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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

Transcriptomic analysis of rice responses to low phosphorus stress

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Chinese Science Bulletin 2010年第3期55卷 251-258页

作者： LI LiHua QIU XuHua LI XiangHua WANG ShiPing ZHANG QiFa lian xingming National Key Laboratory of Crop Genetic Improvement. National Center of Plant Gene Research (Wuhan) Huazhong Agricultural UniversityWuhan 430070 China

Phosphorus is one of the essential macronutrients required for plant growth and development. The plants increase the absorption of phosphorus through an expansion of the root system in the soil when they are in low-phosphorus conditions. At the same time, the changes in biochemical metabolic pathways and the increase of secretion of phosphatase and organic acids activate the insoluble phosphate fixed in the soil. The expression profile in response to low phosphorus was investigated for rice at 6, 24 and 72 h after low-phosphorus stress compared with normal phosphorus conditions as a control with DNA chip. A total of 1207 differen- tially expressed genes were found in our study; 795 and 450 genes exhibited alterations in their RNA expression in response to inorganic phosphate (Pi) starvation in at least one of the three time points in roots and shoots. Thirty-eight genes overlapped in shoots and roots. The functional classification of these genes indicated their involvement in various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. A large number of transposable elements changed the expression in rice after low-phosphorus stress. The results may provide useful information about molecular processes associated with Pi deficiency and facilitate the identification of key molecular determinants for improving Pi use by crop species.

关键词：低磷胁迫转录调控胁迫反应水稻差异表达基因植物生长发育代谢途径 DNA芯片

Rice transcription factors OsLBD37/38/39 regulate nitrate uptake by repressing OsNRT2.1/2.2/2.3 under high-nitrogen conditions

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The Crop Journal 2022年第6期10卷 1623-1632页

作者： Xinxin Zhu Dujun Wang Lijuan Xie Tao Zhou Jingyi Zhao Qian Zhang Meng Yang Wenjuan Wu xingming lian National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070HubeiChina

Nitrate(NO_(3)^(-)) uptake involves a finely regulated and complex multilevel response *** the molecular mechanism of nitrate uptake may lead to improving the growth and productivity of plants in the presence of dynamic variation in nitrate *** this study,we identified three lateral organ boundaries domain(LBD)transcription factors,OsLBD37,OsLBD38,and OsLBD39,as regulators of nitrate uptake in response to nitrogen(N)***37,OsLBD38,and OsLBD39 were induced by ammonium and glutamine in rice *** or collective knockout of OsLBD37,OsLBD38,and OsLBD39 led to increased concentrations of nitrate and increased expression of OsNRT2.1,OsNRT2.2,and OsNRT2.3respectively under high-N conditions,whereas overexpression of each of these three LBD genes produced opposite effects where N accumulation was ***-luciferase reporter assay further confirmed that OsLBD37,OsLBD38,and OsLBD39 possessed transcription inhibitory activities in rice protoplast cells,downregulating the expression of OsNRT2.1/OsNRT2.2/*** two-hybrid and bimolecular fluorescence complementation assays showed that OsLBD37 interacted with OsLBD37,OsLBD38,and OsLBD39in the ***,these results show that OsLBD37,OsLBD38,and OsLBD39 collaborate to inhibit the expression of OsNRT2.1/OsNRT2.2/OsNRT2.3 transporters under N-sufficient conditions,thereby helping rice plants avoid excessive nitrate accumulation that may affect their growth.

关键词： Oslbd37/Oslbd38/Oslbd39 Transcription factor Nitrate uptake Rice

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

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Molecular Plant 2015年第6期8卷 946-957页

作者： Quanxiu. Wang Weibo Xie Hongkun Xing Ju Yan Xiangzhou Meng Xinglei Li Xiangkui Fu Jiuyue Xu xingming lian Sibin Yu Yongzhong Xing Gongwei Wang National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070China

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photo- synthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice （Oryza sativa） and the extent of variations explored is very limited. We con- ducted a genome-wide association study （GWAS） using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demon- strated that Grain number, plant height, andheading date7 （GhdT） was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down- regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 （NAL1） corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5＇ UTR and four non-synonymous SNPs in the cod- ing region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes iden- tified would help to fine-tune and optimize the antenna size of canopies in rice breeding.

关键词： chlorophyll GWAS Ghd7 NAL 1 pleiotropic effect Oryza sativa

The origin of Wx^(la) provides new insights into the improvement of grain quality in rice

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Journal of Integrative Plant Biology 2021年第5期63卷 878-888页

作者： Hao Zhou Duo Xia Da Zhao Yanhua Li Pingbo Li Bian Wu Guanjun Gao Qinglu Zhang Gongwei Wang Jinghua Xiao Xianghua Li Sibin Yu xingming lian Yuqing He National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China

Appearance and taste are important factors in rice(Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of533 diverse cultivars to assess the relationships between—and genetic basis of—rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy(Wx) allele, Wx^(la), which combined two mutations from Wx^(b) and Wx^(in), exhibited a unique phenotype. Reduced GBSSI activity conferred Wx^(la) rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wx^(la) was derived from intragenic recombination. In fact,the recombination rate at the Wx locus was estimated to be 3.34 kb/c M, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.

