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Genome-wide identification and characterization of the PbrATG family in Pyrus bretschneideri and functional analysis of PbrATG1a in response to Botryosphaeria dothidea

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Horticultural Plant Journal 2024年第2期10卷 327-340页

作者： Yun Wang Xun Sun Zhenwu zhang Zhihua Xie Kaijie Qi shaoling zhang Center of Pear Engineering Technology Research State Key Laboratory of Crop Genetics and Germplasm EnhancementCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China

The pear is an economic fruit that is widely planted around the world and is loved by people for its rich nutritional value. Autophagy is a self-protection mechanism in eukaryotes, and its occurrence often accompanied by the degradation of damaged substances in cells and the recycling of nutrients. Autophagy is one of the mechanisms through which plants respond to environmental stress and plays an important role in plant development and stress resistance. Functional studies of autophagy-related genes (ATGs) have been performed on a variety of plant species, but little information is available on the ATG family in pear (Pyrus bretschneideri Rehd). Therefore, we analyzed the evolutionary dynamics and performed a genome-wide characterization of the PbrATG gene family. A total of 28 PbrATG members were identified.Phylogenetic analysis showed that PbrATGs were more closely related to ATGs of European pear and apple. Evolutionary analysis revealed that whole-genome duplication (WGD) and dispersed duplication events were the main driving forces of PbrATG family expansion.Expression analysis of different pear tissues showed that all the genes were expressed in different pear tissues, and different PbrATGs are expressed at different times and in different locations. Moreover, all PbrATGs also responded to different abiotic stresses, especially salt and drought stress, which elicited the highest expression levels. Pear seedlings were subsequently infected with Botryosphaeria dothidea (B.dothidea). The results showed that different PbrATGs had different expression patterns at different infection stages. According to the gene expression data, PbrATG1a was selected as a key autophagy gene for further analysis. Silencing of PbrATG1a reduced the resistance of pear to B. dothidea, which resulted in increased lesions, reactive oxygen species (ROS) contents, antioxidant enzyme activity, and gene expression levels in the silenced pear seedlings after B. dothidea inoculation. In this study, a comprehensive bioinformatic analysis of

关键词： Autophagy Pear PbrATGs Abiotic stress Botryosphaeria dothidea PbrATG1a

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E3 ubiquitin ligase PbrATL18 is a positive factor in pear resistance to drought and Colletotrichum fructicola infection

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Horticultural Plant Journal 2024年第3期10卷 698-712页

作者： Likun Lin Qiming Chen Kaili Yuan Caihua Xing Qinghai Qiao Xiaosan Huang shaoling zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement/College of Horticulture Nanjing Agricultural UniversityNanjingJiangsu210095China

The Arabidopsis Toxicos en Levadura(ATL)protein is a subfamily of the E3 ubiquitin ligases,which exists widely in plants and is extensively involved in plant growth and development.Although the ATL family has been identified in other species,such as Arabidopsis,Oryza sativa,and grapevine,few reports on pear ATL gene families have been reported.In this study,92 PbrATL genes were identified and analyzed from the Pyrus breschneideri genome.Motif analysis and phylogenetic tree generation divided them into nine subgroups,and chromosome localization analysis showed that the 92 PbrATL genes were distributed in 16 of 17 pear chromosomes.Transcriptome data and quantitative real-time polymerase chain reaction(qRT-PCR)experiments demonstrated that PbrATL18,PbrATL41,and PbrATL88 were involved in both pear drought resistance and Colletotrichum fructicola infection.In addition,Arabidopsis thaliana overexpressing PbrATL18 showed greater resistance to drought stress than the wild type(WT),and PbrATL18-silenced pear seedlings showed greater sensitivity to drought and C.fructicola infection than the controls.PbrATL18 regulated plant resistance by regulating chitinase(CHI),phenylalanine ammonia-lyase(PAL),polyphenol oxidase(PPO),catalase(CAT),peroxidase(POD),and superoxide dismutase(SOD)activities.This study provided a reference for further exploring the functions of the PbrATL gene in drought resistance and C.fructicola infection.

