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Identification and functional verification of Y-chromosome-specific gene typo-gyf in Bactrocera dorsalis

Insect Science 2024年第4期31卷 1270-1284页

作者： Peipei Liu Shuning Yu Wenping Zheng Qiuyuan Zhang Jiao Qiao Ziniu Li Zhurong Deng Hongyu Zhang National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable horticultural Crops Hubei Hongshan LaboratoryChina-Australia Joint Research Centre for Horticultural and Urban PestsInstitute of Urban and Horticultural EntomologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina

Genes on the Y chromosome play important roles in male sex determination and *** identification of Y-chromosome-specific genes not only provides a theoretical basis for the study of male reproductive development,but also offers genetic control targets for agricultural ***,Y-chromosome genes are rarely characterized due to their high repeatability and high heterochromatinization,especially in the oriental fruit *** this study,1011 Y-chromosome-specific candidate sequences were screened from 2 to 4 h Bactrocera dorsalis embryo datasets with the chromosome quotient method,6 of which were identified as Y-chromosome-specific sequences by polymerase chain reaction,including typo-gyf,a 19126-bp DNA sequence containing a 575-amino acid open reading *** deformation and a significant reduction in sperm number were observed after typo-gyf knockdown with RNA interference in *** typo-gyf knockout with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9 in the embryonic stage,the sex ratio of the emergent adults was unbalanced,with far more females than males.A genotype analysis of these females with the Y-chromosome gene MoY revealed no sex ***-gyf knockout led to the death of XY individuals in the embryonic *** conclude that typo-gyf is an essential gene for male survival,and is also involved in testicular development and *** identification of typo-gyf and its functional verification provide insight into the roles of Y-chromosome genes in male development.

关键词： Bactrocera dorsalis spermatogenesis testis typo-gyf gene Y-specific gene

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Comparative transcriptome analysis reveals key genes and pathways in response to Alternaria alternata apple pathotype infection

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horticultural Plant Journal 2024年第3期10卷 641-656页

作者： Kai Liu Zhaolin Liang An Yang Jiadi Yan Peihua Cong Xiaolei Han Caixia Zhang Key Laboratory of horticultural Crop Germplasm Utilization of the Ministry of Agriculture and Rural Affairs(MOA) Research Institute of PomologyChinese Academy of Agricultural SciencesXingchengLiaoning 125100China

Apple leaf spot,caused by the Alternaria alternata apple pathotype(AAAP),is an important fungal disease of *** understand the molecular basis of resistance and pathogenesis in apple leaf spot,the transcriptomes of two apple cultivars‘Hanfu'(HF)(resistant)and‘Golden Delicious'(GD)(susceptible)were analyzed at 0,6,18,24 and 48 h after AAAP inoculation by *** each time point,a large number of significantly differentially expressed genes(DEGs)were screened between AAAP-inoculated and uninoculated apple *** of the common DEGs at four time points revealed significant differences in the resistance of‘HF'and‘GD'apple to AAAP ***,RNL,and JA signal-related genes were upregulated in both cultivars to restrict AAAP ***,genes encoding CNLs,TNLs,WRKYs,and AP2s were only activated in‘HF'as part of the resistance response,of which,some play major roles in the regulation of ET and SA signal *** analysis showed that many DEGs with opposite expression trends in the two hosts may play important regulatory roles in response to AAAP *** expression of one such gene MdERF110 in‘GD'apple leaves improved AAAP ***,this study highlights the reasons for differential resistance to AAAP infection between‘HF'and‘GD'apples which can theoretically assist the molecular breeding of disease-resistant apple crops.

关键词： Apple Transcriptome Alternaria alternata apple pathotype Infection Defense response

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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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Melatonin mitigates cold-induced damage to pepper seedlings by promoting redox homeostasis and regulating antioxidant profiling

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horticultural Plant Journal 2024年第2期10卷 532-544页

作者： Muhammad Ahsan Altaf Yuanyuan Hao Huangying Shu Weiheng Jin Chuhao Chen Lin Li Yu Zhang Muhammad Ali Mumtaz Huizhen Fu Shanhan Cheng Guopeng Zhu Zhiwei Wang Key Laboratory for Quality Regulation of Tropical horticultural Crops of Hainan Province Sanya Nanfan Research InstituteHainan UniversitySanyaHainan 572025China Key Laboratory for Quality Regulation of Tropical horticultural Crops of Hainan Province School of HorticultureHainan UniversityHaikouHainan 570228China Hainan Yazhou Bay Seed Laboratory SanyaHainan 572025China

