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Combining QTL mapping and expression profile analysis to identify candidate genes of cold tolerance from Dongxiang common wild rice(Oryza rufipogon Griff.)

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Journal of Integrative Agriculture 2016年第9期15卷 1933-1943页

作者： ZHAO Jie QIN Jing-jing SONG Qian SUN Chuan-qing LIU Feng-xia state key laboratory of plant Physiology and Biochemistry National Center for Evaluation of Agricultural Wild Plants (Rice)/Beijing Key Laboratory of Crop Genetic Improvement/Department of Plant Genetics and Breeding China Agricultural University

Rice（Oryza sativa L.）, a tropical and subtropical crop, is susceptible to low temperature stress during seedling, booting, and flowering stages, which leads to lower grain quality levels and decreasing rice yields. Cold tolerance is affected by multiple genetic factors in rice, and the complex genetic mechanisms associated with chilling stress tolerance remain unclear. Here, we detected seven quantitative trait loci（QTLs） for cold tolerance at booting stage and identified one cold tolerant line, SIL157, in an introgression line population derived from a cross between the indica variety Guichao 2, as the recipient, and Dongxiang common wild rice, as the donor. When compared with Guichao 2, SIL157 showed a stronger cold tolerance during different growth stages. Through an integrated strategy that combined QTL-mapping with expression profile analysis, six candidate genes, which were up-regulated under chilling stress at the seedling and booting developmental stages, were studied. The results may help in understanding cold tolerance mechanisms and in using beneficial alleles from wild rice to improve the cold tolerance of rice cultivars through molecular marker-assisted selection.

关键词： common wild rice introgression line low temperature tolerance different growth stages candidate genes

Genetic Identification of Quantitative Trait Loci for Contents of Mineral Nutrients in Rice Grain

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Journal of Integrative plant Biology 2009年第1期51卷 84-92页

作者： Ana Luisa Garcia-Oliveira department of plant genetics and breeding and state key laboratory of plant Physiology and Biochemistry China Agricultural University National Centre for Evaluation of Agricultural Wild plant Rice Beijing key laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture

In present study, Fe, Zn, Mn, Cu, Ca, Mg, P and K contents of 85 introgression lines （ILs） derived from a cross between an elite indica cultivar Teqing and the wild rice （Oryza rufipogon） were measured by inductively coupled argon plasma （ICAP） spectrometry. Substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for Fe with Cu. A total of 31 putative quantitative trait loci （QTLs） were detected for these eight mineral elements by single point analysis. Wild rice （O. rufipogon） contributed favorable alleles for most of the QTLs （26 QTLs）, and chromosomes 1,9 and 12 exhibited 14 QTLs （45%） for these traits. One major effect of QTL for zinc content accounted for the largest proportion of phenotypic variation （11%-19%） was detected near the simple sequence repeats marker RM152 on chromosome 8. The co-locations of QTLs for some mineral elements observed in this mapping population suggested the relationship was at a molecular level among these traits and could be helpful for simultaneous improvement of these traits in rice grain by marker assisted selection.

关键词： introgression lines mineral elements Oryza sativa Oryza rufipogon quantitative trait loci.

Carotenoid Metabolism:Biosynthesis,Regulation,and Beyond

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Journal of Integrative plant Biology 2008年第7期50卷 778-785页

作者： Shan Lu Li Li state key laboratory of Pharmaceutical biotechnology School of Life Sciences Nanjing University Nanjing 210093 China US department of Agriculture-Agricultural Research Service Plant Soil and Nutrition Laboratory Department of Plant Breeding and Genetics Cornell University Ithaca New York 14853 USA

Carotenoids are indispensable to plants and play a critical role in human nutrition and health. Significant progress has been made in our understanding of carotenoid metabolism in plants. The biosynthetic pathway has been extensively studied. Nearly all the genes encoding the biosynthetic enzymes have been isolated and characterized from various organisms. In recent years, there is an increasing body of work on the signaling pathways and plastid development, which might provide global control of carotenoid biosynthesis and accumulation. Herein, we will highlight recent progress on the biosynthesis, regulation, and metabolic engineering of carotenoids in plants, as well as the future research towards elucidating the regulatory mechanisms and metabolic network that control carotenoid metabolism.

