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Selecting SNP markers reflecting population origin for cacao(Theobroma cacao L.)germplasm identification

Beverage plant Research 2021年第1期1卷 133-141页

作者： Osman A.Gutiérrez Kathleen Martinez Dapeng Zhang Donald S.Livingstone Chris J.Turnbull Juan Carlos Motamayor USDA-ARS Subtropical Horticulture Research Station 13601 Old Cutler RoadMiamiFL 33158USA USDA-ARS Beltsville Agricultural Research CenterSPCL10300 Baltimore AvenueBldg.001Rm.223BARC-WBeltsvilleMD 20705USA mars wrigley plant science laboratory DavisCA 95616USA School of Agriculture Policy and DevelopmentUniversity of ReadingRG66ARUK Universal GeneticSolutions LLCOrlandoFLUSA

Cacao is one of the most economically important agricultural commodities in the world,providing the principal ingredient for the global chocolate *** genotype identification is essential for effective conservation and utilization of cacao ***,we report the screening of 956 candidate SNPs,pre-selected from the 6 and 15K Theobroma cacao SNP Arrays using targeted Genotyping-by-Sequencing on 451 cacao germplasm accessions,representing ten known genetic groups from the tropical *** on call rate(No call rate0.15)and Linkage Disequilibrium(LD≤0.5),a total of 219 SNPs were *** efficacy of these SNP markers for population classification was compared with the previous SSR-based analysis in *** population assignment results of the retained 420 cacao accessions was highly comparable with the SSR *** matrix of genetic distance between SSR and SNP markers is highly correlated(r=0.718;P<0.001).These results demonstrated the consistency in using the present SNP markers for cacao germplasm *** is our pilot project for the development of SNP markers reflecting population origin for cacao germplasm *** SNP markers and the selected reference germplasm for different populations are suitable for use in cacao germplasm management and crop improvement,including genotype identification,seed gardens and nursery accreditation,and cocoa *** is being continued with the emphasis on selecting SNP markers for the detection of sub-population structures in the primary gene pool of ***.

关键词： germplasm origin continued

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Genetic diversity of rhizobial populations recovered from three Lotus species cultivated in the infra-arid Tunisian soils

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Progress in Natural science:Materials International 2009年第9期19卷 1079-1087页

作者： Mokhtar Rejili Maria Josè Lorite Mosbah Mahdhi Juan Sanjuan Pinill Ali Ferchichi Mohamed mars Arid & Oases Cropping laboratory Arid Area Institute (IRA) laboratory of plant Biotechnology Applied to Crop Improvement Faculty of Sciences of Gabès Soil Microbiology & Symbiotic Systems Department Experimental Station of Zaidìn

Eighty-three bacterial strains isolated from root nodules of Lotus creticus, L. pusillus, and L. arabicus grown in infra-arid Tunisian soils were characterized using a polyphasic approach including phenotypic analysis, rep-PCR and PCR-RFLP analyses of the 16S rRNA gene. Phenotypically, all isolates are fast growers the majority of which grow at a pH of between 5.5 and 9. Most of the tested isolates tolerate NaCl concentrations from 1.39% to 3.48%. By rep-PCR fingerprinting, the genomic similarity varied from 30% to 98%. All tested isolates were clustered into 32 rep-PCR clusters at the similarity level of 80%. The genomic divergence of strains revealed by rep/PCR analysis appeared to be very important since a molecular polymorphism delimiting symbionts for each species of Lotus was identified. With the high-resolution of rep-PCR profiles of the isolates obtained using Pearson’s/UPGMA analysis, the isolates were resolved into 60 different profiling groups to undergo 16S ARDRA analyses. The analysis of all restriction fragments from each strain based on the UPGMA algorithm from the combined patterns showed that Lotus isolates are very diverse and that they were affiliated to Sinorhizobium, Rhizobium, and Mesorhizobium genera.

关键词： Lotus sp. rep-PCR fingerprinting PCR-RFLP 16S rRNA Rhizobia Arid habitat

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Characterization of root-nodulating bacteria on Retama raetam in arid Tunisian soils

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Progress in Natural science:Materials International 2008年第1期18卷 43-49页

作者： Mosbah Mahdhi Angèle Nzoué Philippe de Lajudie Mohamed mars laboratory of plant Biotechnology Applied to Crop Improvement Faculty of Sciences of Gabès Erriadh City Zrig 6072 Gabès Tunisia laboratory of Tropical and Mediterranean Symbioses IRD/INRA/CIRAD/UM2/AGRO-M (UMR 113) Montpellier F34398 France

The aim of this study is to investigate the diversity of Retama raetam root-nodule bacteria isolated from arid regions of Tunisia. Twelve isolates, chosen as representative for difierent 16S rRNA gene patterns, were characterized by 16S rRNA gene sequencing and phenotypic analysis. Isolates were assigned to Sinorhizobium, Rhizobium and Agrobacterium. Symbiotic properties of Sinorhizobium and Rhizobium isolates showed a large diversity in their capacity to infect their host plant and fix atmospheric nitrogen. Strain RK 22 identified as Rhizobium was the most effective isolate.

