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GmSTF accumulation mediated by DELLA protein GmRGAs contributes to coordinating light and gibberellin signaling to reduce plant height in soybean

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The crop Journal 2024年第2期12卷 432-442页

作者： Zhuang Li Qichao Tu Xiangguang Lyu Qican Cheng Ronghuan Ji Chao Qin Jun Liu Bin Liu Hongyu Li Tao Zhao State Key Laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Plant height influences plant architecture,lodging resistance,and yield performance.It is modulated by gibberellic acid(GA)metabolism and signaling.DELLA proteins,acting as central repressors of GA signaling,integrate various environmental and hormonal signals to regulate plant growth and development in Arabidopsis.We examined the role of two DELLA proteins,GmRGAa and GmRGAb,in soybean plant height control.Knockout of these proteins led to longer internodes and increased plant height,primarily by increasing cell elongation.GmRGAs functioned under different light conditions,including red,blue,and far-red light,to repress plant height.Interaction studies revealed that GmRGAs interacted with the blue light receptor GmCRY1b.Consistent with this,GmCRY1b partially regulated plant height via GmRGAs.Additionally,DELLA proteins were found to stabilize the protein GmSTF1/2,a key positive regulator of photomorphogenesis.This stabilization led to increased transcription of GmGA2ox-7b and subsequent reduction in plant height.This study enhances our understanding of DELLA-mediated plant height control,offering Gmrgaab mutants for soybean structure and yield optimization.

关键词： DELLA protein GmRGAs GmSTFs Plant height Soybean

A novel pathogen Fusarium cuneirostrum causing common bean(Phaseolus vulgaris)root rot in China

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Journal of Integrative Agriculture 2024年第1期23卷 166-176页

作者： Dong Deng Wenqi Wu Canxing Duan Suli Sun Zhendong Zhu Institute of crop sciences Chinese Academy of Agricultural SciencesBeijing 100081China

Several fungal pathogens cause root rot of common bean,among which Fusarium spp.are the most common pathogens causing Fusarium root rot(FRR)worldwide.FRR has been becoming an increasingly severe disease of common bean in China,but the species of Fusarium spp.have remained unclear.Thus,this study was performed to identify the pathogen causing common bean root rot in Liangcheng County,Inner Mongolia,China.Nineteen Fusarium-like isolates were obtained after pathogen isolation and purification.The pathogenicity test indicated that eight isolates caused severe disease symptoms on common bean,while 11 other isolates were not pathogenic.The eight pathogenic isolates,FCL1–FCL8,were identified as Fusarium cuneirostrum by morphological characterization and phylogenetic analysis using partial sequences of EF-1α,ITS,28S,and IGS regions.Host range test showed that the representative F.cuneirostrum isolate FCL3 was also pathogenic to mung bean,while not pathogenic to adzuki bean,chickpea,cowpea,faba bean,pea,and soybean.Moreover,50 common bean and 50 mung bean cultivars were screened for resistance to FRR,and seven highly resistant or resistant cultivars of common bean were identified,while no resistant cultivars of mung bean were screened.This study revealed that F.cuneirostrum was one of common bean FRR pathogens in Inner Mongolia and it could induce mung bean root rot as well.To our knowledge,this is the first report of F.cuneirostrum causing FRR of common bean in China.

关键词： Fusarium cuneirostrum fusarium root rot pathogenicity molecular phylogenetic analysis Phaseolus vulgaris

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 toF.pseudograminearumand 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

Natural variation of GmFNSII-2 contributes to drought resistance by modulating enzyme activity in soybean

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The crop Journal 2024年第2期12卷 529-539页

作者： Huihui Gao Pengcheng Wei Yongzhe Gu Pengbin Tang Yifan Shen Lei Yang Linxin Dong Haowei Zheng Kuo Shu Mayamiko Masangano Bin Dong Long Miao Jiajia Li Lijuan Qiu Xiaobo Wang School of Agronomy Anhui Agricultural UniversityHefei 230036AnhuiChina State Key Laboratory of crop Gene Resources and Breeding The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the world.However,the scarcity of water resources worldwide has seriously impacted on the quality and yield of soybean.To address this,exploring excellent genes for improving drought resistance in soybean is crucial.In this study,we identified natural variations of GmFNSII-2(flavone synthase II)significantly affect the drought resistance of soybeans.Through sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were identified.The full-length allele GmFNSII-2^(C),but not the truncated allele GmFNSII-2^(A) possessing a nonsense nucleotide variation,increased enzyme activity.Further research found that GmDREB3,known to increase soybean drought resistance,bound to the promoter region of GmFNSII-2^(C).GmDREB3 positively regulated the expression of GmFNSII-2^(C),increased flavone synthase abundance and improved the drought resistance.Furthermore,a singlebase mutation in the GmFNSII-2^(C) promoter generated an additional drought response element(CCCCT),which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought conditions.The frequency of drought-resistant soybean varieties with Hap 1(Pro:GmFNSII-2^(C))has increased,suggesting that this haplotype may be selected during soybean breeding.In summary,GmFNSII-2^(C) could be used for molecular breeding of drought-tolerant soybean.