关键词： allelic variation appearance and eating quality intragenic recombination Oryza sativa waxy

The expression profile of genes in rice roots under low phosphorus stress

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Science China(Life Sciences) 2009年第11期52卷 1055-1064页

作者： LI LiHua, QIU XuHua, LI XiangHua, WANG ShiPing & lian xingming National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 1. National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China

Phosphorus (P) is one of the most essential macronutrients required for plant growth. Although it is abundant in soil, P is often the limiting nutrient for crop yield potential because of the low concentration of soluble P that plants can absorb directly. The gene expression profile was investigated in rice roots at 6, 24 and 72 h under low P stress and compared with a control (normal P) profile, using a DNA chip of 60000 oligos (70 mer) that represented all putative genes of the rice genome. A total of 795 differentially expressed genes were identified in response to phosphate (Pi) starvation in at least one of the treatments. Based on the analysis, we found that: (i) The genes coding for the Pi transporter, acid phosphatase and RNase were up-regulated in rice roots; (ii) the genes involved in glycolysis were first up-regulated and then down-regulated; (iii) several genes involved in N metabolism and lipid metabolism changed their expression patterns; (iv) some genes involved in cell senescence and DNA or protein degradation were up-regulated; and (v) some transmembrane transporter genes were up-regulated. The results may provide useful information in the molecular process associated with Pi deficiency and thus facilitate research in improving Pi utilization in crop species.

关键词： phosphorus rice DNA chip expression profile

Genetic architecture and key genes controlling the diversity of oil composition in rice grains

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Molecular Plant 2021年第3期14卷 456-469页

作者： Hao Zhou Duo Xia Pingbo Li Yiting Ao Xiaodong Xu Shanshan Wan Yanhua Li Bian Wu Huan Shi Kaiyue Wang Guanjun Gao Qinglu Zhang Gongwei Wang Jinghua Xiao Xianghua Li Sibin Yu xingming lian Yuqing He National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China

Rice grain oil is a valuable nutrient ***,the genetic basis of oil biosynthesis in rice grains remains *** this study,we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice *** variation for 11 oil-related traits was observed,and the oil composition of rice grains showed differentiation among the *** identified 46 loci that are significantly associated with grain oil concentration or composition,16 of which were detected in three recombinant inbred line ***-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci,four of which(PAL6,LIN6,MYR2,and ARA6)were found to contribute to natural variation in oil composition and to show differentiation among the ***,population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica *** on these results,we propose a possible oil biosynthetic pathway in rice ***,our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.

关键词： Oryza sativa L grain oil genome-wide association study genetic basis oil biosynthesis

RiceVarMap:a comprehensive database of rice genomic variations

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RiceVarMap:a comprehensive database of rice genomic variatio...

Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice

第十四届全国植物基因组学大会

作者： Hu Zhao Wen Yao Gongwei Wang xingming lian Qifa Zhang Weibo Xie National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University

We constructed a database of rice genomic variations,Rice Variation Map (RiceVarMap,http://***).The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms(SNP) and 1,214,627 insertion... 详细信息

关键词： single nucleotide polymorphism(SNP) insertion/deletions(INDEL) rice(Oryza sativa L.) database

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Molecular Plant 2017年第4期10卷 634-644页

作者： Hao Zhou Pingbo Li WeiboXie Saddam Hussain Yibo Li Duo Xia Hu Zhao Shengyuan Sun Junxiao Chen Hong Ye Jun Hou Da Zhao Guanjun Gao Qinglu Zhang Gongwei Wang xingming lian Jinghua Xiao Sibin Yu Xianghua Li Yuqing He National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070China

Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. Although a few quantitative trait loci associated with stigma exsertion have been fine map- ped or cloned, the underlying genetic architecture remains unclear. We performed a genome-wide associ- ation study on stigma exsertion and related floral traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 genomic loci that are significantly associated with stigma exsertion and related traits, three of which are co-localized with three major grain size genes GS3, GW5, and GW2. Further analyses indicated that these three genes affected the stigma exsertion by controlling the size and shape of the spikelet and stigma. Combinations of GS3 and GW5 largely defined the levels of stigma exsertion and related traits. Selections of these two genes resulted in specific distributions of floral traits among subpopulations of O. sativa. The low stigma exsertion combination gw5GS3 existed in half of the cultivated rice varieties; therefore, introducing the GW5gs3 combination into male sterile lines is of high potential for improving the seed production of hybrid rice.

关键词： stigma exsertion GWAS hybrid seed production floral traits grain shape rice