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

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 species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA 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 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The 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 color.Taken 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 species.For 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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Targeting Cancers: Uncovering the Potential Roles of potato Tissue Culture as Anti-Cancer Agents - A Secondary Publication

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Proceedings of Anticancer Research 2024年第3期8卷 36-50页

作者： Tehseen Sajid Jallat Khan Zulqarnain Abbas Hafiz Muhammad Sultan Mahnoor Mazhar Muhammad Zubair Muhammad Dilshad Kashif Kareem Institute of Biological Science Ground FloorBasic Sciences and Humanities BuildingKhwaja Fareed University of Engineering&Information TechnologyKFUEITRYKPakistan Institute of Plant Protection(Plant Pathology) MNS-University of Agriculture MultanPakistan Crop Diseases Research Institute(CDRI) National Agricultural Research Centre NARCIslamabadPakistan School of Chemistry University of Punjab LahorePakistan

Plant tissue culture is a technique that enhances the quality and quantity of potatoes. potatoes are a significant crop and are primarily used in the world. It is a staple food in many countries, where millions of tonnes are produced annually. It is an essential source of many nutrients, such as proteins, carbohydrates, vitamins, and beta-carotene. In addition, potatoes are being used as therapeutic agents against cancer and other human diseases as well. potatoes are on the third list after wheat and rice. To overcome food shortages and malnutrition, there are two methods used for producing potatoes: the first is sexual, which is seed propagation, and the second is asexual, which is plant tissue culture propagation. Conventional potato breeding is a uniform method, but it is unsafe because there is a risk of pathogen attack. In a laboratory setting, the tissue culture of potatoes produced millions of plants with nutrient-rich medium under controlled environmental conditions that prevent pest attacks. Some environmental stresses, such as salinity and water scarcity, affect potato yield and production;however, applying nanoparticles like organic, inorganic, and silicon dioxide enhances potato quality and combats stress. Biotechnology has proven to be helpful in addressing all these issues. This review discusses the significance of potatoes, their production through the tissue culture technique, and the application of nanoparticles to improve the growth, and impact of potatoes on human health.

关键词： Cancer Nanoparticle potato Tissue culture

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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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Molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes Marie E.Bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde Maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan Mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis Max J.Feldman Kyle M.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum M.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.Endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome.Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous chromosomes.Wild species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding efforts.As a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid potato.Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic load.The StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner.Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

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High non-photochemical quenching of VPZ transgenic potato plants limits CO_(2) assimilation under high light conditions and reduces tuber yield under fluctuating light

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Journal of Integrative Plant Biology 2022年第9期64卷 1821-1832页

作者： Günter G.Lehretz Anja Schneider Dario Leister Uwe Sonnewald Department of Biology Division of BiochemistryFriedrich-Alexander-University Erlangen-NürnbergStaudtstrasse 5Erlangen91058 Germany Plant Molecular Biology Faculty of BiologyLudwig Maximilians University of MunichGroßhaderner Str.2-482152 Planegg-MartinsriedMunichGermany

Under natural conditions,photosynthesis has to be adjusted to fluctuating light intensities.Leaves exposed to high light dissipate excess light energy in form of heat at photosystem II(PSII)by a process called non-photochemical quenching(NPQ).Upon fast transition from light to shade,plants lose light energy by a relatively slow relaxation from photoprotection.Combined overexpression of violaxanthin de-epoxidase(VDE),PSII subunit S(PsbS)and zeaxanthin epoxidase(ZEP)in tobacco accelerates relaxation from photoprotection,and increases photosynthetic productivity.In Arabidopsis,expression of the same three genes(VPZ)resulted in a more rapid photoprotection but growth of the transgenic plants was impaired.Here we report on VPZ expressing potato plants grown under various light regimes.Similar to tobacco and Arabidopsis,induction and relaxation of NPQ was accelerated under all growth conditions tested,but did not cause an overall increased photosynthetic rate or growth of transgenic plants.Tuber yield of VPZ expressing plants was unaltered as compared to control plants under constant light conditions and even decreased under fluctuating light conditions.Under control conditions,levels of the phytohormone abscisic acid(ABA)were found to be elevated,indicating an increased violaxanthin availability in VPZ plants.However,the increased basal ABA levels did not improve drought tolerance of VPZ transgenic potato plants under greenhouse conditions.The failure to benefit from improved photoprotection is most likely caused by a reduced radiation use efficiency under high light conditions resulting from a too strong NPQ induction.Mitigating this negative effect in the future might help to improve photosynthetic performance in VPZ expressing potato plants.

