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EPSPS regulates cell elongation by disrupting the balance of lignin and flavonoid biosynthesis in cotton

Journal of Integrative Agriculture 2024年第10期23卷 3437-3456页

作者： Qingdi Yan Wei Hu Chenxu Gao Lan Yang Jiaxian Yang Renju Liu Masum Billah Yongjun Lin Ji Liu Pengfei Miao Zhaoen Yang Fuguang Li Wenqiang Qin State key laboratory of Cotton Bio‑breeding and Integrated Utilization/Institute of Cotton Research Chinese Academy ofAgricultural SciencesAnyang 455000China National key laboratory of Crop genetic Improvement and National Center of Plant Gene Research Huazhong AgriculturalUniversityWuhan 430070China State key laboratory of Cotton Bio-breeding and Integrated Utilization/Zhengzhou University Zhengzhou 450066China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572025China

EPSPS is a key gene in the shikimic acid synthesis pathway that has been widely used in breeding crops with herbicide ***,its role in regulating cell elongation is poorly *** the overexpression of EPSPS genes,we generated lines resistant to glyphosate that exhibit an unexpected dwarf phenotype.A representative line,DHR1,exhibits a stable dwarf phenotype throughout its entire growth *** for plant height,the other agronomic traits of DHR1 are similar to its transgenic explants *** section observations showed that DHR1 internodes are shortened due to reduced elongation and division of the internode *** hormones confirmed that DHR1 is not a classical brassinolide(BR)-or gibberellin(GA)-related dwarfing *** analysis and fine mapping confirmed that the EPSPS gene is the causal gene for dwarfism,and the phenotype can be inherited in different *** and metabolome analyses showed that genes associated with the phenylpropanoid synthesis pathway are enriched in DHR1 compared with *** metabolites are enriched in DHR1,whereas lignin metabolites are *** enhancement of flavonoids likely results in differential expression of auxin signal pathway genes and alters the auxin response,subsequently affecting cell *** study provides a new strategy for generating dwarfs and will accelerate advancements in light simplification in the cultivation and mechanized harvesting of cotton.

关键词： EPSPS cotton T-DNA dwarfism herbicide resistance

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genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice

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Journal of genetics and Genomics 2024年第6期51卷 583-593页

作者： Chaolong Wang Xiaowen Yu Jian Wang Zhigang Zhao Jianmin Wan State key laboratory for Crop genetics&Germplasm Enhancement and Utlization Nanjing Agricultural UniversityZhongshan Biological Breeding LaboratoryNanjingJiangsu210095China State key laboratory of Crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Heterosis,also known as hybrid vigor,is commonly observed in rice *** hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive ***,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific *** review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this ***,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive ***,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in *** on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.

关键词： Hybrid vigor Reproductive isolation Hybrid ricebreeding

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Intergeneric chromosome-specific painting reveals differential chromosomal transmission from Tripidium arundinaceum in sugarcane progeny

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Journal of Integrative Agriculture 2024年第11期23卷 3751-3762页

作者： Fan Yu Zehuai Yu Jin Chai Xikai Yu Chen Fu Xinwang Zhao Hailong Chang Jiawei Lei Baoshan Chen Wei Yao Muqing Zhang Jiayun Wu Qinnan Wang Zuhu Deng State key laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangxi key laboratory for Sugarcane biology College of Agriculture Guangxi University National Engineering Research Center for Sugarcane Fujian Agriculture and Forestry University Institute of Nanfan & Seed Industry Guangdong Academy of Sciences key laboratory of Sugarcane biology and genetic breeding Ministry of Agriculture and Rural Affairs/Fujian Agriculture and Forestry University

