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Fine-tuning the spatial allocation of phytohormones for smart canopy, smart breeding, and smart agriculture

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Science China Life Sciences 2024年

作者： Tao Zhou Lin Li National key laboratory of Crop genetic Improvement Huazhong Agricultural University HuBei HongShan laboratory

The dual challenges of global climate change and population growth have increased demand for higher crop yields per unit area. The innovative technology of smart agriculture aims to synergize breeding, cultivation, and production through the application of biological and informatics technologies. Historically, the“Green Revolution” introduced semidwarf varieties of certain key crops by utilizing mutations affecting gibberellin pathways, which significantly increased planting densities and yields.

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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

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Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun Wang Tianze Zhu Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Chenwu Xu Zefeng Yang Jiangsu key laboratory of Crop genetics and Physiology/key laboratory of Plant Functional Genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination. We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

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The Crop Journal 2024年第3期12卷 866-879页

作者： Haozhe Tan Binghui Tang Mengling Sun Qiulu Yin Yizan Ma Jianying Li Pengcheng Wang Zhonghua Li Guannan Zhao Maojun Wang Xianlong Zhang Chunyuan You Lili Tu National key laboratory of Crop genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina Cotton Research Institute Shihezi Academy of Agriculture ScienceShihezi 832000XinjiangChina

Cotton fiber is one of the main raw materials for the textile *** recent years,many cotton fiber quality QTL have been identified,but few were applied in *** this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(Ghbreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 *** of these QTL were ignored by only using *** CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain *** these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in ***,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated *** findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

关键词： Cotton fiber quality breeding GWAS Genome-wide selective sweep analysis Genomic selection InDel markers

Rice AGL1 determines grain size and sterile lemma identity

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The Crop Journal 2024年第2期12卷 630-634页

作者： Haiping Yu An Wang Guangheng Zhang Guojun Dong Longbiao Guo Qian Qian Deyong Ren State key laboratory of Rice biology and breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina Hainan Yazhou Bay Seed laboratory Sanya 572024HainanChina National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024HainanChina

The grass spikelet is a unique inflorescence structure that determines grain *** many genetic factors have been well characterized for grain size and glume development,the underlying molecular mechanisms in rice are far from ***,we isolated rice gene,AGL1 that controlled grain size and determines the fate of the sterile *** of function of AGL1 produced larger grains and reduced the size of the sterile *** grains in the agl1 mutant were caused by a larger number of cells that were longer and wider than in the wild *** sterile lemma in the mutant spikelet was converted to a rudimentary glume-like *** findings showed that the AGL1(also named LAX1)protein positively regulated G1 expression,and negatively regulated NSG1 expression,thereby affecting the fate of the sterile *** together,our results revealed that AGL1 played a key role in negative regulation of grain size by controlling cell proliferation and expansion,and supported the opinion that rudimentary glume and sterile lemma in rice are homologous organs.

关键词： Abnormal grain and sterile lemma 1 Oryza sativa Grain size Rudimentary glume

Development and identification of two novel wheat-rye 6R derivative lines with adult-plant resistance to powdery mildew and high-yielding potential

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The Crop Journal 2024年第1期12卷 308-313页

作者： Guohao Han Jing Wang Hanwen Yan Tiantian Gu Lijun Cao Shiyu Liu Xiuquan Li Yilin Zhou Jieru Fan Zhipeng Shi Hong Liu Lihui Li Diaoguo An Center for Agricultural Resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050021HebeiChina The National key Facility for Crop Gene Resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China The State key laboratory for biology of Plant Disease and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China

Powdery mildew,caused by Blumeria graminis ***(Bgt),is a devastating disease that seriously threatens wheat yield and *** control this disease,host resistance is the most effective *** with the resistance genes from common wheat,alien resistance genes can better withstand infection of this highly variable *** of elite alien germplasm resources with powdery mildew resistance and other key breeding traits is an attractive strategy in wheat *** this study,three wheat-rye germplasm lines YT4-1,YT4-2,and YT4-3 were developed through hybridization between octoploid triticale and common wheat,out of which the lines YT4-1 and YT4-2 conferred adult-plant resistance(APR)to powdery mildew while the line YT4-3 was susceptible to powdery mildew during all of its growth *** genomic in situ hybridization,multi-color fluorescence in situ hybridization,multi-color GISH,and molecular marker analysis,YT4-1,YT4-2,and YT4-3 were shown to be cytogenetically stable wheat-rye 6R addition and T1RS.1BL translocation line,6RL ditelosomic addition and T1RS.1BL translocation line,and T1RS.1BL translocation line,*** with previously reported wheat-rye derivative lines carrying chromosome 6R,YT4-1 and YT4-2 showed stable APR without undesirable pleiotropic effects on agronomic ***,these novel wheat-rye 6R derivative lines are expected to be promising bridge resources in wheat disease breeding.