关键词： Pear Colletotrichum fructicola Arabidopsis Toxicos en Levadura(ATL) Drought stress

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Genomic selection of eight fruit traits in pear

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Horticultural Plant Journal 2024年第2期10卷 318-326页

作者： Manyi Sun Mingyue zhang Satish Kumar Mengfan Qin Yueyuan Liu Runze Wang Kaijie Qi shaoling zhang Wenjing Chang Jiaming Li Jun Wu College of Horticulture State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingJiangsu 210095China State Key Laboratory of Crop Biology College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anShandong 271018China The New Zealand Institute for Plant and Food Research Limited Private Bag 1401Havelock North 4157New Zealand Zhongshan Biological Breeding Laboratory NanjingJiangsu 210014China

Genomic selection (GS) has the potential to improve selection efficiency and shorten the breeding cycle in fruit tree breeding. In this study,we evaluated the effect of prediction methods, marker density and the training population (TP) size on pear GS for improving its performance and reducing cost. We evaluated GS under two scenarios:(1) five-fold cross-validation in an interspecific pear family;(2) independent validation. Based on the cross-validation scheme, the prediction accuracy (PA) of eight fruit traits varied between 0.33 (fruit core vertical diameter)and 0.65 (stone cell content). Except for single fruit weight, a slightly better prediction accuracy (PA) was observed for the five parametrical methods compared with the two non-parametrical methods. In our TP of 310 individuals, 2 000 single nucleotide polymorphism (SNP) markers were sufficient to make reasonably accurate predictions. PAs for different traits increased by 18.21%-46.98%when the TP size increased from 50to 100, but the increment was smaller (-4.13%-33.91%) when the TP size increased from 200 to 250. For independent validation, the PAs ranged from 0.11 to 0.45 using rrBLUP method. In summary, our results showed that the TP size and SNP numbers had a greater impact on the PA than prediction methods. Furthermore, relatedness among the training and validation sets, and the complexity of traits should be considered when designing a TP to predict the test panel.

关键词： Pear Pyrus Prediction method TP size SNP marker number

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BreedingEIS: An Efficient Evaluation Information System for Crop Breeding

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Plant Phenomics 2023年第2期5卷 368-377页

作者： Kaijie Qi Xiao Wu Chao Gu Zhihua Xie Shutian Tao shaoling zhang Jiangsu Engineering Research Center for Pear National Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing 210095China

Crop breeding programs generate large datasets.Thus,it is difficult to ensure the accuracy and integrity of all the collected data in the breeding process.To improve breeding efficiency,we established an open source and free breeding evaluation information system(BreedingEIS).The full system is composed of a web client and a mobile client.The web client is used to name the individual breeding offspring plants and analyze data.The mobile client is based on the technology of widely used smartphones and is suitable for Android and iOS systems.Its functions focus on field evaluation,including quick response code recognition,evaluation data entry,and real-time viewing.In addition,near-field communication technology and portable label machines are introduced to enable breeders to quickly locate each individual plant and accurately label any samples collected from it.Generally,BreedingEIS enables users to accurately and conveniently register phenotypic data and quickly lock target individual plants from large volumes of data.The system provides a low-cost and highly efficient solution for crop information evaluation and enables breeders to better collect,manage,and use breeding data for decision making,which is a valuable resource for crop breeding.

关键词： client breeding enable

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Involvement of long non-coding RNAs in pear fruit senescence under high-and low-temperature conditions

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Horticultural Plant Journal 2023年第2期9卷 224-236页

作者： Yuhang Zhou Xueping Wang Kaijie Qi Jianping Bao shaoling zhang Chao Gu Centre of Pear Engineering Technology Research State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China College of Plant Science Tarim UniversityAlaer843300XinjiangChina

Pear fruit senescence under high-and low-temperature conditions has been reported to be mediated by microRNAs.Long non-coding RNAs(lncRNAs),which can function as competing endogenous RNAs that interact with microRNAs,may also be involved in temperature-affected fruit senescence.Based on the transcriptome and microRNA sequencings,in this study,3330 lncRNAs were isolated from Pyrus pyrifolia fruit.Of these lncRNAs,2060 and 537 were responsive to high-and low-temperature conditions,respectively.Of these differentially expressed lncRNAs,82 and 24 correlated to the mRNAs involved in fruit senescence under high-and low-temperature conditions,respectively.Moreover,three lncRNAs were predicted to be competing endogenous RNAs(ceRNAs)that interact with the microRNAs involved in fruit senescence,while one and two ceRNAs were involved in fruit senescence under high-and low-temperature conditions,respectively.A dual-luciferase assay showed that the interaction of an lncRNA with a microRNA disrupts the action of the microRNA on the expression of its target mRNA(s).Furthermore,four alternative splicing-derived lncRNAs interacted with miR172i homologies(Novel_88 and Novel_69)to relieve the repressed expression of their target and produce an miR172i precursor.Correlation analysis of microRNA expression suggested that Novel_69 is likely involved in the cleavage of the pre-miR172i hairpin to generate mature miR172i.Taken together,lncRNAs are involved in pear fruit senescence under high-or low-temperature conditions through ceRNAs and the production of microRNA.