Sugarcane has recently attracted increasing attention for its potential as a source of sugar and bioethanol, so increasing its yield is essential to ensure the sugar security and bioenergy production. Intergeneric hybridization is a highly efficient method to produce new genetic variants of crop plants, particularly those species with high ploidy such as sugarcane(Saccharum spp.). Tripidium arundinaceum exhibits many desirable agronomic traits, and has been widely studied to produce hybrids with improved stress tolerance and other characteristics in sugarcane breeding. However, the genetic relationship between T. arundinaceum and Saccharum species, and the individual T. arundinaceum chromosomal compositions in sugarcane hybrids are still elusive. Here we used whole-genome single-nucleotide polymorphisms(SNPs) to ascertain the phylogenetic relationships between these species and found that T. arundinaceum is more closely related to Saccharum than Sorghum, in contrast to the previous narrow genetic analyses using chloroplast DNA. Additionally, oligonucleotide(oligo)-based chromosome-specific painting derived from Saccharum officinarum was able to distinctly identify the chromosomes of T. arundinaceum. We developed the oligo-genomic in situ hybridization(GISH) system for the first time, to unveil the novel chromosome translocations and the transmission of individual T. arundinaceum chromosomes in sugarcane progeny. Notably,we discovered that the chromosomal transmission of T. arundinaceum exhibited several different inheritance modes,including n, 2n, and over 2n in the BC1 progenies. Such inheritance patterns may have resulted from first division restitution(FDR) or FDR+nondisjunction of a chromosome with the sister chromatids in the second meiosis division/second division restitution(FDR+NSC/SDR) model during meiosis. These results will be of substantial benefit for the further selection of T. arundinaceum chromosomes for sugarcane genetic improvement.

关键词： sugarcane Tripidium arundinaceum chromosome painting Oligo-FISH chromosomal transmission

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Small particles,big effects:How nanoparticles can enhance plant growth in favorable and harsh conditions

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Journal of Integrative Plant biology 2024年第7期66卷 1274-1294页

作者： Jie Wang Honghong Wu Yichao Wang Wuwei Ye Xiangpei Kong Zujun Yin Zhengzhou Research Base State Key Laboratory of Cotton Bio‐breeding and Integrated UtilizationSchool of Agricultural SciencesZhengzhou UniversityZhengzhou 450001China State key laboratory of Cotton Bio‐breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000China National key laboratory of Crop genetic Improvement Huazhong Agricultural UniversityWuhan 430070China School of Engineering Design and Built EnvironmentWestern Sydney UniversityPenrith NSW 2751Australia Western Agricultural Research Center Chinese Academy of Agricultural SciencesChangji 831100China The key laboratory of Plant Development and Environmental Adaptation biology Ministry of EducationCollege of Life SciencesShandong UniversityQingdao 266237China

By 2050,the global population is projected to reach 9 billion,underscoring the imperative for innovative solutions to increase grain yield and enhance food *** has emerged as a powerful tool,providing unique solutions to this ***(NPs)can improve plant growth and nutrition under normal conditions through their high surface-to-volume ratio and unique physical and chemical ***,they can be used to monitor crop health status and augment plant resilience against abiotic stresses(such as salinity,drought,heavy metals,and extreme temperatures)that endanger global *** of NPs can enhance stress tolerance mechanisms in plants,minimizing potential yield losses and underscoring the potential of NPs to raise crop yield and *** review highlights the need for a comprehensive exploration of the environmental implications and safety of nanomaterials and provides valuable guidelines for researchers,policymakers,and agricultural *** thoughtful stewardship,nanotechnology holds immense promise in shaping environmentally sustainable agriculture amid escalating environmental challenges.

关键词： abiotic stress agricultural defense system nano-particles nanotechnology oxidative stress reactive oxygen species toxicity

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Natural variation of an autophagy-family gene among rice subspecies affects grain size and weight

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The Crop Journal 2024年第1期12卷 121-132页

作者： Shiying Huang Peng Wang Caijing Li Qingwen Zhou Tao Huang Yicong Cai Qin Cheng Hui Wang Qi Zhong Zhihao Chen Liping Chen Haohua He Jianmin Bian key laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education.Jiangxi Agricultural UniversityNanchang 330045JiangxiChina Weill Cornell Medical Immunology and Microbiology1300 York AvenueBox 62New YorkNY 10065USA

