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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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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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Fluctuation of Vegetative Storage Proteins in the Seedlings of Swietenia macrophylla, Analogous to the Seasonal Changes of Those in the Shoot of the Adult Tree

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Journal of Integrative Plant Biology 2007年第3期49卷 362-367页

作者： Ya-Qin Han Xing-Fu Yan Hua Zhang Zheng-Hai Hu Bing-Zhong Hao Wei-Min Tian Key Laboratory of Ministry of Agriculture for tropical crop Physiology Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou 571737 China College of horticulture Shandong Agricultural University Tai'an 271018 China Institute of Botany the Chinese Academy of Sciences Beijing 100093 China Institute of Botany Northwest University Xi'an 710069 China

In order to Identify appropriate plant materials for studying the gene expression and biological function of vegetative storage proteins （VSPs） in woody plants, the VSPs in the seedlings of Swietenla rnacrophylla King were investigated by using light microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis （SDS-PAGE） and ***. The seed of S. macrophylla was rich in storage proteins that accumulated In the vacuoles of cotyledon parenchyma cells in appearance of compact spherical grains. The growth and development of S. macrophylla seedlings were characterized by an obvious growth rhythm. The storage proteins In seeds disappeared during seedling growth while VSPs appeared in the stem 2 weeks after seedling leaves matured. Thereafter, the VSPs In the seedling stem almost exhausted during new shoot growth, and when the leaves of new shoot Just matured, both the stem beneath the new shoot of seedlings and the stem of new shoot started to accumulate VSPs. Nitrogen application dramatically Increased the level of VSPs, but had little influence on the dynamics of VSP consumption and accumulation in seedling stem. Together with these data, the fluctuation of VSPs in seedlings was very similar to that in the branches of the adult trees. In addition, seedlings are easy to be treated due to their small size. Our results suggested that S. rnacrophylla seedlings were suitable for Investigating the biological roles of VSPs and the mechanism of nitrogen storage in trees.

关键词： rhythmical growth seedlings Swietenia macrophylla King vegetative storage proteins

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The dynamic arms race during the early invasion of woodland strawberry by Botrytis cinerea revealed by dual dense high-resolution RNA-seq analyses

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horticulture Research 2023年第12期10卷 175-189页

作者： Yibo Bai Haibin Wang Kaikai Zhu Zong-Ming Cheng College of horticulture Nanjing Agricultural UniversityNanjing 210095China Key Laboratory of crop Gene Resources and Germplasm Enhancement in Southern China Ministry of AgricultureTropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China Co-innovation Center for Sustainable Forestry in Southern China Nanjing Forestry UniversityNanjingJiangsu 210037China

Necrotrophic pathogens replicate massively upon colonizing plants,causing large-scale wilting and death of plant ***-standing both mechanisms of pathogen invasion and host response processes prior to symptom appearance and their key regulatory networks is therefore important for defense against pathogen ***,we investigated the mechanisms of interaction between woodland strawberry(Fragaria vesca)leaves and gray mold pathogen(Botrytis cinerea)at 14 infection time points during the first 12 hours of the infection period using a dense,high-resolution time series dual transcriptomic analysis,characterizing the arms race between strawberry *** and *** before the appearance of localized *** leaves rapidly initiated strong systemic defenses at the first sign of external stimulation and showed lower levels of transcriptomic change later in the infection *** the host plants,*** showed larger-scale transcriptomic changes that persisted throughout the infection *** gene co-expression network analysis identified highly correlated genes in 32 gene expression modules between *** and *** two-hybrid and bimolecular fluorescence complementation assays revealed that the disease response protein FvRLP2 from woodland strawberry interacted with the cell death inducing proteins BcXYG1 and BcPG3 from *** of FvRLP2 in both strawberry and Arabidopsis inhibited *** infection,confirming these genes’respective *** findings shed light on the arms race process by which *** invades host plants and strawberry to defend against pathogen infection.

关键词： straw fir invasion

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Interactive Effect of Blackeye cowpea mosaic virus and Cucumber mosaic virus on Vigna unguiculata

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Horticultural Plant Journal 2019年第2期5卷 88-92页

作者： Ayodele Anthony Fajinmi Faculty of Agriculture Department of Crop Science and Horticulture Federal UniversityOye-Ekiti P.M.B. 374 Nigeria

This research tries to demonstrate physiological effect of combined infection of two viruses on growth parameter of cowpea plant as demonstrated through symptom expression. Blackeye cowpea mosaic virus(BlCMV) and Cucumber mosaic virus(CMV) were transmitted to cowpea plants by mechanical rub inoculation. This study showed that the differences in stem height and final aboveground fresh weight of cowpea plants inoculated with mixed infection with CMV and BlCMV were significantly less than those of plants inoculated with a single virus. Likewise cowpea plants inoculated with either virus alone or with CMV and BlCMV mixed infection had less stem height and aboveground fresh weight than the control. The mixed infection of BlCMV and CMV caused significant increase in the severity of symptoms in cowpea and also in the height using factors analysis and Abbott's equation. Symptom severity rating scale used, demonstrated statistical proof for physiological effect based on symptom severity for co-infection. A three phase disease symptom severity expression revealed disease severity for each viral treatment associated with host plant.