关键词： Powdery mildew Secale cereale Triticum aestivum Wheat-rye 6R derivatives Agronomic performance

Establishing VIGS and CRISPR/Cas9 techniques to verify RsPDS function in radish

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Journal of Integrative Agriculture 2024年第5期23卷 1557-1567页

作者： Jiali Ying Yan Wang Liang Xu Tiaojiao Qin Kai Xia Peng Zhang Yinbo Ma keyun Zhang Lun Wang Junhui Dong Lianxue Fan Yuelin Zhu Liwang Liu National key laboratory of Crop genetics&Germplasm Enhancement and Utilization/key laboratory of Horticultural Crop biology and genetic Improvement(East China)of Ministry of Agriculture and Rural Affairs/College of Horticulture Nanjing Agricultural UniversityNanjing210095China College of Horticulture and Landscape Architecture Yangzhou UniversityYangzhou 225009China College of Life Sciences Nanjing Agricultural UniversityNanjing 210095China

Virus-induced gene silencing(VIGS)and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein(CRISPR/Cas)systems are effective technologies for rapid and accurate gene function verification in modern plant ***,the investigation of gene silencing and editing in radish remains *** this study,a bleaching phenotype was generated through the knockdown of RsPDS using tobacco rattle virus(TRV)-and turnip yellow mosaic virus(TYMV)-mediated gene silencing *** TYMV-mediated gene silencing efficiency was higher than the TRV-based VIGS system in *** expression level of RsPDS was significantly inhibited using VIGS in'NAU-067'radish *** rootless seedlings of‘NAU-067'were infected with Agrobacterium rhizogenes using the 2300GN-Ubi-RsPDS-Cas9 vector with two target *** adventitious roots were blue with GUs staining,and four of these adventitious roots were edited at target sequence 1 of the RsPDS gene as indicated by Sanger ***,albino lines were generated with ***-mediated transformation of radish *** base substitutions and three base deletions occurred at target sequence 2 in Line 1,and three base insertions and three base substitutions occurred at target sequence 1 in Line *** study shows that VIGS and CRISPR/Cas9 techniques can be employed to precisely verify the biological functions of genes in radish,which will facilitate the genetic improvement of vital horticultural traits in radish breeding programs.

关键词： Raphanus sativus L. VIGS CRISPR/Cas9 Agrobacterium rhizogenes A.tumefaciens RsPDS

Most Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley

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Plant Communications 2024年第5期5卷 163-175页

作者： Guangqi Gao Luxi Yan Yu Cai Yu Guo Congcong Jiang Qiang He Sarah Tasnim Zongyun Feng Jun Liu Jing Zhang Takao Komatsuda Martin Mascher Ping Yang State key laboratory of Crop Gene Resources and breeding/key laboratory of Grain Crop genetic Resources Evaluation and Utilization(MARA)/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China College of Agronomy Sichuan Agricultural UniversityChengdu 611130China Leibniz Institute of Plant genetics and Crop Plant Research 06466 SeelandGermany Crop Research Institute Shandong Academy of Agricultural SciencesJinan 250100China

Tibetan weedy barleys reside at the edges of qingke(hulless barley)fields in Tibet(Xizang).The spikes of these weedy barleys contain or lack a brittle rachis,with either two-or six-rowed spikes and either hulled or hulless grains at *** the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley(Hordeum vulgare *** Thell.),these plants share genetic similarity with domesticated *** origin of Tibetan weedy barleys continues to be ***,we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys,followed by hybrid self-pollination and recombination between Non-brittle rachis 1(btr1)and 2(btr2).We discovered the specific genetic ancestry of these weedy barleys in South Asian *** weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke,genetically differing from typical eastern and western barley *** classified Tibetan weedy barleys into two groups,brittle rachis(BR)and non-brittle rachis(NBR);these traits align with the haplotypes of the btr1 and btr2 *** wild barleys carry haplotype combinations of Btr1 and Btr2,each showing lower proportions in a population,the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR *** block analysis based on whole-genome sequencing revealed two recombination breakpoints,which are present in 80.6%and 16.8%of BR acces-sions according to marker-assisted *** events between wild and domesticated barley were rarely *** support the notion that Tibetan weedy barleys originated via recom-bination between Btr1 and Btr2 in domesticated barley.

