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GSW3.1,a novel gene controlling grain size and weight in rice

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The Crop Journal 2024年第3期12卷 796-802页

作者： Yifei Jiang Mingao Zhou Simin Ke Xiaoxiao Deng Yangsheng Li State Key Laboratory of Hybrid Rice Key Laboratory for Research and Utilization of Heterosis in Indica RiceMinistry of AgricultureCollege of Life SciencesWuhan UniversityWuhan 430072HubeiChina

Grain size and weight are closely related traits determining yield in rice(Oryza sativa L.).Since indica and japonica rice varieties differ significantly in multiple traits,a high-generation recombinant inbred line(RIL)population derived from the crossing LH9(indica)and RPY(japonica)was used to map grainrelated traits in six *** of the quantitative trait loci(QTL)for thousand-grain weight showed that combinations of multiple QTL significantly increased the phenotypic effect.A novel gene named GSW3.1 controlling grain size and weight was discovered using the major QTL for the colocalization of grain width and thousand-grain weight on chromosome *** editing revealed that GSW3.1(LOC_Os03g16850)was pleiotropic,positively regulating grain size and weight while affecting several other agronomic *** analysis indicated that some traits,including grain width and weight,were highly correlated with indica-japonica differentiation.

关键词： Rice Grain size and weight 3.1(GSW3.1) Quantitative trait locus Haplotype analysis

TaRLK-6A promotes Fusarium crown rot resistance in wheat

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Journal of Integrative Plant Biology 2024年第1期66卷 12-16页

作者： Haijun Qi Xiuliang Zhu Wenbiao Shen Xia Yang Chaozhong Zhang Genying Li Feng Chen Xuening Wei Zengyan Zhang Institute of Special Animal and Plant Sciences Chinese Academy of Agricultural SciencesChangchun 130000China The national Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of Life Science Nanjing Agricultural UniversityNanjing 210095China Agronomy College/national Key Laboratory of Wheat and Maize Crop Science/CIMMYT‐china(Henan)Joint Center of Wheat and Maize Henan Agricultural UniversityZhengzhou 450002China Department of Plant Sciences University of CaliforniaDavisCA 95616USA Crop Research Institute Shandong Academy of Agricultural SciencesJinan 250100China

Fusariumcrown rot(FCR),mainly caused by the soil‐borne fungus Fusarium pseudograminearum,is a devastatingdisease of wheat(Triticum aestivum(Ta)).Fusariumcrown rotcauses substantial yield losses and generates mycotoxins inwheat grains that can cause serious health problems in hu-mans and livestock(Powell et al.,2017).Identifying genes thatprovide resistance *** character-izing the molecular mechanisms underlying such resistance arekey to breeding wheat varieties that are resistant to this dev-astating fungus.

关键词： aestivum breeding soil

Sexual compatibility of transgenic soybean and different wild soybean populations

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Journal of Integrative Agriculture 2022年第1期21卷 36-48页

作者： HU Yu-qi SHENG Ze-wen LIU Jin-yue LIU Qi QIANG Sheng SONG Xiao-ling LIU Biao Weed Research Laboratory College of Life SciencesNanjing Agricultural UniversityNanjing 210095P.R.China Nanjing Institute of Environmental Sciences Ministry of Ecology and EnvironmentNanjing 210042P.R.China

The introduction of genetically modified(GM) soybean into farming systems raises great concern that transgenes from GM soybean may flow to endemic wild soybean via pollen. This may increase the weediness of transgenic soybean by increasing the fitness of hybrids under certain conditions and threaten the genetic diversity of wild soybean populations. Although pollen-mediated gene flow between GM crops and wild relatives is dependent on many factors, the sexual compatibility(SC)determined by their genetic backgrounds is the conclusive factor. The considerable genetic variation among wild soybean populations may cause compatibility differences between different wild and cultivated soybeans. Thus, an evaluation of the SC between transgenic soybean and different wild soybeans is essential for assessing the environmental consequences of cultivated soybean–wild soybean transgene flow. The podding and seed sets were assessed after artificial hybridization using transgenic glyphosate-resistant soybean as the paternal parent and 18 wild soybean populations as the maternal parents. Then, the average number of filled seeds produced in 200 flowers(AFS) was calculated for each wild soybean under natural self-pollination as well as under artificial crossing with transgenic soybean. Finally, the index of cross-SC was calculated(ICSC) as the ratio of the AFS of wild soybean artificially crossed with transgenic soybean and the AFS of naturally self-pollinated wild soybean. The results demonstrated that after self-pollination and crossing with transgenic soybean, the average podding rates of 18 wild soybean populations ranged within 96.50–99.50% and 4.92–18.03%, and the average filled seed numbers per pod varied from 1.70 to 2.69 and 0.20 to 0.48, respectively. The results showed that approximately 89% of wild soybeans displayed either medium or higher than medium SC with transgenic soybean(ICSC>1.0%). This implied the high possibility of gene flow via pollen from transgenic soybean t

关键词： transgenic soybean wild soybean sexual compatibility artificial hybridization gene flow

