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Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

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The crop Journal 2024年第1期12卷 232-243页

作者： Yanzhu Su Xiaoshuai Hao Weiying Zeng Zhenguang Lai Yongpeng Pan Can Wang Pengfei Guo Zhipeng Zhang Jianbo He Guangnan Xing Wubin Wang Jiaoping Zhang Zudong Sun Junyi Gai Soybean Research Institute/MARA National center for Soybean Improvement MARA Key Laboratory of Biology and Genetic Improvement of Soybean/State Key Laboratory for crop Genetics and Germplasm Enhancement/State innovation Platform for Integrated production and Education in Soybean Bio-breeding/jiangsu collaborative innovation center for modern crop production Nanjing Agricultural UniversityNanjing 210095JiangsuChina Guangxi Academy of Agricultural Sciences Nanning 530007GuangxiChina

Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade *** improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with *** of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth *** the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the ***,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.

关键词： Soybean(Glycine max(L.)Merr.) Shade-tolerance Restricted two-stage multi-locus genomewide association study based on gene/allele sequence markers(GASM-RTM-GWAS) Shade-tolerance index(STI) Relative cell length(RCL) Transcriptome

Irrigation regimes modulate non-structural carbohydrate remobilization and improve grain filling in rice(Oryza sativa L.)by regulating starch metabolism

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Journal of Integrative Agriculture 2024年第5期23卷 1507-1522页

作者： Yuguang Zang Gaozhao Wu Qiangqiang Li Yiwen Xu Mingming Xue Xingyu Chen Haiyan Wei Weiyang Zhang Hao Zhang Lijun Liu Zhiqin Wang Junfei Gu Jianchang Yang jiangsu Key Laboratory of crop Genetics and Physiology/jiangsu Key Laboratory of crop Cultivation and Physiology/Agricultural College YangzhouUniversityYangzhou225009China jiangsu Co-innovation center for modern production Technology of Grain crops Yangzhou UniversityYangzhou 225009China

Recently developed ‘super’ rice cultivars with greater yield potentials often suffer from the problem of poor grain filling, especially in inferior spikelets. Here, we studied the activities of enzymes related to starch metabolism in rice stems and grains, and the microstructures related to carbohydrate accumulation and transportation to investigate the effects of different water regimes on grain filling. Two ‘super’ rice cultivars were grown under two irrigation regimes of well-watered(WW) and alternate wetting and moderate soil drying(AWMD). Compared with the WW treatment,the activities of ADP glucose pyrophosphorylase(AGPase), starch synthase(StSase) and starch branching enzyme(SBE), and the accumulation of non-structural carbohydrates(NSCs) in the stems before heading were significantly improved, and more starch granules were stored in the stems in the AWMD treatment. After heading, the activities of α-amylase, β-amylase, sucrose phosphate synthase(SPS) and sucrose synthase in the synthetic direction(SSs)were increased in the stems to promote the remobilization of NSCs for grain filling under AWMD. During grain filling, the enzymatic activities of sucrose synthase in the cleavage direction(SSc), AGPase, StSase and SBE in the inferior spikelets were increased, which promoted grain filling, especially for the inferior spikelets under ***, there were no significant differences in vascular microstructures. The grain yield and grain weight could be improved by 13.1 and 7.5%, respectively, by optimizing of the irrigation regime. We concluded that the low activities of key enzymes in carbon metabolism is the key limitation for the poor grain filling, as opposed to the vascular microstructures, and AWMD can increase the amount of NSC accumulation in the stems before heading, improve the utilization rate of NSCs after heading, and increase the grain filling, especially in the inferior spikelets, by altering the activities of key enzymes in carbon metabolism.

关键词： rice(Oryza sativa L.) non-structural carbohydrates(NsCs) enzymatic activity grain illing starch granules vascular bundle

Optimized tillage methods increase mechanically transplanted rice yield and reduce the greenhouse gas emissions

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Journal of Integrative Agriculture 2024年第4期23卷 1150-1163页

作者： Shuang Cheng Zhipeng Xing Chao Tian Mengzhu Liu Yuan Feng Hongcheng Zhang jiangsu Key Laboratory of crop Cultivation and Physiology/jiangsu Co-innovation center for modern production Technology of Grain crops/Research Institute of Rice Industrial Engineering Technology Yangzhou UniversityYangzhou 225009China

