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Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance

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Science China(Life Sciences) 2024年第1期67卷 149-160页

作者： Haofei Luo Xiaofei Wang Changqing You Xuedan Wu Duofeng Pan Zhiyao Lv Tong Li Dongmei Zhang Zhongbao Shen Xiaodong Zhang Guodao Liu Kaixuan He Qingtong Ye Yajun Jia Qinghua Zhao Xian Deng Xiaofeng Cao Xianwei Song Gai Huang State Key Laboratory of plant Genomics and National Center for plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay Seed Lab Sanya 572025China University of Chinese Academy of Sciences Beijing 100049China Institute of Forage and Grassland Sciences Heilongjiang Academy of Agricultural SciencesHarbin 150086China Shandong Academy of Agricultural Sciences Jinan 250100China National Center of Technology Innovation for comprehensive Utilization of Saline-Alkali Land Dongying 257345China Shandong Green Manure Ecological Technology co. LtdDongying 257345China State Key Laboratory of Tropical Crop breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline soil.To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of S.cannabina spanning~2,087 Mb.The assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric characteristics.Further genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years ago.comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A homoeolog.We further identified four specific alkali-induced phosphate transporter genes in S.cannabina;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil.Our work highlights the significance of S.cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.

关键词： Sesbania cannabina alkaline stress telomere-to-telomere genome legume green manure phosphate transporter allotetraploid

Knockout of miR396 genes increases seed size and yield in soybean

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Journal of Integrative plant Biology 2024年第6期66卷 1148-1157页

作者： Hongtao Xie Fei Su Qingfeng Niu Leping Geng Xuesong Cao Minglei Song Jinsong Dong Zai Zheng Rui Guo Yang Zhang Yuanwei Deng Zhanbo Ji Kang Pang Jian-Kang Zhu Jianhua Zhu School of Life Sciences Anhui Agricultural University Research Center for Biological breeding Technology Research Institute of Frontier Science Anhui Agricultural University Bellagen Biotechnology co.ltd Institute of Crop Sciences/National Nanfan Research Institute Chinese Academy of Agricultural Sciences Key Laboratory of Gene Editing Technologies (Hainan) Ministry of Agriculture and Rural Affairs Southern University of Science and Technology Hainan Yazhou Bay Seed Laboratory

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed. mi R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is unknown. Here, we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302). Four triple mutants (mir396aci, mir396acd, mir396adf, and mir396cdf), two quadruple mutants(mir396-abcd and mir396acfi), and two quintuple mutants(mir396abcdf and mir396bcdfi) were characterized. We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants. Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude. In contrast, mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues, but they are suited for low latitude growth zones with increased yield without lodging problems.Taken together, our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean, providing valuable germplasms for breeding high-yield soybean.

关键词： Cas12SF01 CRISPR/Cas miR396 seed size soybean yield

Creating large EMS populations for functional genomics and breeding in wheat

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Journal of Integrative Agriculture 2024年第2期23卷 484-493页

作者： Wenqiang Wang Xizhen Guan Yong Gan Guojun Liu Chunhao Zou Weikang Wang Jifa Zhang Huifei Zhang Qunqun Hao Fei Ni Jiajie Wu Lynn Epstein Daolin Fu Spring Valley Agriscience co. Ltd.Jinan 250300China college of Life Sciences Zaozhuang UniversityZaozhuang 277160China National Key Laboratory of Wheat Improvement College of AgronomyShandong Agricultural UniversityTai’an 271018China Department of plant Pathology University of CaliforniaDavisCA 95616USA

Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introducing mutagenesis materials.Ethyl methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.In this study,we created a million-scale EMS population(MEP)that started with the Chinese wheat cultivars‘Luyan 128’,‘Jimai 38’,‘Jimai 44’,and‘Shannong 30’.In the M1 generation,the MEP had numerous phenotypical variations,such as>3,000 chlorophyll-deficient mutants,2,519 compact spikes,and 1,692 male sterile spikes.There were also rare mutations,including 30 independent tillers each with double heads.Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 generations.To advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)approach.All other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide quizalofop-P-methyl.The MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

关键词： wheat germplasm ethyl methane sulfonate genetics and breeding

Usefulness of LED lightings in cereal breeding on example of wheat,barley and oat seedlings

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International Journal of Agricultural and Biological Engineering 2019年第6期12卷 32-37页

作者： Piotr Stefański Patrycja Siedlarz Przemysław Matysik Krystyna Rybka plant breeding strzelce ltd.co. ul.Główna 2099-307 StrzelcePoland plant breeding and Acclimatization Institute-National Research Institute 05-870 RadzikówPoland

