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| 1 | Varietal identification of tea(Camellia sinensis)using nanofluidic array of single nucleotide polymorphism(SNP)markers显示文摘Apart from water,tea is the world’s most widely consumed beverage.Tea is produced in more than 50 countries with an annual production of approximately 4.7 million tons.The market segment for specialty tea has been expanding rapidly owing to increased demand,resulting in higher revenues and profits for tea growers and the industry.Accurate varietal identification is critically important to ensure traceability and authentication of premium tea products,which in turn contribute to on-farm conservation of tea genetic diversity.Using a set of single nucleotide polymorphism(SNP)markers developed from the expressed sequence tag(EST)database of Camilla senensis,we genotyped deoxyribonucleic acid(DNA)samples extracted from a diverse group of tea varieties,including both fresh and processed commercial loose-leaf teas.The validation led to the designation of 60 SNPs that unambiguously identified all 40 tested tea varieties with high statistical rigor(p<0.0001).Varietal authenticity and genetic relationships among the analyzed cultivars were further characterized by ordination and Bayesian clustering analysis.These SNP markers,in combination with a high-throughput genotyping protocol,effectively established and verified specific DNA fingerprints for all tested tea varieties.This method provides a powerful tool for variety authentication and quality control for the tea industry.It is also highly useful for the management of tea genetic resources and breeding,where accurate and efficient genotype identification is essential. | Wan-Ping Fang Lyndel W Meinhardt Hua-Wei Tan Lin Zhou Sue Mischke Dapeng Zhang | 2014 | Horticulture Research2014，1，1： | 13 |
| 2 | Exogenous abscisic acid significantly affects proteome in teaplant (Camellia sinensis) exposed to drought stress显示文摘Tea[Camellia sinensis(L.)O.Kuntze]is an important economic crop,and drought is the most important abiotic stress affecting yield and quality.Abscisic acid(ABA)is an important phytohormone responsible for activating drought resistance.Increased understanding of ABA effects on tea plant under drought stress is essential to develop drought-tolerant tea genotypes,along with crop management practices that can mitigate drought stress.The objective of the present investigation is evaluation of effects of exogenous ABA on the leaf proteome in tea plant exposed to drought stress.Leaf protein patterns of tea plants under simulated drought stress[(polyethylene glycol(PEG)-treated]and exogenous ABA treatment were analyzed in a time-course experiment using two-dimensional electrophoresis(2-DE),followed by matrix-assisted laser desorption/ionization time-of-flight(MALDI-TOF)mass spectrometry(MS).Among the 72 protein spots identified by MALDI-TOF MS,16 proteins were downregulated and two were upregulated by exogenous ABA.The upregulated proteins have roles in glycolysis and photosystem II stabilization.Twenty-one protein spots were responsive to drought stress and most participate in carbohydrate and nitrogen metabolism,control of reactive oxygen species(ROS),defense,signaling or nucleic acid metabolism.The combined treatments of exogenous ABA and drought showed upregulation of 10 protein spots at 12 h and upregulation of 11 proteins at 72 h after initiation of drought stress.The results support the importance of the role that ABA plays in the tea plant during drought stress,by improving protein transport,carbon metabolism and expression of resistance proteins. | Lin Zhou Hui Xu Sue Mischke Lyndel W Meinhardt Dapeng Zhang Xujun Zhu Xinghui Li Wanping Fang | 2014 | Horticulture Research2014，1，1： | 12 |
| 3 | Developing single nucleotide polymorphism(SNP)markers from transcriptome sequences for identification of longan(Dimocarpus longan)germplasm显示文摘Longan(Dimocarpus longan Lour.)is an important tropical fruit tree crop.Accurate varietal identification is essential for germplasm management and breeding.Using longan transcriptome sequences from public databases,we developed single nucleotide polymorphism(SNP)markers;validated 60 SNPs in 50 longan germplasm accessions,including cultivated varieties and wild germplasm;and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor(P<0.0001).Multiple trees from the same clone were verified and off-type trees were identified.Diversity analysis revealed genetic relationships among analyzed accessions.Cultivated varieties differed significantly from wild populations(Fst=0.300;P<0.001),demonstrating untapped genetic diversity for germplasm conservation and utilization.Within cultivated varieties,apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation.These SNP markers provide a powerful tool to manage longan genetic resources and breeding,with accurate and efficient genotype identification. | Boyi Wang Hua-Wei Tan Wanping Fang Lyndel W Meinhardt Sue Mischke Tracie Matsumoto Dapeng Zhang | 2015 | Horticulture Research2015，2，1： | 6 |