Elucidating the genetic basis of natural variation in grain size and weight among rice varieties can help breeders develop high-yielding *** identified a novel gene,GW3a(Grain Weight 3a)(LOC_Os03g27350),that affects rice grain size and ***3a mutants showed higher total starch content and dry matter accumulation than the wild type(WT),Nipponbare,suggesting that GW3a negatively regulates grain size and ***,our study found that GW3a interacted with OsATG8 by cleaving it,suggesting that GW3a may be involved in the assembly of autophagosomes and starch degradation in *** haplotype analysis of GW3a showed functional differences between indica and japonica *** together,we conclude that GW3a is expressed in the autophagosome pathway regulating starch metabolism in rice,affecting yield-related traits,such as grain size,grain weight and thousand grain weight(TGW).Our findings also shed new light on autophagy-mediated yield trait regulation,proposing a possible strategy for the genetic improvement of high-yield germplasm in rice.

关键词： Grain size GW3a Autophagy Starch content

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Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia

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Journal of genetics and Genomics 2024年第1期51卷 87-95页

作者： Liu Yang Xing Zhang Yaning Hu Piao Zhu Hua Li Zhenyu Peng Hai Xiang Xinying Zhou Xingbo Zhao National Engineering laboratory for Animal breeding Key Laboratory of AnimalGeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Guangdong Provincial key laboratory of Animal Molecular Design and Precise breeding School of Life Science and EngineeringFoshan UniversityFoshanGuangdong 528225China State key laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China key laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China

Sheep have been one of the most important groups of animals since ancient ***,the knowledge of their migration routes and genetic relationships is still poorly *** investigate sheep maternal migration histories alongside Eurasian communications routes,in this study,we obtain mitochondrial genomes(mitogenomes)from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429–3100 years before present(BP).By obtaining the mitogenomes from the sheep(4429–3556 BP)found in the Tongtian Cave site in Xinjiang,Altai region of northwest China,our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429–3556 *** combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern *** least two migration events have taken place for sheep crossing Eurasia to China,one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 ***,this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.

关键词： Sheep Ancient DNA Eastern Asia Mitochondrial genome Migration Altai

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Developing a CRISPR/FrCas9 system for core promoter editing in rice

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aBIOTECH 2024年第2期5卷 189-195页

作者： Hui Wang Jian Ding Jingyan Zhu Xiaoshuang Liu Rongfang Xu Ruiying Qin Dongfang Gu Min Li Pengcheng Wei Juan Li College of Agronomy Anhui Agricultural UniversityHefei 230036China key laboratory of Rice genetic breeding of Anhui Province Rice Research InstituteAnhui Academy of Agricultural SciencesHefei 230031China Research Centre for Biological breeding Technology Advance AcademyAnhui Agricultural UniversityHefei 230036China

Small mutations in the core promoter region of a gene may result in substantial changes in expression ***,targeting TA-rich sequences of core promoters may pose a challenge for Cas9 variants such as SpCas9 and other G-rich PAM-compatible *** this study,we engineered a unique FrCas9 system derived from Faecalibaculum rodentium for plant genome *** findings indicate that this system is efficient in rice when the TATA sequence is used as a *** addition,FrCas9 demonstrated activity against all 16 possible NNTA PAMs,achieving an efficiency of up to 35.3%in calli and generating homozygous or biallelic mutations in 31.3%of the T_(0)transgenic plants.A proof-ofconcept experiment to examine editing of the rice WX core promoter confirmed that FrCas9-induced mutations could modify gene expression and amylose *** mutations and deletions were produced by bidirectional editing,mediated by FrCas9,using a single palindromic TATA sequence as a ***,we developed FrCas9-derived base editors capable of programmable conversion between AT and GC pairs in *** study highlights a versatile FrCas9 toolset for plant core promoter editing,offering great potential for the fine-tuning of gene expression and creating of new germplasms.

