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

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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Codon Usage Biases of Transposable Elements and Host Nuclear Genes in Arabidopsis thaliana and oryza sativa

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Genomics, Proteomics & Bioinformatics 2009年第4期7卷 175-184页

作者： Jia Jia Qingzhong Xue James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310008 China Department of Agronomy College of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 China.

Transposable elements （TEs） are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa （r=0.944 and 0.839, respectively, P〈0.0001） but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species.

关键词： transposable elements transposase codon usage Arabidopsis thaliana oryza sativa

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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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Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.)

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Journal of Genetics and Genomics 2009年第7期36卷 435-442页

作者： Xiangqian Zhao Long Yang Yan Zheng Zhaohua Xu WeirenWu Department of Agronomy College of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 China College of Life Science Fujian Agriculture and Forestry University Fuzhou 350002 China

It is generally accepted that oryza rufipogon is the progenitor of Asian cultivated rice （O. sativa）. However, how the two subspecies of O. sativa （indica and japonica） were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism （SSILP） markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups： one group （Group I） comprises all the O. rufipogon accesions from tropical （South and Southeast） Asia as well as the standard indica rice; the other group （Group II） comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. ruffpogon might occur after its speciation from other AA-genome species.

关键词： oryza sativa oryza rufipogon evolution SSILP marker

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Developing herbicide resistant Sri-lankan rice(oryza sativa L.)varieties:An application of Self Organizing Map

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Information Processing in Agriculture 2017年第2期4卷 140-149页

作者： E.M.S.I.Ekanayaka S.R.Weerakoon S.Somaratne O.V.D.S.J.Weerasena Department of Botany The Open University of Sri LankaP.O.Box 21NawalaSri Lanka Institutes of Biochemistry Molecular Biology and BiotechnologyUniversity of ColomboSri Lanka

Application of high concentrations of post-emergent broad spectrum systemic herbicide,glyphosate is prevalently used to control rice weeds in Asian countries including Sri Lanka.Off target movements of glyphosate adversely affect growth of the rice plant reducing the yield.Inducing herbicide resistance(HR)in cultivated rice is a novel approach to enhance selectivity and crop safety.Studies on induced HR in Sri Lankan rice varieties are limited and studies are required to include HR rice in a cropping program.Ethyl Methyl Sulfonate(EMS),a chemical mutagen is used for functional mutations.The present study is an attempt of raising HR rice lines through conventional breeding methods.A suitable glyphosate concentration was determined by a preliminary study using five rice varieties(Bg300,Bg352,At362,Bg379-2 and H4)and varying glyphosate concentrations(0.25 g/l,0.5 g/l,1 g/l,2 g/l and 3 g/l).Resistance percentage50%was arbitrary considered as resistant varieties.Complete Randomized Design with three replicates was used in the experiment.Agromorphological characters were recorded for the survived plants.Twelve varieties(Bg359,At362,Bw364,Ld365,Bg366,Bg369,Bg379-2,Bg403,Bg454“Pachcha perumal”,“Kalu heenati”and“Kurulu thuda”)showed natural resistance to glyphosate and fourteen varieties have increased resistance after mutagenesis by EMS(S0-First generation).HR resistance percentage of S1(Second generation)plants was similar to S0 plants indicating HR was transferred to new generation.Conventional statistics was supplemented with Self-Organizing Maps(SOM)to visualize variation of agro-morphological characters under treatment.The result proved that EMS application is an effective method in breeding new rice germplasm with HR and SOM is an important tool for visualizing the multi-dimensional dataset in lower dimensions.

关键词： Ethyl Methyl Sulfonate Glyphosate Herbicide resistance oryza sativa Self-Organizing Map

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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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Molecular Mapping of QTLs for Yield and Yield-Related Traits in oryza sativa cv Swarna × O. nivara (IRGC81848) Backcross Population

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Rice science 2011年第3期18卷 178-186页

作者： B. P. MALLIKARJUNA SWAMY K. KALADHAR M. S. RAMESHA B. C. VIRAKTAMATH N. SARLA Directorate of Rice Research Rajendranagar Hyderabad India - 500030 Plant Breeding Genetics and Biotechnology Division International Rice Research Institute DAPO Box 7777 Metro Manila Philippines

