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 ex...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.展开更多
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...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.展开更多
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 man...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.展开更多
基金This work was partially supported by the National Natural Science Foundation of China(30800884,31370688)References to a company and/or product by the USDA are only for the purposes of information and do not imply approval or recommendation of the product to the exclusion of others that may also be suitable.
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.
基金This work was partially supported by the National Natural Science Foundation of China(31100248).
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.
基金This work was partially supported by the National Natural Science Foundation of China(30800884,31370688).
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.