关键词： Tibetan weedy barley agriocrithon de-domestication out-pollination recombination brittle rachis

Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

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Molecular Plant 2024年第6期17卷 867-883页

作者： Fan Zhang Ruicai Long Zhiyao Ma Hua Xiao Xiaodong Xu Zhongjie Liu Chunxue Wei Yiwen Wang Yanling Peng Xuanwen Yang Xiaoya Shi Shuo Cao Mingna Li Ming Xu Fei He Xueqian Jiang Tiejun Zhang Zhen Wang Xianran Li Long-Xi Yu Junmei Kang Zhiwu Zhang Yongfeng Zhou Qingchuan Yang Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China National key laboratory of Tropical Crop breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China School of Grassland Science Beijing Forestry UniversityBeijing 100083China Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68583USA Department of Crop and Soil Sciences Washington State UniversityPullmanWA 99163USA U.S.Department of Agriculture-Agricultural Research Service Plant Germplasm Introduction and Testing ResearchProsserWA 99350USA National key laboratory of Tropical Crop breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China

Given the escalating impact of climate change on agriculture and food security,gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate ***(Medicago sativa ***),the queen of forages,shows remarkable adaptability across diverse global environments,making it an excellent model for investigating species responses to climate *** this study,we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa’s climatic adaptation and genetic susceptibility to future climate *** found that interspecific genetic exchange has contributed to the gene pool of alfalfa,particularly enriching defense and stress-response *** introgression between *** ***(***)and alfalfa not only aids alfalfa’s climatic adaptation but also introduces genetic burden.A total of 1671 genes were associated with climatic adaptation,and 5.7%of them were introgressions from *** integrating climate-associated variants and climate data,we identified populations that are vulnerable to future climate change,particularly in higher latitudes of the Northern *** findings serve as a clarion call for targeted conservation initiatives and breeding *** also identified preadaptive populations that demonstrate heightened resilience to climate fluctuations,illuminating a pathway for future breeding ***,this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars,contributing to effective agricultural strategies for facing future climate change.

关键词： Medicago local adaptation population genetics adaptive introgression genetic vulnerability alfalfa breeding

Antagonistic MADS-box transcription factors SEEDSTICK and SEPALLATA3 form a transcriptional regulatory network that regulates seed oil accumulation

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Journal of Integrative Plant biology 2024年第1期66卷 121-142页

作者： Shuangcheng He Yuanchang Min Zijin Liu Fang Zhi Rong Ma Ankang Ge Shixiang Wang Yu Zhao Danshuai Peng Da Zhang Minshan Jin Bo Song Jianjun Wang Yuan Guo Mingxun Chen State key laboratory for Crop Stress Resistance and High‐Efficiency Production National Yangling Agricultural Biotechnology&Breeding CenterShaanxi Key Laboratory of Crop HeterosisCollege of AgronomyNorthwest A&F UniversityYangling 712100China State key laboratory for Crop Stress Resistance and High‐Efficiency Production Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYangling 712100China

Transcriptional regulation is essential for balancing multiple metabolic pathways that influence oil accumulation in *** far,the transcriptional regulatory mechanisms that govern seed oil accumulation remain largely ***,we identified the transcriptional regulatory network composed of MADS-box transcription factors SEEDSTICK(STK)and SEPALLATA3(SEP3),which bridges several key genes to regulate oil accumulation in *** found that STK,highly expressed in the developing embryo,positively regulates seed oil accumulation in Arabidopsis(Arabidopsis thaliana).Furthermore,we discovered that SEP3 physically interacts with STK in vivo and in *** oil content is increased by the SEP3 mutation,while it is decreased by SEP3 *** chromatin immunoprecipitation,electrophoretic mobility shift assay,and transient dual-luciferase reporter assays showed that STK positively regulates seed oil accumulation by directly repressing the expression of MYB5,SEP3,and SEED FATTY ACID REDUCER 4(SFAR4).Moreover,genetic and molecular analyses demonstrated that STK and SEP3 antagonistically regulate seed oil production and that SEP3 weakens the binding ability of STK to MYB5,SEP3,and ***,we demonstrated that TRANSPARENT TESTA 8(TT8)and ACYL-ACYL CARRIER PROTEIN DESATURASE 3(AAD3)are direct targets of MYB5 during seed oil accumulation in ***,our findings provide the transcriptional regulatory network antagonistically orchestrated by STK and SEP3,which fine tunes oil accumulation in seeds.

关键词： seed oil accumulation SEP3 STK transcription factor transcriptional regulation