关键词： Pyrus pyrifolia Long non-coding RNA(lncRNA) Fruit senescence High-temperature Low-temperature lncRNA-microRNA-mRNA interaction

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Genome-wide identiﬁcation of the mitogen-activated protein kinase kinases in pear and their functional analysis in response to black spot

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Horticultural Plant Journal 2023年第4期9卷 681-692页

作者： Zan zhang Qiming Chen Luting Jia Ming Qian Qinghai Qiao Xiaosan Huang shaoling zhang College of Horticulture State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingJiangsu 210095China

The mitogen-activated protein kinase(MAPK)cascade is crucial to plant growth,development,and stress responses.MAPK kinases(MAPKK)play a vital role in linking upstream MAPKK kinases(MAPKKK)with the downstream MAPK.Black spot is one of the most serious fungal diseases of pear which is an important part of the fruit industry in China.The MAPKK genes have been identified in many plants,however,none has been reported in pear(Pyrus bretschneideri).In order to explore whether MAPK gene of pear is related to black spot disease,we designed this experiment.The present study investigated eight putative PbrMAPKK genes obtained from the Chinese white pear genome.The phylogenetic analysis revealed that PbrMAPKK genes were divided into A,B,C,and D groups.These PbrMAPKK genes are randomly distributed on 7 out of 17 chromosomes and mainly originated from the whole-genome duplication(WGD)event.The expression analysis of PbrMAPKK genes in seven pear tissues and the leaves of susceptible and resistant varieties after Alternaria alternata infection by quantitative real-time PCR(qRT-PCR)identified seven candidate genes associated with resistance.Furthermore,virus-induced gene silencing(VIGS)indicated that PbrMAPKK6 gene enhanced resistance to pear black spot disease in pear.

关键词： Pyrus bretschneideri Mitogen-activated protein kinase kinase(MAPKK) Gene family Disease resistance Pear black spot

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Comparative genomic analysis of N6-methyladenosine regulators in nine rosaceae species and functional characterization in response to drought stress in pear

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Horticultural Plant Journal 2023年第4期9卷 693-704页

作者： Chenyang Han Huizhen Dong Qinghai Qiao Yuqin Dai Xiaosan Huang shaoling zhang College of Horticulture State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingJiangsu 210095China

N 6-methylated adenine(m6 A)is an emerging epigenetic marker in eukaryotic organisms that plays an important role in biological functions and in enriching genetic information.m6 A exerts these functions via the dynamic interplay among m6 A writers,erasers,and readers.However,little is known about the underlying mechanisms of m6 A in plant growth and stress responses.Here,we identified 276 masked m6 A regulators from nine Rosaceae species(Pyrus bretschneideri,Pyrus betulifolia,Pyrus communis,Malus domestica,Fragaria vesca,Prunus avium,Prunus mume,Prunus persica,and Rubus occidentalis).We classified and named these genes in more detail based on phylogenetic and synteny analysis.The expansion of m6 A regulators in Maloideae was dated back to the recent whole-genome duplication(WGD)in Rosaceae.Based on the expression pattern analysis and gene structure analysis of m6 A regulators,m6 A was shown to be a significant factor in regulating plant development and resistance.In addition,PbrMTA1-silenced pear plants displayed significantly reduced drought tolerance and chlorophyll content,as well as increased electrolyte leakage and concentrations of malondialdehyde and H2 O2.

关键词： Pyrus bretschneideri RNA methylation m6A regulators Rosaceae Evolution Transcriptome Drought stress VIGS

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Identification of S-genotypes and a novel S-RNase in 84 native Chinese pear accessions

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Horticultural Plant Journal 2022年第6期8卷 713-726页

作者： Min He Lufei Li Ying Xu Jianxin Mu Zhihua Xie Chao Gu shaoling zhang Pear Engineering and Technology Research Center State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing 210095China

The Chinese pear(Pyrus spp.)exhibits typical gametophytic self-incompatibility(GSI),which inhibits self-crossing and promotes outcrossing,similar to other fruit species in the Rosaceae family.Thus,S-compatible cultivars are required in pear orchards to ensure successful pollination and stable yields.In this study,84 native Chinese pear accessions were genotyped by allele-specific PCR using one pair allele consensus primers and 29 pairs of S-allele-specific primers that were designed in this study.After cloning and sequencing the PCR products,the S-genotypes of all 84 pear accessions,including wild and cultivated accessions,were determined.The reported 34 S-alleles and a novel S-allele were isolated from these pear accessions.These S-alleles were expressed specifically in the style.Sequence analysis identified that six pear cultivars originated in China shared the same S-RNases with P.communis(Pc).These findings supported the hypothesis that oriental and occidental Pyrus spp.may share the same pool of alleles at the S-locus.A novel S-RNase was isolated in ‘Putiandouli’,‘Daguoshanli’,‘Yunhongli1,and‘Dianli’and deposited as S67-RNase under accession number MT773568.Furthermore,the deduced amino acid sequences exhibited high similarity(99.56%)to S32-RNase in Malus.The high similarity between S-RNase in Pyrus and Malus indicated that the existence of S-RNase could have predated speciation between Pyrus and Malus.Furthermore,S-allele information was rearranged in Asian and European pears to provide information for selecting the best pollinator for widely cultivated pear cultivars in China.This information is useful for pear production,cross-breeding,and understanding the mechanism of the self-incompatibility reaction.