关键词： Genome editing FrCas9 CRISPR Core promoter Base editing

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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(***),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 *** a foundational crop for ancient east Asian agriculture civilization,it possesses remarkable drought and soil-nutrient deficiency tolerance.

关键词： comprehensive soil cultivated

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An orchestrated ethylene-gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

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Journal of Integrative Plant biology 2024年第7期66卷 1427-1439页

作者： Yusong Lyu Xinli Dong Shipeng Niu Ruijie Cao Gaoneng Shao Zhonghua Sheng Guiai Jiao Lihong Xie Shikai Hu Shaoqing Tang Xiangjin Wei Peisong Hu State key laboratory of Rice biology and breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006China College of Agriculture and Biotechnology Zhejiang UniversityHangzhou 310058China

A mechanized direct seeding of rice with less labor and water usage,has been widely ***,this approach requires varieties that exhibit uniform seedling *** elongation(ME)offers the main drive of fast emergence of rice seedlings from soils;nevertheless,its genetic basis remains ***,we identify a major rice quantitative trait locus Mesocotyl Elongation1(qME1),an allele of the Green Revolution gene Semi-Dwarf1(SD1),encoding GA20-oxidase for gibberellin(GA)***1 expression is strongly induced by soil depth and *** rice grains are direct-seeded in soils,the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription,accelerating bioactive GA *** GAs further degrade the DELLA protein SLENDER RICE 1(SLR1),alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13(OsPIL13)to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and *** ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process,and an elite ME1-R allele(D349H)is found in some modern Geng varieties(long mesocotyl lengths)in northern China,which can be used in the direct seeding and dwarf breeding of Geng ***,the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield ***,we reveal the molecular mechanism of rice ME,and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.

关键词： rice(Oryza sativa L.) direct seeding Green Revolu-tion mesocotyl elongation ethylene gibberellin semi-dwarf1(SD1)

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RETINOBLASTOMA RELATED 1 switches mitosis to meiosis in rice

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Plant Communications 2024年第6期5卷 193-212页

作者： Yongjie Miao Hanli You Huixin Liu Yangzi Zhao Jiangzhe Zhao Yafei Li Yi Shen Ding Tang Baohui Liu Kewei Zhang Zhukuan Cheng Guangdong Provincial key laboratory of Plant Adaptation and Molecular Design Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China 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 State key laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China Zhejiang Provincial key laboratory of Biotechnology on Specialty Economic Plants Department of BiologyCollege of Life SciencesZhejiang Normal UniversityJinhua 321004China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu key laboratory of Crop genetics and Physiology Yangzhou UniversityYangzhou 225009China

The transition from mitosis to meiosis is a critical event in the reproductive development of all sexually reproducing ***,the mechanisms that regulate this process in plants remain largely ***,we find that the rice(Oryza sativa L.)protein RETINOBLASTOMA RELATED 1(RBR1)is essential to the transition from mitosis to *** of RBR1 function results in hyper-proliferative sporogenous-celllike cells(SCLs)in the anther locules during early stages of reproductive *** hyperproliferative SCLs are unable to initiate meiosis,eventually stagnating and degrading at late developmental stages to form pollen-free *** results suggest that RBR1 acts as a gatekeeper of entry into ***,cytokinin content is significantly increased in rbr1 mutants,whereas the expression of type-B response factors,particularly LEPTO1,is significantly *** the known close association of cytokinins with cell proliferation,these findings imply that hyper-proliferative germ cells in the anther locules may be attributed to elevated cytokinin concentrations and disruptions in the cytokinin *** a genetic strategy,the association between germ cell hyper-proliferation and disturbed cytokinin signaling in rbr1 has been *** summary,we reveal a unique role of RBR1 in the initiation of meiosis;our results clearly demonstrate that the RBR1 regulatory module is connected to the cytokinin signaling pathway and switches mitosis to meiosis in rice.

关键词： RETINOBLASTOMA RELATED1 meiosis initiation cytokinin rice

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