns, exoteric purple stigma, grain shattering, dispersed panicles, and culm mechanical strength. Genomic in situ hybridization （GISH） analysis was subsequently performed on the mitotic metaphase chromosome of the root tips, and we determined that the hybrid is an allotriploid with 36 chromosomes and its genomic constitution is AHJ. Chemical analyses conducted on the culm of O. sativa, O. ridleyi, and their interspecific hybrids showed that major changes occurred in the xylose, glucose, and arabinose concentrations, which are correlated with the specific hemicellulose polymer and cellulose components that are important in the primary cell walls of green plants. Meanwhile, the culm anatomical analyses indicated that additional large vascular bundles and an extra sclerenchyma cell layer were found in O. ridleyi. Additionally, further thickening of the secondary cell walls of the cortical fiber sclerenchyma cells and the phloem companion cells was discovered in O. ridleyi and in the interspecific hybrids. These results imply that there may be a potential link between culm mechanical strength and culm anatomical structure.

关键词： oryza sativa oryza ridleyi interspecific hybrid genomic in situ hybridization cell wall

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Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (oryza sativa L.) grown at two nitrogen levels

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Progress in Natural Science:Materials International 2008年第12期18卷 1539-1547页

作者： Hua Jiang~(a,b) Liang Jiang~b Longbiao Guo~b Zhenyu Gao~b Dali Zeng~b Lihuang Zhu~c Guohua Liang~a Qian Qian~b a State Key Laboratory of Rice Biology/Key Laboratory of Plant Functional Genomies,Ministry of Education of China,Yangzhou University,Yangzhou 225009,China b State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China c Institute of Genetics,Chinese Academy of Sciences,Beijing 100101,China State Key Laboratory of Rice Biology/Key Laboratory of Plant Functional Genomics Ministry of Education of China Yangzhou University Yangzhou 225009 China State Key Laboratory of Rice Biology China National Rice Research Institute Hangzhou 310006 China Institute of Genetics Chinese Academy of Sciences Beijing 100101 China

In this study,we used 127 double haploid (DH) lines to analyze agricultural traits of *** DH lines,derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture,contained 160 RFLP and 83 SSR *** and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at five growth stages that were grown at two nitrogen *** PH and 13 TP unconditional QTL were identified in the different growth stages,including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) *** conditional QTL for 14 genomic regions under LN/HN con- ditions showed that there was a significant effect on PH and TP across the different *** one conditional QTL,ph2-3,was unable to be detected in unconditional *** QTL were detected in the first four rice growth stages than in the final ***- more,a line from the DH mapping population,DH78,was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) *** gene dft1 was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a map- based cloning *** location of dft1 coincided with the mapping region of the small-LOD peak,QTL ph2 and tp2,which were identified in plants grown in low-nitrogen *** backcrossing and fine-mapping successfully delimited the dft1 locus to a 91 kb region.

关键词： oryza sativa Quantitative trait loci Double haploid (DH) population Developmental behavior Nitrogen Map-based cloning

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Cytological Behavior of Hybridization Barriers Between oryza sativa and oryza officinalis

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Agricultural Sciences in China 2011年第10期10卷 1489-1500页

作者： FU Xue-lin LU Yong-gen LIU Xiang-dong LI Jin-quan ZHAO Xing-juan Key Laboratory of Plant Molecular Breeding Guangdong Province/College of Agriculture South China Agricultural University Guangzhou510642 P.R. China

oryza officinalis is one of the important wild species in the tertiary gene pool of oryza sativa. It has a number of elite genes for rice breeding in resistance or tolerance. However, breeding barriers are so serious that the gene transfer is much difficult by sexual cross method between O. sativa and O. officinalis. Characteristics of the breeding barriers were systemically studied in this paper. When both the diploid （AA, 2n=2x=24） and autotetraploid （AAAA, 2n=4x=48） cultivated rice were crossed as maternal parents with O. officinalis （CC, 2n=2x=24）, none F1 hybrid seeds were obtained. The young hybrid ovaries aborted at 13-16 d after pollinations （DAP）. By rescuing hybrid embryos, in vitro F1 plantlets were obtained in 2x×2x combinations with the crossabilities lower than 0.5%. Lower rates of double-fertilization and abnormal development of hybrid embryo and endosperm were mainly observed in both combinations of 2x×2x and 4x×2x. Free endosperm nuclei in hybrid degenerated early at 1 DAP in a large scale. Almost no normal endosperm cells formed at 3 DAP. Development of a lot of embryos ceased at globularor pear-shaped stage as well as some degenerated gradually. The hybrid plantlets were both male and female sterility. Due to the abnormal development, a diversity of abnormal embryo sacs formed in hybrids, and hybrid pollen grains were typically abortive. It showed that conflicts of genome A and C in hybrid induced abnormal meioses of meiocytes.

