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

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

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TaRLK-6A promotes Fusarium crown rot resistance in wheat

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Journal of Integrative plant Biology 2024年第1期66卷 12-16页

作者： Haijun Qi Xiuliang Zhu Wenbiao Shen Xia Yang Chaozhong Zhang Genying Li Feng Chen Xuening Wei Zengyan Zhang institute of Special Animal and plant Sciences Chinese Academy of Agricultural SciencesChangchun 130000China The National Key Facility for Crop Gene resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of Life Science Nanjing Agricultural UniversityNanjing 210095China Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/CIMMYT‐China(Henan)Joint Center of Wheat and Maize Henan Agricultural UniversityZhengzhou 450002China department of plant Sciences University of CaliforniaDavisCA 95616USA Crop Research institute Shandong Academy of Agricultural SciencesJinan 250100China

Fusariumcrown rot(FCR),mainly caused by the soil‐borne fungus Fusarium pseudograminearum,is a devastatingdisease of wheat(Triticum aestivum(Ta)).Fusariumcrown rotcauses substantial yield losses and generates mycotoxins inwheat grains that can cause serious health problems in hu-mans and livestock(Powell et al.,2017).Identifying genes thatprovide resistance *** character-izing the molecular mechanisms underlying such resistance arekey to breeding wheat varieties that are resistant to this dev-astating fungus.

关键词： aestivum breeding soil

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Exploring the genetic basis of pre-harvest sprouting in rice through a genome-wide association study-based haplotype analysis

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Journal of Integrative Agriculture 2024年第8期23卷 2525-2540页

作者： Myeong-Hyeon Min Aye Aye Khaing Sang-Ho Chu Bhagwat Nawade Yong-Jin Park department of plant resources College of Industrial SciencesKongju National UniversityYesan 32439Republic of Korea department of Agronomy Yezin Agricultural UniversityNay Pyi Taw 15013Myanmar

Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and *** this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated *** assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice *** analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine *** haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,*** identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.

关键词： rice PHS dormancy germination GWAS haplotype abiotic stress

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Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

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Journal of Integrative Agriculture 2024年第3期23卷 769-780页

作者： Shuliang Jiao Qinyan Li Fan Zhang Yonghong Tao Yingzhen Yu Fan Yao Qingmao Li Fengyi Hu Liyu Huang Key Laboratory of Biology and Germplasm Innovation of Perennial Rice Ministry of Agriculture and Rural Affairs/School of AgricultureYunnan UniversityKunming 650091China State Key Laboratory of Crop Gene resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Wenshan Academy of agricultural Sciences Wenshan 663000China

Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides

关键词： Green Revolution Semidwarf 1 high-yield breeding upland rice plant height

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Global wild rice germplasm resources conservation alliance:World Wild-Rice Wiring

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Molecular plant 2024年第4期17卷 516-518页

