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NRL3 Interacts with OsK4 to Regulate Heading Date in Rice

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Rice science 2022年第3期29卷 237-246页

作者： CHEN Wei CAI Yicong Shakeel AHMAD WANG Yakun AN Ruihu TANG Shengjia GUO Naihui WEI Xiangjin TANG Shaoqing SHAO Gaoneng jiao guiai XIE Lihong HU Shikai SHENG Zhonghua HU Peisong Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education/Collaboration Center for Double-Season Rice Modernization ProductionJiangxi Agricultural University/Research Center of Super Rice Engineering and TechnologyJiangxi ProvinceNanchang 330045China State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding Ministry of Agriculture and Rural Affairs/China National Rice Improvement Center/China National Rice Research InstituteHangzhou 310006China

NRL3 is essential for the growth and development of rice leaves.In this study,we found that the loss function of NRL3 also delayed heading date under natural long daylight and short daylight conditions.The yeast two-hybrid and the bimolecular fluorescence complementation proved that NRL3interacts with OsK4,a Snf1-related kinase.OsK4 localized to the nucleus and expressed in various rice tissues.The rhythmic expression pattern of Os K4 was similar to NRL3 under long daylight and short daylight conditions.Knock-out mutants of Os K4 exhibited early heading under long daylight conditions,indicating that it acts as a negative regulator of heading date in rice.Interestingly,the OsK4 mutant under the nrl3 mutant background rescued the late heading phenotype of nrl3 under long daylight conditions,suggesting that Os K4 functions downstream of NRL3.Moreover,both NRL3 and Os K4 controlled heading date through regulating the expression of Hd3a and RFT1 genes.These findings shed light on the heading date regulation in rice and provide a sound theoretical base to improve regional adaptability of rice.

关键词： Oryza sativa heading date NRL3 gene OsK4 gene negative regulator loss function

Editing of Rice Isoamylase Gene ISA1 Provides Insights into Its Function in Starch Formation

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Rice science 2019年第2期26卷 77-87页

作者： CHAO Shufen CAI Yicong FENG Baobing jiao guiai SHENG Zhonghua LUO Ju TANG Shaoqing WANG Jianlong HU Peisong WEI Xiangjin State Key Laboratory of Rice Biology China National Rice Research Institute Southern Regional Collaborative Innovation Center for Grain and Oil Crops College of Agronomy Hunan Agricultural University

Isoamylase 1(ISA1) is an isoamylase-type debranching enzyme which plays a predominant role in amylopectin synthesis. In this study, the clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated endonuclease 9(CRISPR/Cas9) system was used to edit ISA1 gene in rice via Agrobacterium-mediated transformation. We identified 36 genetic edited lines from 55 T_0 transgenic events, and classified the mutation forms into 7 types. Of those, two homozygous mutants, cr-isa1-1(type 1, with an adenine insertion) and cr-isa1-2(type 3, with a cytosine deletion) were selected for further analysis. Seed sizes of both cr-isa1-1 and cr-isa1-2 were affected, and the two mutants also displayed a shrunken endosperm with significantly lower grain weight. Electron microscopy analysis showed that abnormal starch granules and amyloplasts were found in cr-isa1-1 and cr-isa1-2 endosperm cells. The contents of total starch, amylose and amylopectin in the endosperm of the cr-isa1 mutants were significantly reduced, whereas sugar content and starch gel consistency were observably increased compared to the wild-type. The gelatinization temperature and starch chain length distributions of the cr-isa1 mutants were also altered. Moreover, transcript levels of most starch synthesis-related genes were significantly lower in cr-isa1 mutants. In conclusion, the results indicated that gene edition of ISA1 affected starch synthesis and endosperm development, and brought potential implications for rice quality breeding.

关键词： ISA1 rice starch biosynthesis starch granule physicochemical property CRISPR Cas9

Improved Eating and Cooking Quality of indica Rice Cultivar YK17 via Adenine Base Editing of Wx^(a)Allele of Granule-Bound Starch Synthase I(GBSS I)

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Rice science 2021年第5期28卷 427-430,I0010-I0017页

作者： Mahmuda Binte Monsur Cao Ni Wei Xiangjin Xie Lihong jiao guiai TAng Shaoqing Nese Sreeniwsulu Shao Gaoneng Hu Peisong State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China Applied Functional Genomics Cluster Grain Quality and Nutrition CentreStrategic innovation PlatformInternational Rice Research InstituteLos Banos 4030the Philippines

Amylose content(AC)is the key determinant of eating and cooking quality(ECQ)of rice.The major Wxa allele of granule-bound starch synthase I(GBSS I)in indica rice produces higher AC,making rice hard and dry after cooking.Recent work has improved ECQ of japonica rice via clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9(CRISPR/Cas9)or cytosine base editing(CBE)techniques.