Genome sequencing reveals the evolution and pathogenic mechanisms of the wheat sharp eyespot pathogen Rhizoctonia cerealis

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The Crop Journal 2023年第2期11卷 405-416页

作者： Lin Lu Feilong Guo Zhichao Zhang Xiuliang Zhu Yu Hao Jinfeng Yu Wenwu Ye Zengyan Zhang national Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops Ministry of Agriculture and Rural Affairs of the People’s Republic ChinaInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Department of Plant Pathology/Key Laboratory of Soybean Disease and Pest Control(Ministry of Agriculture and Rural Affairs of the People’s Republic china) The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095JiangsuChina College of Plant Protection Shandong Agricultural UniversityTai’an 271018ShandongChina

The necrotrophic fungus Rhizoctonia cerealis is the causal agent of devastating diseases of cereal crops including wheat(Triticum aestivum).We present a high-quality genome assembly of *** Rc207,a virulent strain causing wheat sharp *** assembly(56.36 Mb)is composed of 17.87%repeat sequences and 14,433 predicted protein-encoding *** Rc207 genome encodes a large and diverse set of genes involved in pathogenicity,especially rich in those encoding secreted proteins,carbohydrateactive enzymes(CAZymes),peptidases,nucleases,cytochrome P450,and secondary metabolismassociated *** secretory protein-encoding genes,including CAZymes,peroxygenases,dehydrogenases,and cytochrome P450,were up-regulated during fungal infection of *** identified 831 candidate secretory effectors and validated the functions of 10 up-regulated candidate effector *** them,nine were confirmed as necrotrophic pathogen’s effectors promoting fungal *** potential mobile or plastic genomic regions rich in repeat sequences suggest their roles in fungal adaption and virulence-associated genomic *** study provides valuable resources for further comparative and functional genomics on important fungal pathogens,and provides essential tools for development of effective disease control strategies.

关键词： Effector Evolution Pathogenesis Rhizoctonia cerealis Secretory proteins Sharp eyespot Wheat(Triticum aestivum)

The transcription factor HBF1 directly activates expression of multiple flowering time repressors to delay rice flowering

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aBIOTECH 2023年第3期4卷 213-223页

作者： Cong Li Liya Zhang Xin Wang Chunsheng Yu Tao Zhao Bin Liu Hongyu Li Jun Liu Chunyu Zhang Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of South china Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China Institute of Nanfan and Seed Industry Guangdong Academy of SciencesGuangzhou 510316China

Flowering time(or heading date)is an important agronomic trait that determines the environmental adaptability and yield of many crops,including rice(Oryza sativa L.).Hd3a BINDING REPRESSOR FACTOR 1(HBF1),a basic leucine zipper transcription factor,delays flowering by decreasing the expression of Early heading date 1(Ehd1),Heading date 3a(Hd3a),and RICE FLOWERING LOCUS T 1(RFT1),but the underlying molecular mechanisms have not been fully ***,we employed the hybrid transcriptional factor(HTF)strategy to enhance the transcriptional activity of HBF1 by fusing it to four copies of the activation domain from Herpes simplex virus *** discovered that transgenic rice lines overexpressing HBF1-VP64(HBF1V)show significant delays in time to flower,compared to lines overexpressing HBF1-MYC or wild-type plants,via the Ehd1–Hd3a/RFT1 pathway,under both long-day and short-day *** deep sequencing analysis indicated that 19 WRKY family genes are upregulated in the HBF1V overexpression *** demonstrate that the previously unknown gene,OsWRKY64,is a direct downstream target of HBF1 and represses flowering in rice,whereas three known flowering repressor genes,Days to heading 7(DTH7),CONSTANS 3(OsCO3),and OsWRKY104,are also direct target genes of HBF1 in flowering *** these results together,we propose detailed molecular mechanisms by which HBF1 regulates the time to flower in rice.

关键词： HBF1 bZIP transcription factor OsWRKY64 Flowering time Rice

Designing specific bacterial 16S primers to sequence and quantitate plant endo-bacteriome

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Science china(Life Sciences) 2022年第5期65卷 1000-1013页

作者： Liying Chen Mengting Zhang Da Liu Hongbo Sun Jianxiang Wu Yan Huo Xiaoying Chen Rongxiang Fang Lili Zhang State Key Laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China State Key Laboratory of Plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China national Plant Gene Research Center Beijing 100101China

Plant endophytic bacteria colonize the internal tissues of plants and interact with plants *** past two decades have witnessed the increasing application of next-generation 16S r RNA gene sequencing in the investigation of bacterial ***,deciphering plant endo-bacterial communities by this method is difficult because of the co-amplification of massive plant organellar DNAs with bacterial ***,we designed polymerase chain reaction(PCR) primer sets,including799F/1107R,322F/796R,and 322F-Dr/796Rs(primer pair 322F/796R with a penultimate-base substitution in 322F),that can specifically amplify bacterial 16S from plant total *** computationally and experimentally evaluated the specificity,coverage,and accuracy of the newly designed primer *** 799F/1107R and 322F-Dr/796Rs produced plant DNA-free 16S amplicon libraries or reduced plant DNA contamination to lower than 5% for the plant materials with extremely-low-abundance bacterial *** primer set 322F-A/796R was used through absolute quantitative PCR to quantitate the population size of rice leaf or root endo-bacteriome,which revealed 10^(6)–10^(7) and 10^(9)–10^(10) bacteria per gram fresh weight,*** 16S primer sets and amplification methods enable the simple and inexpensive next-generation sequencing and quantification of plant endo-bacteriome,which will significantly advance studies on the plant-related microbiome.