关键词： drought photosynthesis potato non-photochemical quenching xanthophyll cycle

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The multi-omics basis of potato heterosis

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Journal of Integrative Plant Biology 2022年第3期64卷 671-687页

作者： Dawei Li Xiaoyue Lu Yanhui Zhu Jun Pan Shaoqun Zhou Xinyan Zhang Guangtao Zhu Yi Shang Sanwen Huang Chunzhi Zhang Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Synthetic Biology CenterAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518172China Yunnan Key Laboratory of potato Biology The AGISCAAS-YNNU Joint Academy of Potato SciencesYunnan Normal UniversityKunming 650500China

Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents.Although tremendous progress has been reported in seed crops,the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown.potato(Solanum tuberosum L.)is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploidhybrid potato.In our previous study,we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis.Here,we integrated transcriptome,metabolome,and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages.We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation.Flower color,male fertility,and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids,and hybrids devoted more energy to primary metabolism for rapid growth.In addition,we identified~2700 allele-specific expression genes at each stage,which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level.Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.

关键词： allele-specific expression dominance DNA methylation heterosis metabolome multi-omics potato transcriptome

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Applying organic amendment enriches nutrient status of municipal solid waste compost and its application enhances tuber yield and nutrient concentrations of potato

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Waste Disposal and Sustainable Energy 2023年第4期5卷 439-450页

作者： Marufa Sultana M.Jahiruddin Mohammad Golam Kibria Md Hosenuzzaman Md.Anwarul Abedin Department of Soil Science Faculty of AgricultureBangladesh Agricultural UniversityMymensingh2202Bangladesh Bangladesh Agricultural Research Institute JoydebpurBangladesh

Elevated price of chemical fertilizers and poor nutrient content in conventional organic sources such as municipal solid waste(MSW)compost necessitate the production of nutrient enriched compost which could serve as a potential alternative organic fertilizer option.We studied three types of amended compost that were prepared by mixing 20%mustard oil cake(MOC)and 30%poultry manure(PM)or cow dung or sugarcane press mud(SPM)with 50%MSW compost.Trichoderma viride was inoculated into every type of compost.The rate of amended or unamended MSW compost application was 10 t ha^(−1).The use of different amendments improved the nutrient level of MSW compost,of which the N increment was remarkable,ranging from 1.14%N(unamended compost)to 2.9%–3.22%N depending on the types of amendment.A field experiment was conducted to evaluate performances of the amended MSW composts on the yield and nutrient content of potato(variety BARI Alu25).All compost treatments except the sole MSW compost treatment produced significantly higher tuber yields than the sole fertilizer treatment.The press mud based MSW compost+fertilizer treatment produced the highest tuber yield of 31.6 t ha^(−1)(65%increase over 100%fertilizers and 57%increase over 100%compost treatment).The tuber N concentration varied from 0.128%to 0.594%,P from 0.018%to 0.035%,K from 0.213%to 0.313%and S from 0.020%to 0.053%,with the highest result recorded with press mud+fertilizer treatment.The use of amended composts had residual effects on soil N,P,K and S contents.Thus,the treatment containing 50%fertilizer+50%compost mixture(MSW:MOC:SPM in a ratio of 5:2:3)performed the best followed by PM amended compost.It is concluded that integrated use of 10 t ha^(−1) organic amended MSW compost with chemical fertilizers can ensure higher crop yield,nutrient content and sustained soil fertility in nutrient-deficient sub-tropical soil.

关键词： Mustard oil cake MSW compost potato Poultry manure Sugarcane press mud

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The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions

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Molecular Plant 2023年第2期16卷 314-317页

作者： Xiaohui Yang Lingkui Zhang Xiao Guo Jianfei Xu Kang Zhang Yinqing Yang Yu Yang Yinqiao Jian Daofeng Dong Sanwen Huang Feng Cheng Guangcun Li Institute of Vegetables Shandong Academy of Agricultural SciencesJinan 250100China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing100081China Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsBeijing100081China Institute of Vegetables Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-CenterJinan 250100China Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen518120China Chinese Academy of Tropical Agricultural Sciences Haikou 571101China

Dear Editor,potato is a vital food security crop and is ranked as the world’s third most important food crop after rice and wheat.In 2011,the first genome assembly of a doubled monoploid potato DM1-3516 R44(DM)was released(potato Genome Sequencing Consortium,2011),which has been widely used as one of the most popular reference genomes in the last decade and served as a valuable resource in plant genomics and potato genetics community(Leisner et al.,2018;Yang et al.,2020;Zheng et al.,2020).