关键词： CRISPR/Cas9 cooking Starch

Editing of Rice Endosperm Plastidial Phosphorylase Gene OsPho1 Advances Its Function in Starch Synthesis

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Rice science 2021年第3期28卷 209-211页

作者： LIU Song SHAO Gaoneng jiao guiai ZHU Maodi WU Jiamin CAO Ruijie CHEN Yujuan XIE Lihong SHENG Zhonghua TANG Shaoqing China National Rice Research Institute Hangzhou 310006China

OsPho1 in Zhonghua 11(ZH11)was edited using the clustered regularly interspaced short palindromic repeatsassociated endonuclease 9(CRISPR/Cas9)system.Two homozygous T1 mutants(cr-pho1-34 and cr-pho1-37)displayed a chalky endosperm with a white core,which significantly decreased 1000-grain weight.In addition,many rounded starch granules and abnormal amyloplasts were present in the central region of mutant endosperm cells with increased amylose and lipid contents,decreased total protein content,and altered physicochemical properties of starch.The OsPho1 protein is localized in chloroplasts,and quantitative real-time PCR(qRT-PCR)andβ-glucuronidase(GUS)staining indicated that OsPho1 was highly expressed in seeds at 5 d after fertilization(DAF).OsPho1 mutations displayed close relationships with plastidial phosphoglucomutase and ADPGlc pyrophosphorylase based onα-D-glucose-1P at different temperatures.Moreover,the expressions of starch metabolismrelated genes were also altered in the mutant,and the overexpression of OsPho1 may cause grain chalkiness.

关键词： CRISPR/Cas9 Pho Starch

Alanine aminotransferase(OsAlaAT1)modulates nitrogen utilization,grain yield,and quality in rice

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Journal of Genetics and Genomics 2022年第5期49卷 510-513页

作者： Liangbing Fang Liuyang Ma Shaolu Zhao Ruijie Cao guiai jiao Peisong Hu Xiangjin Wei State Key Laboratory of Rice Biology China National Center for Rice ImprovementChina National Rice Research InstituteHangzhouZhejiang 310006China

Widespread use of inorganic nitrogen fertilizers has increased yields of many grains, including rice (Oryza sativa L.);however, fertilizers are costly for farmers and cause serious environmental problems, such as soil acidification and water eutrophication (Guo et al., 2010, 2021;Liu et al., 2021). Improving nitrogen use efficiency(NUE) in rice offers a practical way to enhance grain yield and alleviate the environmental problems caused by overuse of nitrogen fertilizer. Identifying and characterizing genes involved in NUE provides crucial information for this aim.

关键词： soil grain fertilizers

The OsNAC23-Tre6P-SnRK1 a feed-forward loop regulates sugar homeostasis and grain yield in rice

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Molecular Plant 2022年第4期15卷 706-722页

作者： Zhiyong Li Xiangjin Wei Xiaohong Tong Juan Zhao Xixi Liu Huimei Wang Liqun Tang Yazhou Shu Guanghao Li Yifeng Wang Jiezheng Ying guiai jiao Honghong Hu Peisong Hu Jian Zhang State Key Lab of Rice Biology China National Rice Research InstituteHangzhou 311400China College of Life Science and Technology Huazhong Agricultural UniversityWuhan 430070China

Tre6P(trehalose-6-phosphate)mediates sensing of carbon availability to maintain sugar homeostasis in plants,which underpins crop yield and resilience.However,how Tre6P responds to fluctuations in sugar levels and regulates the utilization of sugars for growth remains to be addressed.Here,we report that the sugar-inducible rice NAC transcription factor OsNAC23 directly represses the transcription of the Tre6P phosphatase gene TPP1 to simultaneously elevate Tre6P and repress trehalose levels,thus facilitating carbon partitioning from source to sink organs.Meanwhile,OsNAC23 and Tre6P suppress the transcription and enzyme activity of SnRK1a,a low-carbon sensor and antagonist of OsNAC23,to prevent the SnRK1a-mediated phosphorylation and degradation of OsNAC23.Thus,OsNAC23,Tre6P,and SnRK1a form a feed-forward loop to sense sugar and maintain sugar homeostasis by transporting sugars to sink organs.Importantly,plants over-expressing OsNAC23 exhibited an elevated photosynthetic rate,sugar transport,and sink organ size,which consistently increased rice yields by 13%–17%in three elite-variety backgrounds and two locations,suggesting that manipulation of OsNAC23 expression has great potential for rice improvement.Collectively,these findings enhance our understanding of Tre6P-mediated sugar signaling and homeostasis,and provide a new strategy for genetic improvement of rice and possibly also other crops.