关键词： cowpea virus mixed infection interaction severity symptom

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Molecular identification of the key starch branching enzyme-encoding gene SBE2.3 and its interacting transcription factors in banana fruits

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horticulture Research 2020年第1期7卷 1354-1368页

作者： Hongxia Miao Peiguang Sun Qing Liu Juhua Liu Caihong Jia Dongfang Zhao Biyu Xu Zhiqiang Jin Key Laboratory of tropical crop Biotechnology Ministry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural Sciences571101 HaikouPeople’s Republic of China Key Laboratory of Genetic Improvement of Bananas Haikou Experimental StationChinese Academy of Tropical Agricultural Sciences571101 HaikouHainan ProvincePeople’s Republic of China Commonwealth Scientific and Industrial Research Organization Agriculture and Food CanberraACT 2601Australia College of horticulture Nanjing Agricultural University210095 NanjingPeople’s Republic of China

Starch branching enzyme(SBE)has rarely been studied in common starchy banana *** the first time,we report here the molecular characterization of seven SBE(MaSBE)and six SBE(MbSBE)genes in the banana A-and B-genomes,respectively,which could be classified into three distinct subfamilies according to genome-wide *** transcriptomic analysis revealed that six MaSBEs and six MbSBEs were expressed in the developing banana fruits of two different genotypes,BaXi Jiao(BX,AAA)and Fen Jiao(FJ,AAB),among which MaSBE2.3 and MbSBE2.3 were highly *** silencing of MaSBE2.3 expression in banana fruit discs led to a significant decrease in its transcription,which coincides with significant reductions in total starch and amylopectin contents compared to those of empty vector *** suggested functional role of MaSBE2.3 in banana fruit development was corroborated by its transient overexpression in banana fruit discs,which led to significant enhancements in total starch and amylopectin contents.A number of transcription factors,including three auxin response factors(ARF2/12/24)and two MYBs(MYB3/308),that interact with the MaSBE2.3 promoter were identified by yeast one-hybrid library *** these ARFs and MYBs,MaARF2/MaMYB308 and MaARF12/MaARF24/MaMYB3 were demonstrated via a luciferase reporter system to upregulate and downregulate the expression of MaSBE2.3,respectively.

关键词： branching starch fruits

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5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.)

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horticulture Research 2023年第8期10卷 109-121页

作者： Weilong Kong Qiufang Zhu Qing Zhang Yiwang Zhu Jingjing Yang Kun Chai Wenlong Lei Mengwei Jiang Shengcheng Zhang Jinke Lin Xingtan Zhang National Key Laboratory for tropical crop Breeding Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangzhou 518120China College of horticulture Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China

In plants,5mC DNA methylation is an important and conserved epistatic mark involving genomic stability,gene transcriptional regulation,developmental regulation,abiotic stress response,metabolite synthesis,***,the roles of 5mC DNA methylation modification(5mC methylation)in tea plant growth and development(in pre-harvest processing)and flavor substance synthesis in pre-and post-harvest processing are *** therefore conducted a comprehensive methylation analysis of four key pre-harvest tissues(root,leaf,flower,and fruit)and two processed leaves during oolong tea post-harvest *** found that differential 5mC methylation among four key tissues is closely related to tissue functional differentiation and that genes expressed tissue-specifically,responsible for tissue-specific functions,maintain relatively low 5mC methylation levels relative to non-tissue-specifically expressed ***,hypomethylation modifications of CsAlaDC and TS/GS genes in roots provided the molecular basis for the dominant synthesis of theanine in *** addition,integration of 5mC DNA methylationomics,metabolomics,and transcriptomics of post-harvest leaves revealed that content changes in flavor metabolites during oolong tea processing were closely associated with transcription level changes in corresponding metabolite synthesis genes,and changes in transcript levels of these important synthesis genes were strictly regulated by 5mC *** further report that some key genes during processing are regulated by 5mC methylation,which can effectively explain the content changes of important aroma metabolites,includingα-farnesene,nerolidol,lipids,and taste substances such as *** results not only highlight the key roles of 5mC methylation in important flavor substance synthesis in pre-and post-harvest processing,but also provide epimutation-related gene targets for future improvement of tea quality or breeding of whole-tissue high-theanine varieties.