关键词： Retama raetam Rhizobia 16S rRNA gene sequence Tunisia

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Anterograde and Retrograde Regulation of Nuclear Genes Encoding Mitochondrial Proteins during Growth, Development, and Stress

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Molecular plant 2014年第7期7卷 1075-1093页

作者： Sophia Ng Inge De Clercqc Olivier Van Akena Simon R. Lawd Aneta Ivanovad Patrick Willems Estelle Giraud Frank Van Breusegem James Wheland ARC Centre of Excellence in plant Energy Biology University of Western Australia Australia Joint Research laboratory in Genomics and Nutriomics College of Life Sciences Zhejiang University Hangzhou 310058 RR. China Department of plant Systems Biology VIB and Department of Plant Biotechnology and Bioinformatics Ghent UniversityTechnologiepark 927 B-9052 Gent Belgium Department of Botany ARC Centre of Excellence in Plant Energy Biology School of Life Science La Trobe University Bundoora 3086Victoria Australia Department of Medical Protein Research and Department of Biochemistry 9000 Ghent Belgium Present address: Illumina ANZ 1 International Court Scoresby Victoria 3179 Australia

Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins （NGEMPs）. The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regu- late these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde （nuclear to mitochondrial） and retrograde （mitochondrial to nuclear） signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.

关键词： mitochondria mitochondrial retrograde regulation (MRR) organellar crosstalk signaling.

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The extremotolerant desert moss Syntrichia caninervis is a promising pioneer plant for colonizing extraterrestrial environments

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The Innovation 2024年第4期5卷 130-138,129页

作者： Xiaoshuang Li Wenwan Bai Qilin Yang Benfeng Yin Zhenlong Zhang Banchi Zhao Tingyun Kuang Yuanming Zhang Daoyuan Zhang State Key laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in Arid LandsXinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China University of Chinese Academy of sciences Beijing 100049China National Space science Center Chinese Academy of SciencesBeijing 100190China Institute of Botany Chinese Academy of SciencesBeijing 100093China

Many plans to establish human settlements on other planets focus on adapting crops to growth in controlled ***,these settlements will also require pioneer plants that can grow in the soils and harsh conditions found in extraterrestrial environments,such as those on ***,we report the extraordinary environmental resilience of Syntrichia caninervis,a desert moss that thrives in various extreme *** has remarkable desiccation tolerance;even after losing>98%of its cellular water content,it can recover photosynthetic and physiological activities within seconds after *** plants can tolerate ultra-low temperatures and regenerate even after being stored in a freezer at80C for 5 years or in liquid nitrogen for 1 *** also has super-resistance to gamma irradiation and can survive and maintain vitality in simulated mars conditions;i.e.,when simultaneously exposed to an anoxic atmosphere,extreme desiccation,low temperatures,and intense UV *** study shows that *** is among the most stress tolerant *** work provides fundamental insights into the multi-stress tolerance of the desert moss ***,a promising candidate pioneer plant for colonizing extraterrestrial environments,laying the foundation for building biologically sustainable human habitats beyond Earth.

关键词： crops environments extreme

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Cadmium isotope fractionation reveals genetic variation in Cd uptake and translocation by Theobroma cacao and role of natural resistanceassociated macrophage protein 5 and heavy metal ATPase-family transporters

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Horticulture Research 2020年第1期7卷 2006-2016页

作者： Rebekah E.T.Moore Ihsan Ullah Vinicius Hde Oliveira Samantha J.Hammond Stanislav Strekopytov Mark Tibbett Jim M.Dunwell Mark Rehkämper Department of Earth science and Engineering Imperial CollegeLondon SW72BPUK School of Agriculture Policy and DevelopmentUniversity of ReadingReading RG66BZUK School of Environment Earth and Ecosystem SciencesThe Open UniversityMilton Keynes MK76AAUK Imaging and Analysis Centre The Natural History MuseumLondon SW75BDUK Present address:Department of plant Biology Institute of BiologyUniversity of CampinasCampinasSao Paulo 13083-970Brazil Present address:National Measurement laboratory LGCQueen’s RoadTeddington TW110LYUK