关键词： Drought stress Flavone synthase GmFNSII-2 Natural variation Drought response element

A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria

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Molecular Plant 2024年第2期17卷 219-222页

作者： Qiang He Chunchao Wang Qiang He Jun Zhang Hongkai Liang Zefu Lui Kun Xie Sha Tang Yuhan Zhou Bin Liu Hui Zhi Guanqing Jia Ganggang Guo Huilong Du Xianmin Diao State Key Laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China School of Life sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaoding 071000China State Key Laboratory of Rice Biology&Breeding Zhejang Provincial Key Laboratory of Crop GermplasmThe Advanced Seed InstituteZhejiang UniversityHangzhouChina

Dear Editor,,Foxtail millet(Setaria italica)and its wild ancestor green foxtail(S.viridis),are two C4 genetic model plants known for their desirable traits,such as small size,short life cycle,ease of transformation,and a compact genome size(~420 Mb)(He et al.,2023).Foxtail millet stands out as the only cultivated species within the Setaria genus.As a foundational crop for ancient east Asian agriculture civilization,it possesses remarkable drought and soil-nutrient deficiency tolerance.

关键词： comprehensive soil cultivated

Identification and fine mapping of qSW2 for leaf slow wilting in soybean

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The crop Journal 2024年第1期12卷 244-251页

作者： Shengyou Li Changling Wang Chunjuan Yan Xugang Sun Lijun Zhang Yongqiang Cao Wenbin Wang Shuhong Song Institute of crop Research Liaoning Academy of Agricultural SciencesShenyang 110161LiaoningChina

Drought is one of the abiotic stresses limiting the production of soybean(Glycine max).Elucidation of the genetic and molecular basis of the slow-wilting(SW)trait of this crop offers the prospect of its genetic improvement.A panel of 188 accessions and a set of recombinant inbred lines produced from a cross between cultivars Liaodou 14 and Liaodou 21 were used to identify quantitative-trait loci(QTL)associated with SW.Plants were genotyped by Specific-locus amplified fragment sequencing and seedling leaf wilting was assessed under three water-stress treatments.A genome-wide association study identified 26 SW-associated single-nucleotide polymorphisms(SNPs),including three located in a 248-kb linkage-disequilibrium(LD)block on chromosome 2.Linkage mapping revealed a major-effect QTL,qSW2,associated with all three treatments and adjacent to the LD block.Fine mapping in a BC_(2)F_(3) population derived from a backcross between Liaodou 21 and R26 confined qSW2 to a 60-kb interval.Gene expression and sequence variation analysis identified the gene Glyma.02 g218100,encoding an auxin transcription factor,as a candidate gene for qSW2.Our results will contribute significantly to improving drought-resistant soybean cultivars by providing genetic information and resources.

关键词： Drought GWAS Linkage mapping Slow wilting Soybean(Glycine max)

Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

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Journal of Integrative Plant Biology 2024年第1期66卷 66-85页

作者： Ding Ren Hui Liu Xuejun Sun Fan Zhang Ling Jiang Ying Wang Ning Jiang Peiwen Yan Jinhao Cui Jinshui Yang Zhikang Li Pingli Lu Xiaojin Luo State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China State Key Laboratory of crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China MOE Key Laboratory of crop Physiology Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045China State Key Laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China College of Agronomy Anhui Agricultural UniversityHefei 230036China

RNA-binding proteins(RBPs)are components of the post-transcriptional regulatory system,but their regulatory effects on complex traits remain unknown.Using an integrated strategy involving map-based cloning,functional characterizations,and transcriptomic and population genomic analyses,we revealed that RBP-K(LOC_Os08g23120),RBP-A(LOC_Os11g41890),and RBP-J(LOC_Os10g33230)encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits.Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally.Additionally,RBP-J most likely affects GA pathways,resulting in considerable increases in grain and panicle lengths,but decreases in grain width and thickness.In contrast,RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport,with substantial effects on the rice grain filling process as well as grain length and weight.Evolutionarily,RBP-K is relatively ancient and highly conserved,whereas RBP-J and RBP-A are more diverse.Thus,the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency,efficiency,and versatility,as well as increased evolutionary potential.Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits.Furthermore,rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.

关键词： GL11 grain weight and shape post-transcriptional regulation RNA-binding proteins

A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

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The crop Journal 2024年第1期12卷 142-153页

作者： Anqi Zhang Tangchao Kong Baiquan Sun Shizheng Qiu Jiahe Guo Shuyong Ruan Yu Guo Jirui Guo Zhishuai Zhang Yue Liu Zheng Hu Tao Jiang Yadong Liu Shuqi Cao Shi Sun Tingting Wu Huilong Hong Bingjun Jiang Maoxiang Yang Xiangyu Yao Yang Hu Bo Liu Tianfu Han Yadong Wang Center for Bioinformatics School of Computer Science and TechnologyHarbin Institute of TechnologyHarbin 150001HeilongjiangChina Ministry of Agriculture Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China National Key Facility for crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

关键词： Soybean Telomere-to-Telomere assembly Zhonghuang 13 Structure variations

Orchestrating seed storage protein and starch accumulation toward overcoming yield–quality trade-off in cereal crops

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Journal of Integrative Plant Biology 2024年第3期66卷 468-483页

作者： Shuanghe Cao Bingyan Liu Daowen Wang Awais Rasheed Lina Xie Xianchun Xia Zhonghu He State Key Laboratory of crop Gene Resources and Breeding/National Wheat Improvement Center Institute of Crop SciencesBeijing 100081China College of Agronomy Henan Agricultural UniversityZhengzhou 450002China International Maize and Wheat Improvement Center(CIMMYT)China Office Chinese Academy of Agricultural SciencesBeijing 100081China

Achieving high yield and good quality in crops is essential for human food security and health.However,there is usually disharmony between yield and quality.Seed storage protein(SSP)and starch,the predominant components in cereal grains,determine yield and quality,and their coupled synthesis causes a yield–quality trade-off.Therefore,dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality.Here,we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops,including maize,rice and wheat.We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights.We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding.Finally,future perspectives on major challenges are proposed.

关键词： cereal crops grain yield and quality seed storage protein starch synergistic regulation