关键词： synthesis functional roots

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Genetic Mapping of Root-knot Nematode Resistance Genes in Solanaceous Vegetables

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Agricultural Biotechnology 2021年第1期10卷 6-8,11页

作者： Bingzheng JIANG Ziji LIU Zhenmu CAO Jie ZHU College of horticulture Hainan UniversityHaikou 570228China tropical crop Germplasm Research Institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China 不详

Root-knot nematodes are becoming more and more harmful to solanaceous vegetables. The most economical and effective way to deal with root-knot nematode disease is to breed varieties with disease resistance. This paper reviewed the recent research progress and achievements of tomato, pepper, eggplant and potato on root-knot nematode disease resistance gene characteristics, disease resistance gene mapping and disease resistance gene molecular markers, and prospects for future research directions.

关键词： Solanaceae Root-knot nematode Gene mapping Molecular marker

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Effects of exogenous paclobutrazol and sampling time on the efficiency of in vitro embryo rescue in the breeding of new seedless grape varieties

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Journal of Integrative Agriculture 2022年第6期21卷 1633-1644页

作者： XU Teng-fei GUO Yu-rui WANG Wen-yuan YUAN Xiao-jian CHU Yan-nan WANG Xiao-wei HAN Yu-lei WANG Yue-jin SONG Rui FANG Yu-lin WANG Lu-jun XU Yan State Key Laboratory of crop Stress Biology for Arid Areas College of HorticultureNorthwest A&F UniversityYangling 712100P.R.China College of Plant Science Tibet Agricultural and Animal Husbandry UniversityNyingchi 860000P.R.China Institute for China Wine Industry Technology Yinchuan 750000P.R.China Institute for Weinan Grape Research Weinan 714099P.R.China

Embryo rescue technology plays an important role in seedless grape ***,the efficiency of embryo rescue,including the embryo formation,germination,and seedling rates,is closely related to the parental genotypes,degree of abortion,growth medium,and plant growth *** this study,we investigated the effects of different concentrations of paclobutrazol(PAC),a plant growth regulator,and embryo collection times on the embryo formation,germination,and seedling rates for different hybrid combinations of grape breeding varieties used for their aroma and cold-resistance *** results showed that the different PAC concentrations had varying impacts on the development of ovules and embryos from the different grape *** embryo formation rates of the‘Sultanina Rose’×‘Beibinghong’and‘Kunxiang Seedless’×‘Taishan-2’crosses were the highest under the 5.1μmol L^(-1)PAC *** 1.0μmol L^(-1)PAC treatment was optimal for the germination and seedling development of the‘Sultanina Rose’×‘Beibinghong’embryos,whereas the 0.2μmol L^(-1)PAC treatment induced the highest germination rate for the‘Sultanina Rose’×‘Kunxiang Seedless’*** optimal sampling times for each cross varied as 39 d after pollination(DAP)for the‘Flame Seedless’×‘Muscat Hamburg’cross,46 DAP for the‘Kunxiang Seedless’×‘Beibinghong’cross,and 41 DAP for the‘Ruby Seedless’×‘Beibinghong’and‘Fantasy Seedless’×‘Shuangyou’***,the medium modified with 0.5 g L^(-1)of indole-3-butyric acid allowed the malformed seedlings to develop into plantlets and achieve larger *** study provides a useful basis for further studies into grape embryo rescue and could improve breeding efforts for new seedless grape varieties.

关键词： Vitis grape embryo rescue paclobutrazol malformed seedlings

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TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining

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Molecular Plant 2023年第11期16卷 1733-1742页

作者： Chengjie Chen Ya Wu Jiawei Li Xiao Wang Zaohai Zeng Jing Xu Yuanlong Liu Junting Feng Hao Chen Yehua He Rui Xia State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510640China Key Laboratory of Biology and Germplasm Enhancement of Horticultural crops in South China Ministry of Agriculture and Rural AffairSouth China Agricultural UniversityGuangzhouGuangdong 510640China Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhouGuangdong 510640China Guangdong Key Laboratory of Non-human Primate Research Guangdong-Hongkong-Macao Institute of CNS RegenerationJinan UniversityGuangzhouGuangdong 510632China State Key Laboratory of crop Stress Adaptation and Improvement Henan Joint International Laboratory for Crop Multi-Omics ResearchSchool of Life SciencesHenan UniversityKaifeng 475004China Key Laboratory of Genetic Improvement of Bananas Sanya Research InstituteState Key Laboratory of Tropical Crop BreedingInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China College of Agronomy Hunan Agricultural UniversityChangsha 410128China

Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic ***,TBtools is a commonly used tool in biological *** the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—*** this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data ***,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual *** date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools *** plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data ***,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and *** promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.

关键词： TBtools-ll plugin biological big data BSA-seq

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