关键词： carotenoids isoprenoids metabolism metabolic engineering plastid regulation.

Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci

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Journal of Integrative plant Biology 2007年第6期49卷 871-884页

作者： Lubin Tan department of plant genetics and breeding and state key laboratory of agro-biotechnology China Agricultural University Beijing 100094 China key laboratory of Crop Heterosis and Utilization of Ministry of Education Beijing 100094 China key laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture China Agricultural University Beijing 100094 China Beijing key laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

Introgression lines population was effectively used in mapping quantitative trait loci （QTLs）, identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines （ILs）, which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing （O. sativa L.）, as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats （SSR） markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs （51.4%） were detected at both sites, and the alleles from O. rufipogon at fifteen loci （40.5%） improved the yield and yield components in the Teqing background. These O. rufipogon-O, sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

关键词： common wild rice cultivated rice introgression lines quantitative trait locus yield-related trait.

Cloning and characterization of an up-regulated GA 20-oxidase gene in hybrid maize

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Progress in Natural Science:Materials International 2009年第2期19卷 161-166页

作者： Jinkun Du,Yingyin Yao,Zhongfu Ni,Qixin Sun department of plant genetics & breeding and state key laboratory for agrobiotechnology,key laboratory of Crop Genomics and Genetic Improvement,Ministry of Agriculture/Beijing key laboratory of Crop Genetic Improvement,China Agricultural University,Beijing 100094,China department of plant genetics & breeding and state key laboratory for agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

Previous studies revealed that GA content and metabolism are positively correlated with a faster shoot growth rate of hybrid,and recently,genes participating in both GA biosynthesis and GA response pathways were also found to be differentially expressed between wheat hybrid and its parental inbreds. In this study,an up-regulated GA 20-oxidase gene in a maize hybrid,designated ZmGA20,was cloned. ZmGA20 contains an open reading frame (ORF) encoding 391 amino acid residues. BLASTX searches in GenBank revealed that the ZmGA20 is homologous to the sequences of GA20ox proteins from different species,and analysis also indicated that ZmGA20 had typical features of GA 20-oxidase proteins,including a "LPWKET" sequence. Semi-quantitative RT-PCR analysis showed that ZmGA20 was expressed in different tissues and/or organs. The expression level of ZmGA20 in the hybrid was higher than that in two parents (in roots,leaves,stems and embryo,and ears). The abundance of ZmGA20 transcript was equal to that of the highly expressed parents,which provided molecular evidence for the observed GA content heterosis in maize hybrids.

关键词： GA 20-oxidase Gene expression Maize Heterosis

Genomic decoding of breeding history to guide breeding-by-design in rice

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National Science Review 2023年第5期10卷 124-137页

作者： Zhuo Chen Qingyun Bu Guifu Liu Maoqing Wang Hongru Wang Huazhao Liu Xiufeng Li Hong Li Jun Fang Yan Liang Zhenfeng Teng Sai Kang Hong Yu Zhukuan Cheng Yongbiao Xue Chengzhi Liang Jiuyou Tang Jiayang Li Chengcai Chu state key laboratory of plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences key laboratory of Soybean Molecular Design breeding Northeast Institute of Geography and AgroecologyChinese Academy of Sciences key laboratory of Crop biotechnology breeding of the Ministry of Agriculture and Rural Affairs Beidahuang Kenfeng Seed Co.Ltd Institute of Botany Chinese Academy of Sciences Guangdong laboratory for Lingnan Modern Agriculture and state key laboratory for Conservation and Utilization of Subtropical agro-Bioresources College of AgricultureSouth China Agricultural University University of Chinese Academy of Sciences state key laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Hainan Yazhou Bay Seed laboratory

Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design(BbD),but remains not well ***,we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China(NEC).We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study(GWAS)-detected quantitative trait loci(QTLs),or introgressions from indica sub-species with chronological changes in allele *** we summarized a rice breeding trend/principle in NEC,and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in *** study provides a paradigm for decoding the breeding history of a specific crop to guide BbD,which may have implications in different crop breeding.