This study assessed the influence of exogenous ME in the mitigation of cold damage in pepper seedlings. Melatonin(ME) is a dynamic molecule that helps plants cope with stress in several ways. Cold stress(CS) is one of the most important environmental factors that restrict plant growth and yield. Pepper(Capsicum annuum L.) is a valuable commercial crop, highly sensitive to CS. Thus, identifying an efficient strategy to mitigate cold damage is critical for long-term pepper production. For this purpose, the roots of pepper seedlings were pretreated with ME(5 μmol · L^(-1)) and exposed to CS for 7 d. The results indicated that CS suppressed pepper growth, hampered photosynthetic capacity, and damaged root architecture in pepper plants. In contrast, the production of reactive oxygen species(ROS), malondialdehyde(MDA), electrolyte leakage(EL), proline, and soluble sugars were enhanced in plants under CS. ME(5 μmol · L^(-1)) pretreatment reduced the negative effects of CS by recovering plant growth, root traits, gas exchange elements, and pigment molecules compared to CS control treatment. Furthermore, ME application efficiently reduced oxidative stress markers [hydrogen peroxide(H_(2)O_(2)), superoxide ion(O_(2)^(·-)), EL, and MDA] while increasing proline and soluble sugar content in pepper leaves. ME application combined with CS further increased antioxidant enzymes and related gene expression. Collectively, our results confirmed the mitigating potential of ME supplementation for CS by maintaining pepper seedling growth,improving the photosynthesis apparatus, regulating pigments, and osmolyte content.

关键词： Pepper Melatonin Cold stress Antioxidant enzyme Root trait

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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

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horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang Qi Tang Lingkui Zhang Xing Li Shumin Chen Kang Zhang Ying Li Xilin Hou Feng Cheng State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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Fast,simple,efficient Agrobacterium rhizogenes-mediated transformation system to non-heading Chinese cabbage with transgenic roots

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horticultural Plant Journal 2024年第2期10卷 450-460页

作者： Huiyu Wang Yushan Zheng Qian Zhou Ying Li Tongkun Liu Xilin Hou State Key Laboratory of Crop Genetics&Germplasm Enhancement Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(East China)Ministry of Agriculture and Rural Affairs of ChinaEngineering Research Center of Germplasm Enhancement and Utilization of Horticultural CropsMinistry of Education of ChinaNanjing Agricultural UniversityNanjingJiangsu 210095China Nanjing Suman Plasma Engineering Research institute Nanjing Agricultural UniversityNanjingJiangsu 210095China

Non-heading Chinese cabbage, a variety of Brassica campestris, is an important vegetable crop in the Yangtze River Basin of China. However,the immaturity of its stable transformation system and its low transformation efficiency limit gene function research on non-heading Chinese cabbage. Agrobacterium rhizogenes-mediated(ARM) transgenic technology is a rapid and effective transformation method that has not yet been established for non-heading Chinese cabbage plants. Here, we optimized conventional ARM approaches(one-step and two-step transformation methods) suitable for living non-heading Chinese cabbage plants in nonsterile environments. Transgenic roots in composite non-heading Chinese cabbage plants were identified using phenotypic detection, fluorescence observation, and PCR analysis. The transformation efficiency of a two-step method on four five-day-old non-heading Chinese cabbage seedlings(Suzhouqing, Huangmeigui, Wuyueman, and Sijiu Caixin) was 43.33%-51.09%, whereas using the stout hypocotyl resulted in a transformation efficiency of 54.88% for the 30-day-old Sijiu *** one-step method outperformed the two-step method;the transformation efficiency of different varieties was above 60%, and both methods can be used to obtain transgenic roots for functional studies within one month. Finally, optimized ARM transformation methods can easily,quickly, and effectively produce composite non-heading Chinese cabbage plants with transgenic roots, providing a reliable foundation for gene function research and non-heading Chinese cabbage genetic improvement breeding.

关键词： Agrobacterium rhizogenes Non-heading Chinese cabbage Transgenic roots Composite plant Transformation efficiency

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Accelerating the Digitalization Process in Rural China and Promoting Common Prosperity

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Asian Agricultural Research 2024年第3期16卷 8-13页

作者： Zhongxiong LAI Xiaoqiong XU institute of horticultural Biotechnology Fujian Agriculture and Forestry UniversityFuzhou 350002China

Under the historical background of promoting agricultural and rural modernization in an all-round way,this paper deeply analyzes the practical significance of digital construction in rural China,and explores the problems in the digitalization level of rural infrastructure,farmers digitalization awareness and accomplishment,and agricultural digital *** and suggestions are put forward from four aspects:digital village construction policy system,rural digital infrastructure construction,rural digital talent cultivation system,and agricultural digital system,and the rural digital construction of Huzhou City is taken as an example,in order to further realize the goal of empowering rural farmers with digital technology for common prosperity.