关键词： Pear S-RNase S-genotype Parent assignment

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PbrChiA:a key chitinase of pear in response to Botryosphaeria dothidea infection by interacting with PbrLYK1b2 and down-regulating ROS accumulation

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Horticulture Research 2023年第10期10卷 185-201页

作者： Qiming Chen Huizhen Dong Qionghou Li Xun Sun Xin Qiao Hao Yin Zhihua Xie Kaijie Qi Xiaosan Huang shaoling zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Centre of Pear Engineering Technology ResearchNanjing Agricultural UniversityNanjing 210095China

Pear ring rot,caused by the pathogenic fungi Botryosphaeria dothidea,seriously affects pear production.While the infection-induced reactive oxygen species(ROS)burst of infected plants limits the proliferation of B.dothidea during the early infection stage,high ROS levels can also contribute to their growth during the later necrotrophic infection stage.Therefore,it is important to understand how plants balance ROS levels and resistance to pathogenic B.dothidea during the later stage.In this study,we identified PbrChiA,a glycosyl hydrolases 18(GH18)chitinase-encoding gene with high infection-induced expression,through a comparative transcriptome analysis.Artificial substitution,stable overexpression,and virus induced gene silencing(VIGS)experiments demonstrated that PbrChiA can positively regulate pear resistance as a secreted chitinase to break down B.dothidea mycelium in vitro and that overexpression of PbrChiA suppressed infection-induced ROS accumulation.Further analysis revealed that PbrChiA can bind to the ectodomain of PbrLYK1b2,and this interaction suppressed PbrLYK1b2-mediated chitin-induced ROS accumulation.Collectively,we propose that the combination of higher antifungal activity from abundant PbrChiA and lower ROS levels during later necrotrophic infection stage confer resistance of pear against B.dothidea.

关键词： infection ChiA resistance

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Efficacy and Safety of Iron Isomaltoside Compared with an Oral Iron Supplement in the Management of Patients with Iron Deficiency Anemia

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Open Journal of Blood Diseases 2024年第1期14卷 17-30页

作者： Zhimin Wu Chunxiao Zhou Chunyan Wu Qiao Song Shilyu Chen Wen zhang shaoling Wu Department of Medicine Qingdao University Qingdao China Department of Hematology The Affiliated Hospital of Qingdao University Qingdao China

Objective: To evaluate the treatment outcome of iron isomaltoside compared with an oral iron supplement in the management of iron deficiency anemia (IDA). Methods: The study included patients with IDA who visited the Outpatient Clinic of the Department of Hematology, the Affiliated Hospital of Qingdao University from October 2021 to August 2022 and met the inclusion and exclusion criteria. According to the actual application of iron supplementation, the patients were divided into two groups: iron isomaltoside treatment group and oral iron treatment group. Baseline measurements were collected before the start of treatment, and measurements were collected subsequently at intervals of 1 week, 1 month, and 3 months. The hematological parameters analyzed included Hemoglobin (Hb), Mean corpuscular hemoglobin (MCH), Mean Hemoglobin content (MCH), Mean corpuscular Hemoglobin concentration (MCHC), and Platelet (Plt). Safety data and adverse event profiles were recorded. Results: Intra-group comparisons: After 1 month of treatment, the Hb significantly improved (P 0.05). Inter-group comparisons: The biochemical parameters were significantly improved (P 0.05) in the iron isomaltoside group compared with those in the oral iron group after 1 month of iron supplementation in patients with mild and moderate anemia. Adverse reactions were tolerable for the patients in both iron isomaltoside group and oral iron group. Only 1 patient in iron isomaltoside group developed anaphylactic shock during medication and recovered after aggressive rescue. Conclusions: Iron isomaltoside which increases Hb more rapidly compared with the oral iron supplementation has few adverse reactions and good acceptance.

关键词： Anemia Iron-Deficiency Drug Therapy Iron Isomaltoside 1000 Treatment Outcome

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