关键词： rice breeding-by-design breeding history genome-wide association study genomic decoding

A long noncoding RNA involved in rice reproductive development by negatively regulating osa-miR160

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Science Bulletin 2017年第7期62卷 470-475页

作者： Meng Wang Hua-Jun Wu Jun Fang Chengcai Chu Xiu-Jie Wang state key laboratory of plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences Northeast Institute of Geography and agroecology Key Laboratory of Soybean Molecular Design BreedingChinese Academy of Sciences

Long noncoding RNAs （IncRNAs） participate in the regulation of multiple biological processes via diverse manners, one of which is functioning as endogenous target mimics （eTMs） to modulate microRNAs （miRNAs） by competing for their targets. Previously, we have predicted one IncRNA （osa-eTM160） as an endogenous repressor of osa-miR160 and validated the target mimicry ability of osa-eTM160 for ath-miR160 in Arabidopsis thaliana, yet the functions of osa-eTM160 in rice remain obscure. Here, we demonstrated that osa-eTM160 attenuated the repression of osa-miR160 on osa-ARF18 mRNAs during early anther developmental stages through the target mimicry manner, therefore to regulate rice seed setting and seed size. These findings revealed the roles of osa-eTM160 in rice, and indicated that lncRNAs with eTM functions may serve as temporal regulators to modulate the effects of miRNAs at specific developmental stages.

关键词： microRNA IncRNA miR160 Target mimic

Crop antiviral defense: Past and future perspective

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Science China Life Sciences 2024年第12期67卷 2617-2634页

作者： Zhirui Yang Guangyao Li Yongliang Zhang Fangfang Li Tao Zhou Jian Ye Xianbing Wang Xiaoming Zhang Zongtao Sun Xiaorong Tao Ming Wu Jianguo Wu Yi Li The state key laboratory of Protein and plant Gene Research School of Life Sciences Peking University state key laboratory of plant Environmental Resilience Frontiers Science Center for Molecular Design Breeding College of Biological Sciences China Agricultural University state key laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research Center College of Plant Protection Fujian Agriculture and Forestry University state key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences state key laboratory for agro-biotechnology and department of plant Pathology China Agricultural University state key laboratory of plant Genomics Institute of Microbiology Chinese Academy of Sciences state key laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences state key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of agro-products Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province Institute of Plant Virology Ningbo University department of plant Pathology The Key Laboratory of Plant Immunity Nanjing Agricultural University

Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.

关键词： crops antiviral defense RNA silencing autophagy ubiquitin proteasome system

Role of hydrogen peroxide in stress-induced programmed cell death during somatic embryogenesis in Fraxinus mandshurica

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Journal of Forestry Research 2019年第3期30卷 767-777页

作者： Ling Yang Cheng Wei Chao Huang Hongnan Liu Dongyan Zhang Hailong Shen Yuhua Li state key laboratory of Tree genetics and breeding School of Forestry Northeast Forestry University

We examined how reactive oxygen species, in the form of hydrogen peroxide (H2O2), affect osmotic stress–induced programmed cell death during somatic embryogenesis from cotyledon explants of Manchurian ash (Fraxinus mandshurica Rupr.). We found that substantial osmotic stress was essential for Manchurian ash somatic cells to obtain embryogenic competence. The explant cells displayed hallmarks of programmed cell death, chromatin condensation, and DNA fragmentation to oligonucleotides during somatic embryogenesis. Increasing concentrations of plant growth regulators and sucrose in the medium increased osmotic stress thereby inducing H2O2 accumulation in the explant cells. We found that H2O2 concentration was significantly decreased in explant cells when the induction medium was modified, i.e., when reducing the concentration of sucrose, which reduces the osmotic pressure of the medium, or by withdrawing plant growth regulators at mid-culture. These treatments also decreased the proportion of explant cells undergoing programmed cell death. Accordingly, a decreased rate of somatic embryo induction was observed. These results show that PCD occurred during tissue browning and death of some explant cells during somatic embryogenesis in F. mandshurica. The ROS contributed to PCD in abiotic stress stimulated F. mandshurica cells.

关键词： Manchurian ash Somatic embryos Programmed cell death Reactive oxygen species Osmotic stress