In response to new European Union regulations,studies are underway to mitigate accumulation of toxic cadmium(Cd)in cacao(Theobroma cacao,Tc).This study advances such research with Cd isotope analyses of 19 genetically diverse cacao clones and yeast transformed to express cacao natural resistance-associated macrophage protein(NRAMP5)and heavy metal ATPases(HMAs).The plants were enriched in light Cd isotopes relative to the hydroponic solution withΔ^(114/110)Cd_(tot-sol)=−0.22±0.08‰.Leaves show a systematic enrichment of isotopically heavy Cd relative to total plants,in accord with closed-system isotope fractionation ofΔ^(114/110)C_(dseq-mob)=−0.13‰,by sequestering isotopically light Cd in roots/stems and mobilisation of remaining Cd to *** findings demonstrate that(i)transfer of Cd between roots and leaves is primarily unidirectional;(ii)different clones utilise similar pathways for Cd sequestration,which differ from those of other studied plants;(iii)clones differ in their efficiency of Cd *** yeast that expresses TcNRAMP5(*** natural resistance-associated macrophage gene)had isotopically lighter Cd than did *** suggests that NRAMP5 transporters constitute an important pathway for uptake of Cd by *** isotope signatures of transgenic yeast expressing HMA-family proteins suggest that they may contribute to Cd *** data are the first to record isotope fractionation induced by transporter proteins in vivo.

关键词： roots transformed signature

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Analysis of Genetic Diversity and Relationships in a Tunisian Fig （Ficus carica） Germplasm Collection by Random Amplified Microsatellite Polymorphisms

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Journal of Integrative plant Biology 2007年第3期49卷 386-391页

作者： Khaled Chatti Olfa Saddoud Amel Salhi-Hannachi Messaoud mars Mohamed Marrakchi Mokhtar Trifi laboratory of Molecular Genetics Immunology and Biotechnology Faculty of Sciences Campus University 2092 EI Manar Tunis Tunisia High Institute of Breeding and Horticulture 4042 Chott Mariem Sousse Tunisia

The random amplified mirosatellite polymorphism method was performed in a set of Tunisian fig landraces using eighteen primer combinations. A total of sixty three random amplified microsatellite polymorphism （RAMPO） markers were scored and used either to assess the genetic diversity in these cultivars or to detect cases of mislabeling. Opportunely, data proved that the designed procedure constitutes an attractive and fast method with low costs and prevents radio exposure. As a result, we have identified the primer combinations that are the most efficient to detect genetic polymorphism in this crop. Therefore, the derived unweighted pair-group method with arithmetic averages （UPGMA） dendrogram illustrates the genetic divergence among the landraces studied and exhibits a typically continuous variation. Moreover, no evident correlation between the sexes of trees was observed. In addition, using these markers, discrimination between landraces has been achieved. Thus, random amplified mirosatellite polymor- phism is proved to be powerful for characterizing the local fig germplasm.

关键词： collection Ficus carica genetic diversity germplasm random amplified microsatellite polymorphism Tunisia

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Two response patterns to negative environmental changes:Cases from Populus and Metasequoia

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Global Geology 2023年第2期26卷 63-73页

作者： ZHANG Yi XIONG Zhifeng GUO Shuangxing College of Paleontology Shenyang Normal UniversityShenyang 110034China Key laboratory for Evolution of Past Life in Northeast Asia Ministry of Natural ResourcesShenyang 110034China Nanjing Institute of Geology and Palaeontology Chinese Academy of SciencesNanjing 210008China

Traditionally,plant distribution is thought to be closely related to environmental *** recently,it is found that Populus,quite different from other plant taxa,adapted to negative environmental changes,and successfully migrated to different climate zones from its origin places of warm temperate ***,Metasequoia is gradually tending to extinction from the Miocene to *** on above contrary cases,two response patterns of plant to negative environmental changes are *** is active adaptation represented by Populus,the other is passive adaptation represented by *** plants of passive strategy characterized for desert prevention might be easily replaced by those of active strategy characterized for desert *** growing plants,such as Populus with characteristics of drought and salt tolerance,wind and sand resistance,are selected in Tarim Basin in southern Xinjiang,China,as a good example of desert utilization in the construction of new highways and towns,not only serve as farmland shelterbelt in sandy *** addition,Populus with high-altitude and cold adaptation has also been selected as an ideal tree planted in ***,the idea of using Populus as one of the preferred pioneer trees to colonize mars is proposed.

关键词： active adaptation passive adaptation Populus Metasequoia deserts mars

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