关键词： Tre6P sugar homeostasis carbon partitioning NAC transcription factor grain yield rice

Targeted mutagenesis of POLYAMINE OXIDASE 5 that negatively regulates mesocotyl elongation enables the generation of direct-seeding rice with improved grain yield

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Molecular Plant 2021年第2期14卷 344-351页

作者： Yusong Lv Gaoneng Shao guiai jiao Zhonghua Sheng Lihong Xie Shikai Hu Shaoqing Tang Xiangjin Wei Peisong Hu State Key Laboratory of Rice Biology China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006China National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China

Under conditions of labor or resource scarcity,direct seeding,rather than transplantation,is the preferred mode of rice(Oryza sativa)cultivation.This approach requires varieties that exhibit uniform seedling emergence.Mesocotyl elongation(ME),the main driver of rapid emergence of rice seedlings from soil,is enhanced by darkness and inhibited by light.Plant polyamine oxidases(PAOs)oxidize polyamines(PAs)and release H2O2,Here,we established that OsPAO5 expression in rice seedlings is increased in the presence of light and inhibited by darkness.To determine its role in ME,we created OsPAO5 mutants using CRISPR/Cas9.Compared with the wild type,pao5 mutants had longer mesocotyls,released less H2O2,and synthesized more ethylene.The mutant seedlings emerged at a higher and more uniform rate,indicating their potential for use in direct seeding.Nucleotide polymorphism analysis revealed that an SNP(PAO5-578G/A)located 578 bp upstream of the OsPAO5 start codon alters its expression,and was selected during rice mesocotyl domestication.The PAO5-578G genotype conferring a long mesocotyl mainly exists in wild rice,most Aus accessions,and some Geng(Japonica)accessions.Intriguingly,knocking out OsPAO5 can remarkably increase the grain weight,grain number,and yield potential.In summary,we developed a novel strategy to obtain elite rice with higher emergence vigor and yield potential,which can be conveniently and widely used to breed varieties of direct-seeding rice.

关键词： Oryza sativa direct seeding mesocotyl elongation grain yield polyamine oxidase 5

Mapping of qGL7-2, a grain length QTL on chromosome 7 of rice

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Journal of Genetics and Genomics 2010年第8期37卷 523-531页

作者： Gaoneng Shao Shaoqing Tang Ju Luo guiai jiao Xiangjin Wei Ao Tang Jianli Wu Jieyun Zhuang Peisong Hu State Key Laboratory of Rice Biology China National Rice Research lnstitt~te Hangzhou 310006 China

A residual heterozygous line （RHL） carrying a heterozygous segment between two S SR loci RM 11 and RM134 on the rice chromo- some 7 was selected from a set of recombinant inbred lines from the cross D50 （javanica）/HB277 （indica）. The former parent produces much longer grains than the latter. Selfed progenies of this selection were analyzed genotypically （SSRs） and phenotypically （grain length）. Grain length was discontinuously variable in the mapping populations, allowing for the placement of this QTL qGL7-2 within a -4.8 cM interval defined by RM351 and RM234. A set of new markers within this region were developed, which narrowed the QTL to a 278 kb region defined by the markers Indell and RM21945. This region contains 49 predicted genes. The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.

关键词： grain length mapping quantitative trait locus residual heterozygous line rice

GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development

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Journal of Integrative Plant Biology 2017年第2期59卷 134-153页

作者： Xiangjin Wei guiai jiao Haiyan Lin Zhonghua Sheng Gaoneng Shao Lihong Xie Shaoqing Tang Qingguo Xu Peisong Hu State Key Laboratory of Rice Biology Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture China National Rice Research Institute Hangzhou 310006 China . College of Agronomy Hunan Agricultural University Changsha 410128 China Agricultural Genomes Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518120 China

Rice grain filling determines grain weight, final yield and grain quality. Here, a rice defective grain filling mutant, gif2, was identified. Grains ofgif2 showed a slower filling rate and a significant lower final grain weight and yield compared to wild-type. The starch content in gilt2 was noticeably decreased and its physicochemical properties were also altered. Moreover, gif2 endosperm cells showed obvious defects in compound granule formation. Posi- tional cloning identified GIF2 to encode an ADP-glucose pyrophosphorylase （AGP） large subunit, AGPL2; consequently, AGP enzyme activity in gif2 endosperms was remarkably decreased. GIF2 is mainly expressed in developing grains and the coded protein localizes in the cytosol. Yeast two hybrid assay showed that GIF2 interacted with AGP small subunits OsAGPS% OsAGPS2a and OsAGPS2b. Transcript levels for granule-bound starch synthase, starch synthase, starch branching enzyme and starch debranching enzyme were distinctly elevated in gif2 grains. In addition, the level of nucleotide diversity of the GIF2 locus was extremely low in both cultivated and wild rice. All of these results suggest that GIF2 plays important roles in the regulation of grain filling and starch biosynthesis during caryopsis development, and that it has been preserved during selection throughout domestication of modern rice.

关键词： GIF GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development Figure AGPS RNAi