作者： Xiaoming Zheng Disna Ratnasekera Jiayu Fan Robert J.Henry Beng-Kah Song Kenneth M.Olsen Bal Krishna Joshi Maria Celeste N.Banaticla-Hilario Tonapha Pusadee Adane Getachew Melaku Yeyinou Laura Estelle Loko Koukham Vilayheuang Gavers K.Oppong Samuel Aduse Poku Peterson W.Wambugu Song Ge Aldo Merotto Junior Ohn Mar Aung Ramaiah Venuprasad Ajay Kohli Wenbin Zhou Qian Qian National Key Facility for Crop Gene resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Sanya National Research institute of breeding in Hainan Chinese Academy of Agricultural SciencesBeijing 100081China International Rice Research institute DAPO Box 7777Metro Manila 4031Philippines department of agricultural Biology Faculty of AgricultureUniversity of RuhunaMatara 81000Sri Lanka Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China Hainan University Haikou 570228China ARC Centre of Excellence for plant Success in Nature and Agriculture University of QueenslandBrisbaneQLD4072Australia School of Science Monash University Malaysia47500 Bandar SunwaySelangor 47500Malaysia department of Biology Washington University in St.LouisSt.LouisMO 63130-4899USA National Agriculture genetic resources Center(Genebank) KhumaltarPO Box 3055KathmanduNepal plant Biology Division Insttute of Biological SciencesUniversity of the Pilippines Los BanosLos BanosLaguna 4031Philippines Division of Agronomy Department of Plant and Soil SciencesFaculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Bio and Emerging Technology institute Addis Ababa 1165Ethiopia National University of Sciences TechnologiesEngineering and Mathematics(UNSTIM)Dassa-ZouméBP 14Benin National Genebank Rice and Cash Crops Research CenterNAFRIVientiane 0605Lao PDR plant Sciences and the Bioeconomy Rothamsted ResearchHarpenden AL52JQUK UK Future Food Beacon of Excellence and School of Biosciences and University of Nottingham Nottingham LE125RDUK department of plant and Environmental Biology University of GhanaAccraGhana Kenya agricultural and Livestock Research Organization Genetic Resources Research InstituteNairobi 00200Kenya institute of Botany Chinese Academy of SciencesBeijing 100093China Federal University of Rio Grande do Sul UFRGSPorto Alegre 91501-970RSBrazil department of Agricultur

Wild relatives of crop are key genetic resources serving as diversity reservoirs for crop improvement under changing ***(Oryza sativa)is one of the most important crops in the world,providing staple food for half of the world's *** rice is thus a critical germplasm resource for sustained global food security,ensuring high production yields,improved quality,and stress resistance in the face of climate *** rice is closely related to domesticated rice and has a rich genetic diversity and exceptional adaptability to extreme *** has played a pivotal role in the history of rice hybridization and has become a key resource for rice breeding *** identification of wild-type cytoplasmic male sterility resources paved the way for the achievement of the“three lines”goal in hybrid rice,leading to a significant increase in rice *** addition,the use of resistance alleles found in wild rice is making rice production more resilient to losses caused by environmental ***,wild rice germplasm resources are threatened due to habitat destruction and other anthropogenic *** the same time,the lack of centralized distribution of wild rice has hampered the sharing of basic information on wild rice resources and the utilization and conservation of wild rice in each country,as well as collaboration among scientists.

关键词： germplasm breeding crops

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Exogenous application of bio-stimulants and growth retardants improve nutrient absorption and fiber quality in upland cotton

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Journal of Cotton Research 2024年第2期7卷 137-147页

作者： Al-Khayri Jameel M. Arif Muhammad Kareem Shadia Hama Salih Anwar Adeel Dehghanisanij Hossein Emami Somayeh Yasmeen Azra Aftab Komal Negm Mohamed department of agricultural Biotechnology College of Agriculture and Food SciencesKing Faisal University31982 Al‑AhsaSaudi Arabia Water resources Zone Irrigation Department PunjabD.G.KhanPakistan department of Biotechnology and Crop Science College of Agricultural Engineering SciencesUniversity of SulaimaniSulaimaniIraq department of Agronomy PMAS-Arid Agriculture UniversityRawalpindiPakistan agricultural Research Education and Extension OrganizationAgricultural Engineering Research InstituteKarajAlborzIran department of Water Engineering University of TabrizTabrizIran department of Agronomy Bahauddin Zakariya UniversityMultanPakistan department of plant breeding and genetics Bahauddin Zakariya UniversityMultanPakistan agricultural Research Center Cotton Research InstituteGiza 12619Egypt