The LED lightings in horticulture are becoming prevalent,due to their physical properties allowing reduction of electricity consumption and on modulation of light spectrum and frequency.At present,LED lightings are not widely used by cereal breeding companies despite the fact that use of greenhouses is very common.This is why,the present experiment was run to show the evidence of LED lightings usefulness in a cereal crops breeding processes.Spring wheat(Triticum aestivum,L.),spring barley(Hordeum vulgare,L.)and oat(Avena sativa,L.),one cultivar of each species,were used for the 9 week trial conducted in a greenhouse with strictly controlled temperature(22℃)and humidity(80%).As a light source,4 LED illuminators along with a high-pressure sodium and xenon lamps and a natural sunlight in non-shadowed area of the same greenhouse were used.LED illuminators were characterized by relatively high ratio of blue/red radiation(0.6-1.3)to force the stem shortening,since cereal seedlings with such a growth habit are preferred in greenhouse cultivation of cereals.It was evidenced,that LED illuminators provided light suitable for cereals growth in a greenhouse,however each species had slightly different optimal light requirements.For wheat and barley the best impact on stem shortening and also on time to heading had a LED illuminator with high multi wave-blue radiation whereas on the leaves width the illuminator with lowest blue/red ratio.For oat seedlings a light source with highest light intensity and highest blue/red ratio seemed to be the most proper.Not much differences in seedlings growth and time to heading suggested that there is a chance for construction of one universal type of LED illuminator designed for greenhouse stages of cereal crops breeding.

关键词： greenhouse light emitting diodes cost-effectiveness Triticum aestivum Hordeum vulgare Avena sativa

Development of a single transcript CRISPR/Cas9 toolkit for efficient genome editing in autotetraploid alfalfa

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The Crop Journal 2024年第3期12卷 788-795页

作者： Haixia Zhao Siyi Zhao Yingping Cao Xiping Jiang Lijuan Zhao Zhimeng Li Mengqi Wang Ruijuan Yang Chuanen Zhou Zhaoming Wang Feng Yuan Dongmei Ma Hao Lin Wenwen Liu Chunxiang Fu CAS Key Laboratory of Biofuels Shandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101ShandongChina Shandong Energy Institute Qingdao 266101ShandongChina Qingdao New Energy Shandong Laboratory Qingdao 266101ShandongChina University of Chinese Academy of Sciences Beijing 100049China The Key Laboratory of plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdao 266101ShandongChina Key Laboratory of Forage breeding and Seed Production of Inner Mongolia Inner Mongolia M-Grass Ecology and Environment(Group)Co.Ltd.Hohhot 010016Inner MongoliaChina School of Ecology Environment Ningxia UniversityYinchuan 750021NingxiaChina Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China

Alfalfa(Medicago sativa.L.)is a globally significant autotetraploid legume forage crop.However,despite its importance,establishing efficient gene editing systems for cultivated alfalfa remains a formidable challenge.In this study,we pioneered the development of a highly effective ultrasonic-assisted leaf disc transformation system for Gongnong 1 alfalfa,a variety widely cultivated in Northeast China.Subsequently,we created a single transcript CRISPR/Cas9(CRISPR_2.0)toolkit,incorporating multiplex gRNAs,designed for gene editing in Gongnong 1.Both Cas9 and gRNA scaffolds were under the control of the Arabidopsis ubiquitin-10 promoter,a widely employed polymeraseⅡconstitutive promoter known for strong transgene expression in dicots.To assess the toolkit’s efficiency,we targeted PALM1,a gene associated with a recognizable multifoliate phenotype.Utilizing the CRISPR_2.0 toolkit,we directed PALM1 editing at two sites in the wild-type Gongnong 1.Results indicated a 35.1%occurrence of editing events all in target 2 alleles,while no mutations were detected at target 1 in the transgenic-positive lines.To explore more efficient sgRNAs,we developed a rapid,reliable screening system based on Agrobacterium rhizogenes-mediated hairy root transformation,incorporating the visible reporter MtLAP1.This screening system demonstrated that most purple visible hairy roots underwent gene editing.Notably,sgRNA3,with an 83.0%editing efficiency,was selected using the visible hairy root system.As anticipated,tetra-allelic homozygous palm1 mutations exhibited a clear multifoliate phenotype.These palm1 lines demonstrated an average crude protein yield increase of 21.5%compared to trifoliolate alfalfa.Our findings highlight the modified CRISPR_2.0 system as a highly efficient and robust gene editing tool for autotetraploid alfalfa.

关键词： Alfalfa Gene editing CRISPR_2.0 toolkit Hairy root system Tetra-allelic homozygous mutants

breeding exceptionally fragrant soybeans for soy milk with strong aroma

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Journal of Integrative plant Biology 2024年第4期66卷 642-644页

作者： Hongtao Xie Minglei Song Xuesong Cao Qingfeng Niu Jianhua Zhu Shasha Li Xin Wang Xiaomu Niu Jian-Kang Zhu Bellagen Biotechnology co.ltd. Jinan 250000China Institute of Advanced Biotechnology and School of Life Sciences Southern University of Science and TechnologyShenzhen 518055China School of Life Sciences Anhui Agricultural UniversityHefei 230036China Shandong Normal University Jinan 250000China

Soybean(Glycine max(L.)Merr.)is a major source of vegetable protein and oil in human diet and animal nutrition.Soybean seeds have been extensively used in various food products and snacks.Taste quality,particularly the aroma,affects cooking and eating,and ultimately influences consumer preference.Soy milk is particularly popular in China and has been gaining popularity in many other countries in the world.