| 4 | Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array显示文摘Tea is an important cash crop, representing a $40 billion-a-year global market. Differentiation of the tea market has resulted in increasing demand for tea products that are sustainably and responsibly produced. Tea authentication is important because of growing concerns about fraud involving premium tea products. Analytical technologies are needed for protection and value enhancement of high-quality brands. For loose-leaf teas, the challenge is that the authentication needs to be established on the basis of a single leaf, so that the products can be traced back to the original varieties. A new generation of molecular markers offers an ideal solution for authentication of processed agricultural products. Using a nanofluidic array to identify variant SNP sequences, we tested genetic identities using DNA extracted from single leaves of 14 processed commercial tea products. Based on the profiles of 60 SNP markers, the genetic identity of each tea sample was unambiguously identified by multilocus matching and ordination analysis. Results for repeated samples of multiple tea leaves from the same products(using three independent DNA extractions) showed 100% concordance, showing that the nanofluidic system is a reliable platform for generating tea DNA fingerprints with high accuracy. The method worked well on green, oolong, and black teas, and can handle a large number of samples in a short period of time. It is robust and cost-effective, thus showing high potential for practical application in the value chain of the tea industry. | Wanping Fang Lyndel W.Meinhardt Huawei Tan Lin Zhou Sue Mischke Xinghua Wang Dapeng Zhang | 2016 | The Crop Journal2016，4，4： | 4 |
| 5 | Developing single nucleotide polymorphism markers for the identification of pineapple(Ananas comosus)germplasm显示文摘Pineapple(Ananas comosus[L.]Merr.)is the third most important tropical fruit in the world after banana and mango.As a crop with vegetative propagation,genetic redundancy is a major challenge for efficient genebank management and in breeding.Using expressed sequence tag and nucleotide sequences from public databases,we developed 213 single nucleotide polymorphism(SNP)markers and validated 96 SNPs by genotyping the United States Department of Agriculture-Agricultural Research Service pineapple germplasm collection,maintained in Hilo,Hawaii.The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection.Twenty-four groups of duplicates were detected,encompassing 130 of the total 170 A cosmos accessions.The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple.Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties.Parentage analysis further revealed that both A.comosus var.bracteatus and A.comosus var.ananassoides are likely progenitors of pineapple cultivars.However,the traditional classification of cultivated pineapple into horticultural groups(e.g.‘Cayenne’,‘Spanish’,‘Queen’)was not well supported by the present study.These SNP markers provide robust and universally comparable DNA fingerprints;thus,they can serve as an efficient genotyping tool to assist pineapple germplasm management,propagation of planting material,and pineapple cultivar protection.The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops. | Lin Zhou Tracie Matsumoto Hua-Wei Tan Lyndel W Meinhardt Sue Mischke Boyi Wang Dapeng Zhang | 2015 | Horticulture Research2015，2，1： | 2 |
| 6 | Identification of Erythroxylum taxa by AFLP DNA analysis显示文摘 | EMANUE L JOHNSON JAMES A SAUNDERS SUE MISCHKE CHARLES S ET A L | 2003 | Phytochemistry2003，64，1： | 1 |
| 7 | Traditional varieties of cacao(Theobroma cacao)in Madagascar:their origin and dispersal revealed by SNP markers显示文摘Cacao(Theobroma cacao L.)is an important Neotropical crop originating in South America and dispersed by European explorers,arriving in Madagascar in the late 19th century.Although Madagascar is an important producer of cocoa for the premium chocolate market,the varietal composition and genetic diversity in cacao germplasm from Madagascar,especially in traditional cacao farms,remains unknown.A total of 190 cacao accessions,including 40 farmer accessions collected from traditional cacao farms in Madagascar,and 150 accessions representing seven reference cacao populations,were analyzed using Single Nucleotide Polymorphism(SNP)markers.Multivariate analysis and Bayesian stratification resulted in the clustering of the 40 farmer accessions into three groups:Criollo,Amelonado and Trinitario.These three traditional varieties were commonly cultivated in tropical America in the 18th century,but most of them have been replaced by improved varieties.The present study demonstrated that Madagascar is distinctive in that all three traditional cacao varieties,Criollo,Amelonado and Trinitario,are still maintained on-farm for cocoa production,as in Mesoamerica and the Caribbean several hundred years ago.Results from the present study are significant in terms of understanding the early dispersal of cacao from tropical America and Asia to Africa,in addition to the well-documented route from Brazil to São Tomé&Príncipe.The results also provide new information for planning future conservation and utilization of cacao germplasm in Madagascar. | Yanmei Li Dapeng Zhang Lambert A.Motilal Philippe Lachenaud Sue Mischke Lyndel W.Meinhardt | 2021 | Beverage Plant Research2021，1，1： | 0 |
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