Background Natural and synthetic plant growth regulators are essential for plant health,likewise these regulators also play a role in increasing organic production productivity and improving quality and yield *** the present study,we have evaluated the effects of foliar applied plant growth regulators,i.e.,moringa leaf extract(MLE)and mepiquat chloride(MC)alone and in combination MC and MLE on the conventional cotton cultivar(CIM 573)and transgenic one(CIM 598).The growth regulators were applied at the start of bloom,45 and 90 days after *** The application of MC and MLE at 90 days after blooming significantly improved the relative growth rate,net assimilation rate,the number of bolls per plant,and seed cotton ***,the combined application of MLE and MC at 90 days after blooming significantly boosted the nitrogen uptake in locules,as well as the phosphorus and potassium uptake in the leaves of both cotton *** application of MLE alone has considerably improved the nitrogen uptake in leaves,and phosphorus and potassium contents in locules of Bt and conventional cotton ***,Bt cotton treated with MLE at 90 days after blooming produced significantly higher ginning out turn and oil *** in combination(MLE+MC)at 90 days after blooming produced considerably higher micronaire value,fiber strength,and staple length in conventional *** The natural growth enhancer,MLE is a rich source of minerals and zeatin,improving the nutrient absorption and quality of cotton fiber in both conventional and Bt cotton cultivars.

关键词： Bio-stimulant Cotton Fiber quality Mepiquat chloride Moringa leaf extract Potassium accumulation Oil contents

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Integrating artificial intelligence and high-throughput phenotyping for crop improvement

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Journal of Integrative Agriculture 2024年第6期23卷 1787-1802页

作者： Mansoor Sheikh Farooq Iqra Hamadani Ambreen Kumar A Pravin Manzoor Ikra Yong Suk Chung Phenomics Laboratory Department of Plant Resources and EnvironmentJeju National UniversityJeju 63234Republic of Korea Council of Scientific&Industrial Research Indian Institute of Integrative MedicinePulwamaJ&K 192301India Animal and Dairy Science University of WisconsinMadisonWI 530706United States of America Division of Fruit Science Faculty of HorticultureSher-e-Kashmir University of Agricultural Sciences and Technology of KashmirSrinagar 190025India

Crop improvement is crucial for addressing the global challenges of food security and sustainable *** advancements in high-throughput phenotyping(HTP)technologies and artificial intelligence(AI)have revolutionized the field,enabling rapid and accurate assessment of crop traits on a large *** integration of AI and machine learning algorithms with HTP data has unlocked new opportunities for crop *** algorithms can analyze and interpret large datasets,and extract meaningful patterns and correlations between phenotypic traits and genetic *** technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection,thereby reducing the time and cost required for variety ***,further research and collaboration are needed to overcome the existing challenges and fully unlock the power of HTP and AI in crop *** leveraging AI algorithms,researchers can efficiently analyze phenotypic data,uncover complex patterns,and establish predictive models that enable precise trait selection and crop *** aim of this review is to explore the transformative potential of integrating HTP and AI in crop *** review will encompass an in-depth analysis of recent advances and applications,highlighting the numerous benefits and challenges associated with HTP and AI.

关键词： artificial intelligence crop improvement data analysis high-throughput phenotyping machine learning precision agriculture trait selection

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Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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Molecular plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu Peng Zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State Key Laboratory of Rice Biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan institute of Zhejiang University Sanya 572025China National Key Laboratory of plant Molecular genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China Key Laboratory of plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State Key Laboratory of Rice Biology and breeding China National Rice Research InstituteHangzhou 311400China department of Molecular Biology and Center for Computational and Integrative Biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

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Population genetic insights into the conservation of common walnut(Juglans regia)in Central Asia

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plant Diversity 2024年第5期46卷 600-610页

作者： Linjiang Ye Robabeh Shahi Shavvon Hailing Qi Hongyu Wu Pengzhen Fan Mohammad Nasir Shalizi Safiullah Khurram Mamadzhanov Davletbek Yerlan Turuspekov Jie Liu CAS Key Laboratory for plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Key Laboratory of plant resources and Biodiversity of Jiangxi Province Jingdezhen UniversityJingdezhen 333400JiangxiChina Germplasm Bank of Wild Species&Yunnan Key Laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina department of Biology Faculty of ScienceYasouj UniversityYasouj 75918-74934Iran University of Chinese Academy of Sciences Beijing 100049China department of Forestry and Environmental resources North Carolina State UniversityRaleighNC 27695United States department of Forestry and Natural resources Faculty of AgricultureKabul UniversityKabul D-1006Afghanistan National Academy of Science of the Kyrgyz Republic Jalal-Abad Scientific CenterJalal-Abad 715600Kyrgyzstan Laboratory of Molecular genetics Institute of Plant Biology and BiotechnologyAlmaty 050040Kazakhstan