关键词： exceptional soybean cooking

Expressing a human RNA demethylase as an assister improves gene-editing efficiency in plants

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Molecular plant 2024年第3期17卷 363-366页

作者： Mengyan Bai Wenxin Lin Chunyan Peng Peizhe Song Huaqin Kuang Jieni Lin Jieping Zhang Jiyao Wang Bo Chen Huarong Li Fanjiang Kong Guifang Jia Yuefeng Guan Guangdong Provincial Key Laboratory of plant Adaptation and Molecular Design Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China college of Agronomy China Agricultural UniversityBeijing 100193China college of Life Sciences Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China Synthetic and Functional Biomolecules Center Bejing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China Kingagroot co. Ltd.QingdaoShandong 266000China Tsinghua University-Peking University Joint Center for Life Sciences Bejing 100871China

Dear Editor,Despite myriad successful applications of gene editing in plant functional genomics research and precision breeding,many challenges persist around the efficiency of gene-editing tools for many plant species.For instance,soybean(Glycine max)is a major crop providing oil and protein to human diets and feedstock,but its gene-editing efficiency remains relatively low(Bai et al.,2019).

关键词： editing breeding

Calcium-dependent protein kinase CPK32 mediates calcium signaling in regulating Arabidopsis flowering time

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National Science Review 2022年第1期9卷 56-65页

作者： Xidong Li Limei Chen Li Yao Junjie Zou Jie Hao Weihua Wu State Key Laboratory of plant Physiology and Biochemistry College of Biological Sciences China Agricultural University Center for Crop Functional Genomics and Molecular breeding China Agricultural University Syngenta Biotechnology China co. Ltd. Biotechnology Research Institute Chinese Academy of Agricultural Sciences

Appropriate flowering time is critical for the reproductive success of plant species.Emerging evidence indicates that calcium may play an important role in the regulation of flowering time.However,the underlying molecular mechanisms remain unclear.In this study,we demonstrate that calcium-dependent protein kinase 32(CPK32) regulates flowering time by affecting the alternative polyadenylation of FLOWERING coNTROL LOCUS A(FCA) and altering the transcription of FLO WERING LOCUS C(FLC),a central repressor of flowering time.The knockdown of CPK32 results in an obvious late flowering phenotype and dramatically enhanced FL C transcription.CPK32 interacts with FCA,and phosphorylates the serine592of FCA in a Ca2+-dependent manner.Moreover,the ratio of abundance of the FCA transcripts(FCA-D and FCA-P) changes significantly in the cpk32 mutant,which subsequently affects FLC expression and consequently regulates floral transition.The present evidence demonstrates that CPK32 modulates flowering time by regulating FCA alternative polyadenylation and consequent FL C expression.

关键词： calcium signaling CPK32 FCA FLC flowering time

Analysis on Genetic Diversity of 40 Flowering Cherry Cultivars and construction of Molecular ID Based on SSR Markers

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Agricultural Sciences 2024年第2期15卷 256-273页

作者： Chaoren Nie Xiaoguo Xu Xiaoqin Zhang Hongbing Sun Jingya Yu Wensheng Xia Wuhan Institute of Landscape Architecture Wuhan China Wuhan Landscape Ecology Group co. Ltd. Wuhan China

Studying on the genetic diversity and genetic relationship of flowering cherry cultivars is extremely important for germplasm conservation, cultivar identification and breeding. Flowering cherry is widely cultivated as an important woody ornamental plant in worldwide, especially Japan, China. However, owning to the morphological similarity, many cultivars are distinguished hardly in non-flowering season. Here, we evaluated the genetic diversity and genetic relationship of 40 flowering cherry cultivars, which are mainly cultivated in China. We selected 13 polymorphicprimers to amplify to allele fragments with fluorescent-labeled capillary electrophoresis technology. The population structure analysis results show that these cultivars could be divided into 4 subpopulations. At the population level, Na and Ne were 6.062, 4.326, respectively. Ho and He were 0.458 and 0.670, respectively. The Shannon’s information index (I) was 1.417. The Pop3, which originated from P. serrulata, had the highest Ho, He, and I among the 4 subpopulations. AMOVA showed that only 4% of genetic variation came from populations, the 39% variation came from individuals and 57% (p construct molecular ID code system of these cultivars. This analysis on the genetic diversity and relationship of the 40 flowering cherry cultivars will help to insight into the genetic background, relationship of these flowering cherry cultivars and promote to identify similar cultivars.

关键词： Flowering Cherry SSR Genetic Relationship Molecular ID Identifying Cultivars