关键词： plant endo-bacteriome plant DNA-free amplification 16S rRNA gene next-generation sequencing absolute quantification

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

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The Crop Journal 2022年第1期10卷 47-55页

作者： Fei Ge Jingtao Qu Peng Liu Lang Pan Chaoying Zou Guangsheng Yuan Cong Yang Guangtang Pan Jianwei Huang Langlang Ma Yaou Shen Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Berry Genomics Corporation Beijing 100015China

The current assembled maize genomes cannot represent the broad genetic diversity of maize *** more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in *** we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome *** assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for *** on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten *** analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred *** a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in *** our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.

关键词： Maize Embryonic callus A188 Genome assembly Single-molecule sequencing

GhKNL1 controls fiber elongation and secondary cell wall synthesis by repressing its downstream genes in cotton(Gossypium hirsutum)

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Journal of Integrative Plant Biology 2022年第1期64卷 39-55页

作者： Yao Wang Yang Li Si-Ying Gong Li-Xia Qin Xiao-Ying Nie Dong Liu Yong Zheng Xue-Bao Li Hubei Key Laboratory of Genetic Regulation and Integrative Biology School of Life SciencesCentral China Normal UniversityWuhan 430079China

Cotton which produces natural fiber materials for the textile industry is one of the most important crops in the world. Class II KNOX proteins are often considered as transcription factors in regulating plant secondary cell wall(SCW) formation. However,the molecular mechanism of the KNOX transcription factor-regulated SCW synthesis in plants(especially in cotton) remains unclear in details so far. In this study, we show a cotton class II KNOX protein(Gh KNL1) as a transcription repressor functioning in fiber development. The Gh KNL1-silenced transgeniccotton produced longer fibers with thicker SCWs,whereas Gh KNL1 dominant repression transgenic lines displayed the opposite fiber phenotype, compared with controls. Further experiments revealed that Gh KNL1 could directly bind to promoters of Gh Ces A4-2/4-4/8-2 and Gh MYB46 for modulating cellulose synthesis during fiber SCW development in cotton. On the other hand, Gh KNL1 could also suppress expressions of Gh EXPA2 D/4 A-1/4 D-1/13 A through binding to their promoters for regulating fiber elongation of cotton. Taken together, these data revealed Gh KNL1 functions in fiber elongation and SCW formation by directly repressing expressions of its target genes related to cell elongation and cellulose synthesis. Thus, our data provide an effective clue for potentially improving fiber quality by genetic manipulation of Gh KNL1 in cotton breeding.

关键词： cotton(Gossypium hirsutum) fiber elongation KNOX protein secondary cell wall(SCW)synthesis transcriptional regulation

miR-204 suppresses porcine reproductive and respiratory syndrome virus(PRRSV)replication via inhibiting LC3B-mediated autophagy

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Virologica Sinica 2023年第5期38卷 690-698页

作者： Yao Yao Sihan Li Yingqi Zhu Yangyang Xu Siyuan Hao Shuyuan Guo Wen-Hai Feng State Key Laboratory of Animal Biotech Breeding Frontiers Science Center for Molecular Design BreedingMinistry of Agriculture Key Laboratory of Soil Microbiologyand Department of Microbiology and ImmunologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China

Porcine reproductive and respiratory syndrome(PRRS)caused by PRRS virus(PRRSV)has been regarded as a persistent challenge for the swine farms ***(miRNAs)play key roles in regulating almost every important biological process,including virus-host *** this study,we found that miR-204 was highly expressed in cells that were not permissive to PRRSV infection compared with cells susceptible to PRRSV ***,we demonstrated that overexpression of miR-204 significantly inhibited PRRSV replication in porcine alveolar macrophages(PAMs).Through bioinformatic analysis,we found that there existed a potential binding site of miR-204 on the 30UTR of microtubule associated protein 1 light chain 3B(MAP1LC3B,LC3B),a hallmark of *** experiments including luciferase reporter assay and UV cross-linking and immunoprecipitation(CLIP)assay,we demonstrated that miR-204 directly targeted LC3B,thereby downregulating ***,we investigated the interplay between autophagy and PRRSV replication in PAMs,confirming that PRRSV infection induces autophagy,which in turn facilitates viral ***,we verify that miR-204 suppresses PRRSV replication via inhibiting LC3B-mediated autophagy in *** findings will provide a novel potential approach for us to develop antiviral therapeutic agents and controlling measures for future PRRSV outbreaks.

关键词： Porcine reproductive and respiratory syndrome virus(PRRSV) miR-204 Autophagy LC3B