关键词： Digital village Digital technology Rural farmer Common prosperity

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Quantitative trait loci identification reveals zinc finger protein CONSTANS-LIKE 4 as the key candidate gene of stigma color in watermelon(Citrullus lanatus)

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Journal of Integrative Agriculture 2024年第7期23卷 2292-2305页

作者： Shuang Pei Zexu Wu Ziqiao Ji Zheng Liu Zicheng Zhu Feishi Luan Shi Liu Key Laboratory of Biology and Genetic Improvement of horticultural Crops(Northeast Region) Ministry of Agriculture and RuralAffairs/College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin 150030China institute of Rural Revitalization Science and Technology Heilongjiang Academy of Agricultural SciencesHarbin 150028China

Stigma color is a critical agronomic trait in watermelon that plays an important role in ***,there are few reports on the regulation of stigma color in *** this study,a genetic analysis of the F2 population derived from ZXG1553(P1,with orange stigma)and W1-17(P2,with yellow stigma)indicated that stigma color is a quantitative trait and the orange stigma is recessive compared with the yellow *** segregant analysis sequencing(BSA-seq)revealed a 3.75 Mb segment on chromosome 6 that is related to stigma ***,a major stable effective QTL Clqsc6.1(QTL stigma color)was detected in two years between cleaved amplified polymorphic sequencing(CAPS)markers Chr06_8338913 and Chr06_9344593 spanning a~1.01 Mb interval that harbors 51 annotated ***97C06G117020(annotated as zinc finger protein CONSTANS-LIKE 4)was identified as the best candidate gene for the stigma color trait through RNA-seq,quantitative real-time PCR(qRT-PCR),and gene structure alignment analysis among the natural watermelon *** expression level of Cla97C06G117020 in the orange stigma accession was lower than in the yellow stigma accessions with a significant difference.A nonsynonymous SNP site of the Cla97C06G117020 coding region that causes amino acid variation was related to the stigma color variation among nine watermelon accessions according to their re-sequencing *** color formation is often related to carotenoids,and we also found that the expression trend of ClCHYB(annotated asβ-carotene hydroxylase)in the carotenoid metabolic pathway was consistent with Cla97C06G117020,and it was expressed in low amounts in the orange stigma *** data indicated that Cla97C06G117020 and ClCHYB may interact to form the stigma *** study provides a theoretical basis for gene fine mapping and mechanisms for the regulation of stigma color in watermelon.

关键词： watermelon stigma color gene mapping zinc finger protein CONSTANS-LIKE 4

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Peculiarity of transcriptional and H3K27me3 dynamics during peach bud dormancy

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horticultural Plant Journal 2024年第1期10卷 38-50页

作者： Yalin Zhao Yong Li Ke Cao Weichao Fang Changwen Chen Xinwei Wang Jinlong Wu Wenwu Guo Lirong Wang The Key Laboratory of Biology and Genetic Improvement of horticultural Crops(Fruit Tree Breeding Technology) Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China Western Research institute Chinese Academy of Agricultural SciencesChangjiXinjiang 831100China College of Horticulture and Forestry Science Huazhong Agricultural UniversityWuhanHubei 430070China

Bud dormancy facilitates the survival of meristems under harsh environmental *** elucidate how molecular responses to chilling accumulation controlling dormancy in peach buds,chromatin immunoprecipitation sequencing to identify the H3K27me3 modifications and RNA sequencing of two peach cultivars with pronounced differences in chilling requirement were carried out,the results showed that genes associated with abscisic acid and gibberellic acid signal pathways play key roles in dormancy *** results demonstrated that peach flower bud differentiation occurred continuously in both cultivars during chilling accumulation,which was correlated with the transcript abundance of key genes involved in phytohormone metabolism and flower bud development under adverse *** more increased strength in high chillingrequirement cultivar along with the chilling accumulation at the genome-wide *** function of the dormancy-associated MADS-box gene PpDAM6 was identified,which is involved in leaf bud break in peach and flower development in transgenic Nicotiana tabacum(NC89).In addition,PpDAM6 was positively regulated by PpCBF,and the genes of putative dormancy-related and associated with metabolic pathways were *** together,these results constituted a theoretical basis for elucidating the regulation of peach bud dormancy transition.

关键词： Peach bud Dormancy RNA-seq H3K27me3 Chilling requirement

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Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape

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Journal of Integrative Agriculture 2024年第3期23卷 863-875页

作者： Hainan Liu Maosong Pei Charles Ampomah-Dwamena Yaxin Shang Yihe Yu Tonglu Wei Qiaofang Shi Dalong Guo College of Horticulture and Plant Protection Henan University of Science and TechnologyLuoyang 471000China Henan Engineering Technology Research Center of Quality Regulation and Control of horticultural Plants Luoyang 471000China The New Zealand institute for Plant&Food Research Limited(PFR) Auckland 1010New Zealand

The firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes(DEGs) by comparing the transcriptomes of folic acid(FA)-treated and water-treated(CK) berries at different time points. We then analyzed the sequences to detect alternatively spliced(AS) genes associated with postharvest softening. A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group. There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively. Gene Ontology(GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes,particularly cell wall degradation processes. Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2(VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event. The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated *** study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries.

关键词： grape postharvest softening folic acid alternative splicing Pectinesterase 2 alternative 3'splice site(A3SS)

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