Advanced backcross QTL analysis was used to identify QTLs for seven yield and yield-related traits in a BC2F2 population from the cross between a popular oryza sativa cv Swarna and O. nivara IRGC81848. Transgressive segregants with more than 15% increased effect over Swarna were observed for all the traits except days to heading and days to 50% flowering. Thirty QTLs were detected for seven yield and yield-related traits using interval and composite interval mapping. Enhancing alleles at 13 (45%) of these QTLs were derived from O. nivara, and enhancing alleles at all the QTLs for stem diameter and rachis diameter were derived from O. nivara. Three stem diameter QTLs, two rachis diameter QTLs and one number of secondary branches QTL identified by both Interval and composite interval mapping contributed more than 15% of the total phenotypic variance. The QTL epistasis was significant for stem diameter and plot yield. The most significant QTLs qSD7.2, qSD8.1 and qSD9.1 for stem diameter, qRD9.1 for rachis diameter and qNSB1.1 for number of secondary branches are good targets to evaluate their use in marker-assisted selection. O. nivara is a good source of novel alleles for yield related traits and reveals major effect QTLs suitable for marker-assisted selection.

关键词： oryza sativa oryza nivara stem diameter rachis diameter yield yield components quantitative trait locus

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Prediction and Expression Analysis of miRNAs Associated with Heat Stress in oryza sativa

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Rice science 2014年第1期21卷 3-12页

作者： B.SAILAJA S.R.VOLETI D.SUBRAHMANYAM N.SARLA V.VISHNU PRASANTH V.P.BHADANA S.K.MANGRAUTHIA Biotechnology Section Directorate of Rice Research Rajendranagar

Computational prediction of potential microRNAs （miRNAs） and their target genes was performed to identify the miRNAs and genes associated with temperature response in rice. The data of temperature-responsive miRNAs of Arabidopsis, and miRNAs and the whole genome data of rice were used to predict potential miRNAs in oryza sativa involved in temperature response. A total of 55 miRNAs were common in both the species, and 27 miRNAs were predicted at the first time in rice. Target genes were searched for these 27 miRNAs in rice genome following stringent criteria. Real time PCR based on expression analysis of nine miRNAs showed that majority of the miRNAs were down regulated under heat stress for rice cultivar Nagina 22. Furthermore, miR169, miR1884 and miR160 showed differential expression in root and shoot tissues of rice. Identification and expression studies of miRNAs during heat stress will advance the understanding of gene regulation under stress in rice.

关键词： miRNA oryza sativa Arabidopsis target mRNA regulation

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Development of Simple Functional Markers for Low Glutelin Content Gene 1 (Lgc1) in Rice (oryza sativa)

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Rice science 2010年第3期17卷 173-178页

作者： CHEN Tao TIAN Meng-xiang ZHANG Ya-dong ZHU Zhen ZHAO Ling ZHAO Qing-yong LIN Jing ZHOU Li-hui WANG Cai-lin Jiangsu High Quality Rice Research and Development Center Institute of Food Crops Jiangsu Academy of Agricultural SciencesNanjing 210014 China＂ #These authors contributed equally to this paper

Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelin-content gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5 , which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel- Lgc1- 1 and InDel- Lgc1- 2 were developed to detect the low glutelin-content gene Lgc1 . A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.

关键词： oryza sativa low glutelin-content gene functional marker double polymerase chain reaction

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Spotted-Leaf Mutants of Rice(oryza sativa)

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Rice science 2010年第4期17卷 247-256页

作者： HUANG Qi-na YANG Yang SHI Yong-feng CHEN Jie Wu Jian-li State Key Laboratory of Rice Biology Chinese National Center for Rice Improvement China National Rice Research Institute Hangzhou 310006 China College of Life and Environmental Sciences Hangzhou Normal University Hangzhou 310036 China＂ #These authors contributed equally to this paper

Many rice spotted-leaf （spl） mutants are ideal sources for understanding the mechanisms involved in blast resistance, bacterial blight resistance and programmed cell death in plants. The genetic controls of 50 spotted-leaf mutants in rice have been characterized and a few spotted-leaf genes have been isolated as well. This article reviews the odgin, genetic modes, isolation and characterization of spotted-leaf genes responsible for their phenotypes, and their resistance responses to main rice diseases.

关键词： oryza sativa spotted-leaf mutagenesis disease resistance programmed cell death gene

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