关键词： agronomic doubled potato

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Exogenously applied methyl Jasmonate induces early defense related genes in response to Phytophthora infestans infection in potato plants

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Horticultural Plant Journal 2022年第4期8卷 511-526页

作者： Yu Yang Xiaohui Yang Xiao Guo Xinxi Hu Daofeng Dong Guangcun Li Xingyao Xiong Hunan Provincial Engineering Research Center for potatoes Key Laboratory for Vegetable Biology of Hunan ProvinceCollege of HorticultureHunan Agricultural UniversityChangsha 410128China Institute of Vegetable Research Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility VegetableJi’nan 250100China Institute of Vegetables and Flowers Ministry of Agriculture and Rural AffairsChinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropBeijing 100081China Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhenGuangdong 518120China

In order to elucidate the contributions of JA in orchestrating disease resistance in potato plants,the potato genotype‘SD20’,which exhibits strong resistance against the highly virulent Phytophthora infestans isolate CN152,while infected by the super virulent isolate 2013-18-306,was treated with exogenous JA and then challenged by inoculation with 2013-18-306.The results showed that exogenously applied JA significantly delayed the onset and alleviated the symptoms of late blight,indicating exogenous JA could induce resistance to P.infestans in the early biotrophic stage of infection in‘SD20’plants.To further clarify the role of JA in the early defense response and identify key genes involved in JA signal transduction,gene expression profiling via RNA sequencing(RNA-seq)in‘SD20’plants treated with exogenously applied JA was performed.A total of 2927 differentially expressed genes were specifically induced,the majority encoded transcription factors,protein kinases,secondary metabolites,defense enzymes and disease resistance related proteins.GO functional annotation and KEGG metabolic pathway analysis showed that exogenously applied JA rapidly induced the expression of genes related to immune response regulation,pathogen defense,and other biological processes,and stimulated endogenous JA synthesis and signal transduction,and the overall early pathogen defense response in‘SD20’.These results provide useful information in understanding the JA’s function involved in pathogen defense responses and a theoretical basis for the application of JA in potato production.

关键词： Jasmonic acid potato Phytophthora infestans Pathogen defense Transcriptome

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Horticultural Plant Journal 2022年第3期8卷 369-380页

作者： Yumeng Niu Guangcun Li Yinqiao Jian Shaoguang Duan Ju Liu Jianfei Xu Liping Jin Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropsMinistry of Agriculture and Rural AffairsBeijing 100081China

Early tuberization,a short period from stolon occurrence to tuber formation,is one of the major characteristics of a good early-maturing potato cultivar,while the regulatory mechanism of tuberization time(TT)is still unclear.In this study,two tetraploid cultivars,Zhongshu 3(Z3)and Zhongshu 18(Z18),with short and long TT respectively,were examined to reveal regulatory genes related to TT using RNA sequencing of tissue samples taken during stolon occurrence,stolon swelling and tuber formation.Cluster analysis showed that the gene expression patterns at the stolon swelling and tuber formation stages were significantly different from those at stolon occurrence in both Z3 and Z18.Therefore,we screened the differentially expressed genes(DEGs)at stolon swelling and tuber formation and compared them to those at stolon occurrence.A total of 3085 DEGs were specifically identified and analyzed according to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment,and DEGs involved in starch and sucrose metabolism,plant hormone signal transduction and plant circadian clock were significantly enriched.The circadian clock genes were significantly differentially expressed between Z3 and Z18,revealing an important role for the plant circadian pathway in regulating TT.Furthermore,three candidate genes,StGI,StPRR and StEFM involved in circadian regulation and significantly differentially expressed between Z3 and Z18,were discovered and confirmed by qRT-PCR.The results provide valuable information for understanding the regulatory mechanisms of potato TT and represent a step toward breeding early-maturing potato cultivars.

关键词： potato Tuberization time Transcriptome analysis Circadian rhythm genes

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StOFP20 regulates tuber shape and interacts with TONNEAU1 Recruiting Motif proteins in potato

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Journal of Integrative Agriculture 2023年第3期22卷 752-761页

作者： AI Ju WANG Ye YAN Ya-wen LI Chen-xiao LUO Wei MA Ling SHANG Yi GAO Dong-li Yunnan Key Laboratory of potato Biology the CAAS-YNNU-YINMORE Joint Academy of Potato ScienceYunnan Normal UniversityKunming 650500P.R.China

The OVATE family proteins(OFPs) are plant-specific proteins that modulate diverse aspects of plant growth and development. In tomato, OFP20 has been shown to interact with TONNEAU1 Recruiting Motif(TRM) proteins to regulate fruit shape. In this study, we demonstrated that the mutation of StOFP20 caused a shift from round to oval shaped tubers in a diploid accession C151, supporting the role of StOFP20 in controlling tuber shape. Its expression reached a maximum in the tuber initiation stage and then decreased as the tuber develops. To help elucidate the mechanism of tuber shape regulation by StOFP20, 27 TONNEAU1 Recruiting Motif(TRM) proteins were identified and 23 of them were successfully amplified in C151. A yeast two-hybrid assay identified three TRM proteins that interacted with StOFP20, which was confirmed by firefly luciferase complementation in tobacco leaves. The OVATE domain was indispensable for the interactions, while the necessity of the M10 motif in TRM proteins varied among the interactions between StOFP20 and the three TRMs. In summary, both StOFP20 and SlOFP20 directed interactions with TRM proteins, but the corresponding interactants were not completely consistent, implying that they exert regulatory roles through mechanisms that are only partially overlapping.

关键词： potato tuber shape OFP20 TRM

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