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Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 107-120页

作者： Wanlin Zhou Haoran Shi Zhiqiang Wang Yuxin Huang Lin Ni Xudong Chen Yan Liu Haojie Li Caixia Li Yaxi Liu state Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130China Triticeae research institute Sichuan Agricultural UniversityChengdu 611130China Chengdu Academy of agricultural and Forestry Sciences Chengdu 611130China

Enhancers are DNA sequences that can strengthen transcription ***,the global identification of plant enhancers is complicated due to uncertainty in the distance and orientation of enhancers,especially in species with large *** this study,we performed self-transcribing active regulatory region sequencing(STARR-seq)for the first time to identify enhancers across the barley genome.A total of 7323 enhancers were successfully identified,and among 45 randomly selected enhancers,over 75%were effective as validated by a dual-luciferase reporter assay system in the lower epidermis of tobacco ***,up to 53.5%of the barley enhancers were repetitive sequences,especially transposable elements(TEs),thus reinforcing the vital role of repetitive enhancers in gene *** the common active mark H3K4me3 and repressive mark H3K27me3 were abundant among the barley STARR-seq *** addition,the functional range of barley STARR-seq enhancers seemed much broader than that of rice or maize and extended to±100 kb of the gene body,and this finding was consistent with the high expression levels of genes in the *** study specifically depicts the unique features of barley enhancers and provides available barley enhancers for further utilization.

关键词： Barley Enhancer Transposable element Gene expression Repetitive sequence

Is magnesium deficiency the major cause of needle chlorosis of Pinus taeda in Brazil?

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Journal of Forestry research 2024年第2期35卷 209-221页

作者： Antônio Carlos Vargas Motta Shizuo Maeda Valdécio dos Santos dos Santos Rodrigues Tamires Maiara Ercole Stephen Arthur Prior Ana Elisa Lyra Brumat Amanda Pacheco Cardoso Moura Julierme Zimmer Barbosa João Bosco Vasconcellos Gomes Department of Soil Sciences and Agriculture Engineering Federal University of ParanáR.dos Funcionários1540.CuritibaParanáCEP 80035‑050Brazil Brazilian agricultural research Company Embrapa FlorestasEstr.da Ribeira–Br‑476Km 111–Parque Monte Castelo.ColomboParanáCEP 83411‑000Brazil United states Department of Agriculture‑agricultural research Service USDA-ARS National Soil Dynamics Laboratory411 South Donahue DriveAuburnAL 36832USA Reforestation Remasa Rodovia PR 170–Km 522.BiturunaParanáCEP 84640‑000Brazil Federal institute of Southeast of Minas Gerais R.Luz Interior360.Juiz de ForaMinas Gerais CEP 36030‑713Brazil

Needle chlorosis(NC)in Pinus taeda *** in Brazil becomes more frequent after second and third harvest rotation *** a study to identify factors contributing to yellowing needle chorosis(YNC),trees were grown in soils originating from contrasting parent materials,and soils and needles(whole,green and chlorotic portions)from 1-and 2-year-old branches and the first and second needle flush release at four sites with YNC on *** were analyzed for various elements and *** soils had very low base levels(Ca^(2+),Mg^(2+)and K^(+))and P,suggesting a possible lack of multiple *** symptoms started at needle tips,then extended toward the needle base with *** flush needles had longer portions with YNC than second flush needles *** from the lower crown also had more symptoms along their length than those higher in the *** were similar to those reported for *** chlorotic portions,Mg and Ca concentrations were well below critical values;in particular,Mg levels were only one third of the critical value of 0.3 g kg^(-1).Collectively,results suggest that Mg deficiency is the primary reason for NC of *** in various parent soils in Brazil.

关键词： Nutritional deficiency Forest management Soil depletion Pine foliar analysis Needle chlorosis

Identification of an Aux/IAA regulator for flesh firmness using combined GWAS and bulked segregant RNA-Seq analysis in watermelon

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Horticultural Plant Journal 2024年第5期10卷 1198-1213页

作者： Muhammad Anees Hongju Zhu Muhammad Jawad Umer Chengsheng Gong Pingli Yuan Xuqiang Lu Nan He Mohamed Omar Kaseb Dongdong Yang Yong Zhao Wenge Liu Henan Joint International research Laboratory of South Asian Fruits and Cucurbits Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China Henan Key Laboratory of Fruit and Cucurbit Biology Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China state Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural Science(ICRCAAS)AnyangHenan 455000China National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China

Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit *** various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf life and its commercial *** auxin/indole-3-acetic acid(Aux/IAA)plays a significant role in fruit development and ripening of non-climacteric ***,the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains *** this study,we employed an integrative approach combining genome-wide association study(GWAS)and bulked segregant RNA-Seq analysis(BSR-Seq)to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6,underlying an auxin-responsive gene(Aux/IAA)associated with flesh firmness in *** analysis,followed by real-time quantitative reverse transcription PCR(qRT-PCR),confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh *** sequence alignment revealed a single base mutation in the coding region of Aux/***,the concomitant Kompetitive/Competitive allele-specific PCR(KASP)genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh ***/IAA was enriched in the plant hormone signal transduction pathway,involving cell enlargement and leading to low flesh *** determined the higher accumulation of abscisic acid(ABA)in fruits with low flesh firmness than hard ***,overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell ***,the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication,indicating that soft flesh firmness was a domesticated *** findings significantly enhanced our unders

关键词： Watermelon Flesh firmness GWAS BSR-Seq KASP marker analysis Transient overexpression

Several whitefly genome assemblies and an integrated whitefly gene search platform

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Insect Science 2024年第1期31卷 299-306页

作者： Xingnuo Li Peng Liang Mingyue Wu Shaoli Wang Qingjun Wu Wen Xie Youjun Zhang state Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina Sanya Academy of Troprical agricultural Sciense SanyaHainanChina National research institute of Breeding in Hainan Chinese Academy of Agricultural SciencesSanyaHainanChina

Dear Editor,The characteristics and importance of the whitefly Bemisia tabaci as an economic pest seem to continually get more and more *** the whiteflies *** including,at least 11 genetic groups and 36 morphologically indistinguishable cryptic species,invasive MEAMl(Middle East-Asia Minor 1,"B"type)and MED(the Mediterranean,"Q"type)are the 2 most destructive cryptic species of the B.

关键词： Middle white East

Effect of red clover isoflavones on hormone, immune, inflammatory,and plasma biochemistry in lactating dairy cows

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Animal Nutrition 2024年第1期16卷 306-312页

作者： Shiqi Zhang Xiaoyin Zhang Zhanbo Xiong Kexin Li Yuan Gao Ying Bu Nan Zheng Shengguo Zhao Jiaqi Wang state Key Laboratory of Animal Nutrition Institute of Animal Sciences Chinese Academy of Agricultural Sciences

This study was to conducted to investigate the effect of red clover isoflavones on the health indicated by immune status and blood biochemistry in dairy cows. Sixty-eight healthy Holstein lactating cows were randomly divided into four treatments(n = 17 per treatment) from 5 blocks according to milk yield using a randomized complete block design. No initial differences in parity(2.13 ± 1.21), days in milk(165 ± 21 d), and milk yield(33.93 ± 3.81 kg/d) between groups. Cows were fed the basal diet supplemented with 0, 2, 4, or 8 g/kg red clover extract(RCE) in diet(dry matter based). Feeding, refusal feed weights, and milk yield were recorded three consecutive days in weeks 0, 4, 8, and 12. Blood was collected from the tail vein of the cows on the last day of weeks 4, 8 and 12, 1 h after the morning feeding,and analyzed for hormones, immunoglobulins, inflammatory markers, and markers of liver and kidney activities. The dry matter intake was significantly decreased by 3.7% in the 8 g/kg group(P 0.05). These results recommend the supplementation of RCE at a level from 2 to4 g/kg DM.

关键词： Dairy cow Red clover isoflavone Immunity Anti-inflammatory

Multi-omics analysis reveals the pivotal role of phytohormone homeostasis in regulating maize grain water content

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The Crop Journal 2024年第4期12卷 1081-1092页

作者： Yuanliang Liu Manman Li Jianju Liu Suining Deng Yan Zhang Yuanfeng Xia Baoshen Liu Mingliang Xu state Key Laboratory of Plant Environmental Resilience/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China College of Agronomy/state Key Laboratory of Crop Biology Shandong Agricultural UniversityTai’an 271018ShandongChina institute of agricultural Biotechnology Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina Maize research institute Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina

Grain water content(GWC)is a key determinant for mechanical harvesting of maize(Zea mays).In our previous research,we identified a quantitative trait locus,qGWC1,associated with GWC in ***,we examined near-isogenic lines(NILs)NILL and NILH that differed at the qGWC1 *** GWC in NILL was primarily attributed to reduced grain water weight(GWW)and smaller fresh grain size,rather than the accumulation of dry *** difference in GWC between the NILs became more pronounced approximately 35 d after pollination(DAP),arising from a faster dehydration rate in *** an integrated analysis of the transcriptome,proteome,and metabolome,coupled with an examination of hormones and their derivatives,we detected a marked decrease in JA,along with an increase in cytokinin,storage forms of IAA(IAA-Glu,IAA-ASP),and IAA precursor IPA in immature NILL *** kernel development,genes associated with sucrose synthases,starch biosynthesis,and zein production in NILL,exhibited an initial up-regulation followed by a gradual down-regulation,compared to those in *** discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.

关键词： Grain water content Maize kernel Phytohormone homeostasis

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

An inducible CRISPR activation tool for accelerating plant regeneration

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Plant Communications 2024年第5期5卷 109-122页

作者： Cuimei Zhang Yajun Tang Shanjie Tang Lei Chen Tong Li Haidi Yuan Yujun Xu Yangyan Zhou Shuaibin Zhang Jianli Wang Hongyu Wen Wenbo Jiang Yongzhen Pang Xian Deng Xiaofeng Cao Junhui Zhou Xianwei Song Qikun Liu state Key Laboratory of Protein and Plant Gene research School of Advanced Agricultural SciencesPeking UniversityBeijing 100871China Peking University institute of Advanced agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandong 261000China National Center for Plant Gene research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Grass and Science institute of Heilongjiang Academy of agricultural Sciences Heilongjiang 150086China institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China Key Laboratory of Seed Innovation and National Center for Plant Gene research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant *** this study,we developed a chem-ically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a *** systematically compared different induction strategies and achieved high efficiency in target gene *** demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant *** experiments showed that induced activation of these morphogenic genes can accelerate regenera-tion and improve regeneration efficiency in both eudicot and monocot plants,including alfalfa,woodland strawberry,and *** study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.

关键词： inducible CRISPR activation morphogenic gene genetic transformation plant regeneration

Leaf Morphology Genes SRL1 and RENL1 Co-Regulate Cellulose Synthesis and Affect Rice Drought Tolerance

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Rice science 2024年第1期31卷 103-117,I0020-I0022页

作者： LIU Dan ZHAO Huibo WANG Zi’an XU Jing LIU Yiting WANG Jiajia CHEN Minmin LIU Xiong ZHANG Zhihai CEN Jiangsu ZHU Li HU Jiang REN Deyong GAO Zhenyu DONG Guojun ZHANG Qiang SHEN Lan LI Qing QIAN Qian HU Songping ZHANG Guangheng state Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China research Center of Plant Functional Genes and Tissue Culture Technology College of Bioscience and BioengineeringJiangxi Agricultural UniversityNanchang 330045China Qian Qian Academician Workstation National Nanfan Research Institute(Sanya)Chinese Academy of Agricultural SciencesSanya 572024China

The morphological development of rice(Oryza sativa L.)leaves is closely related to plant architecture,physiological activities,and ***,it is unclear whether there is a co-regulatory relationship between the morphological development of leaves and adaptation to drought *** this study,a drought-sensitive,roll-enhanced,and narrow-leaf mutant(renl1)was induced from a semi-rolled leaf mutant(srl1)by ethyl methane sulfonate(EMS),which was obtained from Nipponbare(NPB)through ***-based cloning and functional validation showed that RENL1 encodes a cellulose synthase,allelic to NRL1/*** RENL1 mutation resulted in reduced vascular bundles,vesicular cells,cellulose,and hemicellulose contents in cell walls,diminishing the water-holding capacity of *** addition,the root system of the renl1 mutant was poorly developed and its ability to scavenge reactive oxygen species(ROS)was decreased,leading to an increase in ROS after drought ***,genetic results showed that RENL1 and SRL1 synergistically regulated cell wall *** results revealed a theoretical basis for further elucidating the molecular regulation mechanism of cellulose on rice drought tolerance,and provided a new genetic resource for enhancing the synergistic regulation network of plant type and stress resistance,thereby realizing simultaneous improvement of multiple traits in rice.

关键词： cellulose cell wall drought tolerance leaf morphology rice