Biaxia lrotary tillage in dryland(DBRT)can complete biaxial rotary tillage with straw incorporation,secondary suppression,and ditching,and it has been previously studied in direct-seeded rice and ***,the effects of DBRT on the mechanically transplanted rice yield and greenhouse gas emissions remain *** evaluate the effects of DBRT on improving the food security of mechanically transplanted rice and reducing the greenhouse gas emissions,we conducted an experiment for two years with wheat straw *** tillage methods were set up:DBRT,uniaxial rotary tillage in dryland and paddy(DPURT),and uniaxial rotary tillage in paddy(PURT).The results showed that compared with DPURT and PURT,DBRT increased the yield of machine-transplanted rice by 7.5-11.0%and 13.3-26.7%,respectively,while the seasonal cumulative CH_(4) emissions were reduced by 13.9-21.2%and 30.2-37.0%,respectively,and the seasonal cumulative N_(2)O emissions were increased by 13.5-28.6%and 50.0-73.1%,***,DBRT reduced the global warming potential by 10.7-15.5%and 23.7-28.6%,respectively,andtheyield-scaledglobalwarmingpotentialby18.2-21.8%and36.4-39.3%,respectively,compared to DPURT and *** results were mainly related to the fact that DBRT significantly reduced soil bulk density and increased soil redox potential(Eh).Therefore,implementing DBRT in machine-transplanted rice fields is feasible,which cannot only increase the rice yield,but also reduce the greenhouse gas emissions.

关键词： integrated tillage rice grain yield CH_(4) N_(2)O

Straw return influences the structure and functioning of arbuscular mycorrhizal fungal community in a rice-wheat rotation system

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Pedosphere 2024年第2期34卷 339-350页

作者： Silong ZHAI Junjie XIE Zongyi TONG Bing YANG Weiping CHEN Roger TKOIDE Yali MENG Xiaomin HUANG Atta Mohi Ud DIN Changqing CHEN Haishui YANG College of Agriculture Nanjing Agricultural UniversityNanjing 210095China Department of Biology Brigham Young UniversityProvo UT 84602USA jiangsu Key Laboratory of crop Genetics and Physiology/jiangsu Key Laboratory of crop Cultivation and Physiology Agricultural College of Yangzhou UniversityYangzhou 225009China National Research center of Intercropping The Islamia University of BahawalpurBahawalpur 63100Pakistan jiangsu collaborative innovation center for modern crop production Nanjing Agricultural UniversityNanjing 210095China

Straw return is a sustainable soil fertility-building practice,which can affect soil microbial ***,how straw return affects arbuscular mycorrhizal fungi(AMF)is not well ***,we studied the impacts of different straw management treatments over eight years on the structure and functioning of AMF communities in a rice-wheat rotation *** straw management treatments included no tillage with no straw(NTNS),rotary tillage straw return(RTSR),and ditch-buried straw return(DBSR).The community structure of AMF was characterized using high-throughput sequencing,and the mycorrhizal functioning was quantified using an in situ mycorrhizal-suppression *** straw management treatments formed unique AMF community structure,which was closely related to changes in soil total organic carbon,available phosphorus,total nitrogen,ammonium,and *** compared with NTNS,RTSR significantly increased Shannon diversity in 0–10 cm soil layer,while DBSR increased it in 10–20 cm soil layer;DBSR significantly increased hyphal length density in the whole ploughing layer(0–20 cm),but RTSR only increased it in the subsurface soil layer(10–20 cm).The mycorrhizal responses of shoot biomass and nutrient(N and P)uptake were positive under both straw return treatments(RTSR and DBSR),but negative under *** community composition of AMF was significantly correlated to hyphal length density,and the latter was further a positive predictor for the mycorrhizal responses of plant growth and nutrient *** findings suggest that straw return can affect AMF community structure and functioning,and farmers should manage mycorrhizas to strengthen their beneficial effects on crop production.

关键词： community structure hyphal length density shoot biomass shoot N uptake shoot P uptake soil physicochemical properties straw management tillage

Inhibition of protein degradation increases the Bt protein concentration in Bt cotton

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Journal of Integrative Agriculture 2024年第6期23卷 1897-1909页

作者： Yuting Liu Hanjia Li Yuan Chen Tambel Leila.I.M Zhenyu Liu Shujuan Wu Siqi Sun Xiang Zhang Dehua Chen jiangsu Key Laboratory of crop Genetics and Physiology/Co-innovation center for modern production Technology of Grain crops Yangzhou UniversityYangzhou 225009China Agricultural Research Cooperation Biotechnology and Biosafety Research CenterKhartoum 13314Sudan

Bacillus thuringiensis(Bt)cotton production is challenged by two main problems,i.e.,the low concentration of Bt protein at the boll setting stage and the lowest insect resistance in bolls among all the cotton plant’s ***,increasing the Bt protein concentration at the boll stage,especially in bolls,has become the main goal for increasing insect resistance in *** this study,two protein degradation inhibitors(ethylene diamine tetra acetic acid(EDTA)and leupeptin)were sprayed on the bolls,subtending leaves,and whole cotton plants at the peak flowering stage of two Bt cultivars(medium maturation Sikang 1(SK1))and early maturation Zhongmian 425(ZM425)in 2019 and *** Bt protein content and protein degradation metabolism were *** results showed that the Bt protein concentrations were enhanced by 21.3 to 38.8%and 25.0 to 38.6%in the treated bolls of SK1 and ZM425 respectively,while they were decreased in the subtending leaves of these treated *** the treated leaves,the Bt protein concentrations increased by 7.6 to 23.5%and 11.2 to 14.9%in SK1 and ZM425,*** combined application of EDTA and leupeptin to the whole cotton plant increased the Bt protein concentrations in both bolls and subtending *** Bt protein concentrations in bolls were higher,increasing by 22.5 to 31.0%and 19.6 to 32.5%for SK1 and ZM425,*** organs treated with EDTA or/and leupeptin showed reduced free amino acid contents,protease and peptidase activities and significant enhancements in soluble protein *** results indicated that inhibiting protein degradation could improve the protein content,thus increasing the Bt protein concentrations in the bolls or/and leaves of cotton ***,the increase in the Bt protein concentration without yield reduction suggested that these two protein degradation inhibitors may be applicable for improving insect resistance in cotton production.