关键词： breeding barriers interspecific hybridization crossability hybrid sterility oryza sativa oryza officinalis

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Characterization of Interspecific Hybrids Between oryza sativa L, and Three Wild Rice Species of China by Genomic In Situ Hybridization

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Journal of Integrative Plant Biology 2006年第9期48卷 1077-1083页

作者： Guang-Xuan Tan Zhi-Yong Xiong Hua-Jun Jin Gang Li Li-Li Zhu Li-Hui Shu Guang-Cun He Key Laboratory of the Ministry of Education for Plant Development Biology Wuhan University College of Life Sciences Wuhan 430072 China Zhoukou Normal University Zhoukou 466001 China

In the genus oryza, interspecific hybrids are useful bridges for transferring the desired genes from wild species to cultivated rice （oryza sativa L.）. In the present study, hybrids between O. sativa （AA genome） and three Chinese wild rices, namely O. rufipogon （AA genome）, O. officinalis （CC genome）, and O. meyeriana （GG genome）, were produced. Agricultural traits of the F1 hybrids surveyed were intermediate between their parents and appreciably resembled wild rice parents. Except for the O. sativa × O. rufipogon hybrid, the other F1 hybrids were completely sterile. Genomic in situ hybridization （GISH） was used for hybrid verification. Wild rice genomic DNAs were used as probes and cultivated rice DNA was used as a block. With the exception of O. rufipogon chromosomes, this method distinguished the other two wild rice and cultivated rice chromosomes at the stage of mitotic metaphase with different blocking ratios. The results suggest that a more distant phylogenetic relationship exists between O. meyeriana and O. sativa and that O. rufipogon and O. sativa share a high degree of sequence homology. The average mitotic chromosome length of O. officinalis and O. meyeriana was 1.25- and 1.51-fold that of O. sativa, respectively. 4＇,6＇-Diamidino- 2-phenylindole staining showed that the chromosomes of O. officinalis and O. meyeriana harbored more heterochromatin, suggesting that the C and G genomes were amplified with repetitive sequences compared with the A genome. Although chromocenters formed by chromatin compaction were detected with wild rice-specific signals corresponding to the C and G genomes in discrete domains of the F1 hybrid interphase nuclei, the size and number of O. meyeriana chromocenters were bigger and greater than those of O. officinalis. The present results provide an important understanding of the genomic relationships and a tool for the transfer of useful genes from three native wild rice species in China to cultivars.

关键词： Chinese wild rice species interspecific hybrids genomic in situ hybridization (GISH) oryza sativa

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Suppression of glutamate synthase genes significantly affects carbon and nitrogen metabolism in rice (oryza sativa L.)

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Science China(Life Sciences) 2011年第7期54卷 651-663页

作者： LU YongEn LUO Feng YANG Meng LI XiangHua LIAN XingMing National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China

Rice (oryza sativa) glutamate synthase (GOGAT,EC 1.***.1.14) enzymes have been proposed to have great potential for improving nitrogen use efficiency,but their functions in vivo and their effects on carbon and nitrogen metabolism have not been systematically *** this research,we analyzed transcriptional profiles of rice GOGAT genes using a genome-wide microarray database,and investigated the effects of suppression of glutamate synthase genes on carbon and nitrogen metabolism using GOGAT co-suppressed rice *** profiles showed that rice GOGAT genes were expressed differently in various tissues and organs,which suggested that they have different roles in *** with the wild-type,tiller number,total shoot dry weight,and yield of GOGAT co-suppressed plants were significantly *** and biochemical studies showed that the contents of nitrate,several kinds of free amino acids,chlorophyll,sugars,sugar phosphates,and pyridine nucleotides were significantly decreased in leaves of GOGAT co-suppressed plants,but the contents of free ammonium,2-oxoglutarate,and isocitrate in leaves were *** conclude that GOGATs play essential roles in carbon and nitrogen metabolism,and that they are indispensable for efficient nitrogen assimilation in rice.

关键词： glutamate synthase oryza sativa co-suppression carbon and nitrogen metabolism

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