The common walnut(Juglans regia)is one of the most economically important nut trees cultivated *** its importance,no comprehensive evaluation of walnut tree population genetics has been undertaken across the range where it originated,Central *** this study,we investigated the genetic diversity and population structure of 1082 individuals from 46 populations across Central *** found moderate genetic diversity of *** across Central Asia,with 46 populations clustered into three groups with a weak relationship between genetic and geographic *** findings reveal that the western Himalaya might be the core region of common walnut genetic diversity in Central Asia and that,except for two populations in Gongliu Wild Walnut Valley,humans might have introduced walnut populations to Xinjiang,*** observed distribution of the genetic landscape has probably been affected by historical climate fluctuation,breeding system,and prolonged anthropogenic *** propose the conservation of the core genetic diversity resources in the western Himalaya and pay special attention to populations from Gongliu in *** findings enhance our understanding of the genetic variation throughout the distribution range of *** in Central Asia,which will provide a key prerequisite for evidence-based conservation and management.

关键词： Central Asia genetic diversity Germplasm management Gongliu wild walnut valley Juglans regia Western Himalaya

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Screening and evaluation of chilli(Capsicum annuum L.)genotypes for waterlogging tolerance at seedling stage

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BIOCELL 2022年第7期46卷 1613-1627页

作者： MDREZWAN MOLLA MDMOTIAR ROHMAN MDROBYUL ISLAM MIRZA HASANUZZAMAN LUTFUL HASSAN plant genetic resources Centre(PGRC) Bangladesh Agricultural Research Institute(BARI)Gazipur1701Bangladesh Molecular breeding Lab Plant Breeding DivisionBangladesh Agricultural Research Institute(BARI)Gazipur1701Bangladesh department of Agronomy Sher-e-Bangla Agricultural UniversityDhaka1207Bangladesh department of genetics and plant breeding Bangladesh Agricultural UniversityMymensingh2202Bangladesh

Waterlogging is an illustrious abiotic stress and the constrictions it enforces on plant roots have negative effects on growth and *** study was undertaken to investigate waterlogging stress tolerant potential in chilli(Capsicum annum L.)genotypes through evaluating morphological,physiological,biochemical and anatomical ***-five days old seedlings of 10 chilli genotypes were exposed to waterlogging stress maintaining water height 3–5 cm over the soil surface artificially for three *** duration(36–38 DAE)was termed as waterlogging period,and subsequent withdrawal of waterlogging condition(39–45 DAE)was regarded as a recovery *** on their survival performance,two tolerant genotypes viz.,SRC-517 and BARI morich-2 and two susceptible genotypes viz.,AHM-206 and RI-1(6)were selected for studying stress tolerance *** waterlogging,however,both genotypes(tolerant and susceptible)exhibited reduced root shoot length,dry weight ratio,petiole weight and leaf area,and noticeable reduction regarding these parameters was observed in susceptible ***,tolerant genotypes displayed a higher recovery than susceptible genotypes after removal of waterlogging *** reduction of leaf area and photosynthetic pigments as well as higher reduction of relative water content(RWC)were noticed in susceptible *** accumulation of proline and total antioxidant capacity(TAC)during waterlogging condition in tolerant genotypes suggested lower oxidative *** both genotypes lost total soluble sugar(TSS)relative to control at waterlogging stress,better performance was recorded in tolerant *** the period after the removal of extra water,a similar genotypic response in terms of TSS gain was ***,under flooding conditions,the development of aerenchyma cells in tolerant genotypes is a means of tolerance mechanism for long-term ***,the morpho-physiological and biochemical changes h

关键词： Abiotic stress Anoxia Flooding Hypoxia Pepper Photosynthetic pigments Proline

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