关键词： Bt cotton Bt protein inhibition of protein degradation protein degradation metabolism

Exploiting viral vectors to deliver genome editing reagents in plants

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aBIOTECH 2024年第2期5卷 247-261页

作者： Yilin Shen Tao Ye Zihan Li Torotwa Herman Kimutai Hao Song Xiaoou Dong Jianmin Wan State Key Laboratory of crop Genetics and Germplasm Enhancement and Utilization Jiangsu Collaborative Innovation Centre for Modern Crop ProductionJiangsu Engineering Research Center for Plant Genome EditingNanjing Agricultural UniversityNanjing 210095China Zhongshan Biological Breeding Laboratory Nanjing 210014China Hainan Seed Industry Laboratory Sanya 572025China State Key Laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Genome editing holds great promise for the molecular breeding of plants,yet its application is hindered by the shortage of simple and effective means of delivering genome editing reagents into *** plant transformation-based methods for delivery of genome editing reagents into plants often involve prolonged tissue culture,a labor-intensive and technically challenging process for many elite crop *** this review,we describe various virus-based methods that have been employed to deliver genome editing reagents,including components of the CRISPR/Cas machinery and donor DNA for precision editing in *** update the progress in these methods with recent successful examples of genome editing achieved through virus-based delivery in different plant species,highlight the advantages and limitations of these delivery approaches,and discuss the remaining challenges.

关键词： Plant genome engineering Genome editing CRISPR/Cas Virus-based delivery

Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating OsGA2ox7 in rice

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Journal of Integrative Plant Biology 2024年第4期66卷 731-748页

作者： Peng Zeng Ting Xie Jiaxin Shen Taokai Liang Lu Yin Kexin Liu Ying He Mingming Chen Haijuan Tang Sunlu Chen Sergey Shabala Hongsheng Zhang Jinping Cheng National Key Laboratory of crop Genetics&Germplasm Enhancement and Utilization Jiangsu Collaborative Innovation Center for Modern Crop ProductionHainan Yazhou Bay Seed LabJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyNanjing Agricultural UniversityNanjing 210095China International Research center for Environmental Membrane Biology Foshan UniversityFoshan 528000China School of Biological Sciences University of Western AustraliaCrawley WA 6009Australia

Soil salinity has a major impact on rice seed germination,severely limiting rice ***,a rice germination defective mutant under salt stress(gdss)was identified by using chemical *** GDSS gene was detected via MutMap and shown to encode potassium transporter *** analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt ***9 is highly expressed in germinating seed *** contents and non-invasive micro-test technology results showed that OsHAK9 restricted K^(+)efflux in salt-exposed germinating seeds for the balance of K^(+)/Na^(+).Disruption of OsHAK9 significantly reduced gibberellin 4(GA4)levels,and the germination defective phenotype of oshak9a was partly rescued by exogenous GA_(3)treatment under salt *** sequencing(RNA-seq)and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress,and the expression of OsGA2ox7 was significantly inhibited by salt *** mutants of OsGA2ox7 created using clustered,regularly interspaced,short palindromic repeat(CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt ***,our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7,which provides a novel clue about the relationship between GA and OsHAKs in rice.

关键词： GDSS gibberellins potassium transporter rice salt tolerance seed germination

Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： Long Chen Guanqing Liu Tao Zhang jiangsu Key Laboratory of crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China jiangsu Co-innovation center for modern production Technology of Grain crops/jiangsu Key Laboratory of crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing crop improvement Molecular design breeding

Combining QTL Mapping and Multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in Maize

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1441-1453页

作者： Pengcheng Li Tianze Zhu Yunyun Wang Shuangyi Yin Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Zefeng Yang Chenwu Xu jiangsu Key Laboratory of crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhou225009China jiangsu Co-innovation center for modern production Technology of Grain crops Yangzhou UniversityYangzhou225009China

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and ***,the genetic basis underlying these nutritional quality traits during grainﬁlling remains poorly *** this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages *** the traits exhibited considerable phenotypic *** the grain-ﬁlling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with signiﬁcant changes observed between 30 and 40 days after *** trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,*** QTLs were consistently detectable across different time *** integrating QTL analysis,glo-bal gene expression proﬁling,and comparative genomics,we identiﬁed 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,*** gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein *** study offers signiﬁcant insights into the genetic architecture of maize kernel nutritional quality and identiﬁes promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.

关键词： Maize protein oil starch QTL mapping candidate genes