Molecular Characterization of a Cacao Germplasm Collection Maintained in Yunnan, China Using Single Nucleotide Polymorphism (SNP) Markers

Anthrax caused byBacillus anthracisis an old and neglected zoonosis that continues to raise concerns in Southern Africa. In this study, twenty (20) slides with suspected isolates ofB. anthracisfrom anthrax cases between 1990 and 2014 and two (2) from that of a vaccine strain were analysed using MLVA with 15 VNTRs and CanSNPs test. The results from the CanSNPs indicate that all anthrax outbreaks in Zambia between 1990 and 2014 were caused by the lineage A.Br.005/006 of the clade A. This indicates a common ancestral origin of theB. anthraciscirculating in the country. This data has described several environmental, wildlife, livestock and human cases that occurred in a 24 year period, from the major areas where anthrax is endemic. The molecular characterization of isolates from anthrax outbreaks in Zambia has revealed a genetic structure in agreement with previous studies from neighbouring countries. Further studies are needed to elucidate how to better manage anthrax outbreaks and define the risk maps of Zambia.

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Development of a New A m –Genome‐Specific Single Nucleotide Polymorphism Marker Set for the Molecular Characterization of Wheat– Triticum monococcum Introgression Lines

The Plant Genome ◽

10.3835/plantgenome2018.12.0098 ◽

2019 ◽

Vol 12 (3) ◽

pp. 180098

Author(s):

Andras Cseh ◽

Maria Megyeri ◽

Caiyun Yang ◽

Stella Hubbart‐Edwards ◽

Duncan Scholefield ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Molecular Characterization ◽

Single Nucleotide Polymorphism Marker ◽

Introgression Lines ◽

Triticum Monococcum ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

M Genome

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Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (Ziziphus jujuba Mill.) Germplasm

Agronomy ◽

10.3390/agronomy11112303 ◽

2021 ◽

Vol 11 (11) ◽

pp. 2303

Author(s):

Lihua Song ◽

Bing Cao ◽

Yue Zhang ◽

Lyndel W. Meinhardt ◽

Dapeng Zhang

Keyword(s):

Single Nucleotide Polymorphism ◽

Germplasm Collection ◽

Snp Markers ◽

High Rate ◽

Pedigree Information ◽

Nucleotide Polymorphism ◽

Chinese Jujube ◽

Single Nucleotide ◽

Climate Conditions ◽

Ziziphus Jujuba

Chinese jujube (Ziziphus jujuba Mill.) is an economically important fruit tree with outstanding adaptability to marginal lands and a broad range of climate conditions. There are over 800 cultivars, mostly landraces from China. However, a high rate of mislabeling in Chinese jujube germplasm restricts the sharing of information and materials among jujube researchers and hampers the use of jujube germplasm in breeding. In the present study, we developed a large panel of single nucleotide polymorphism (SNP) markers and validated 288 SNPs by genotyping 114 accessions of Chinese jujube germplasm. The validation resulted in the designation of a set of 192 polymorphic SNP markers that revealed a high rate of synonymous mislabeling in the jujube germplasm collection in Ningxia, China. A total of 17 groups of duplicates were detected, encompassing 49 of the 114 Chinese jujube cultivars. Model-based population stratification revealed two germplasm groups, and the core members of the two groups showed a significant genetic differentiation (Fst = 0.16). The results supported the hypothesis that the cultivated Chinese jujube had multiple origins and multiple regions of domestication. The Neighbor-Joining dendrogram further revealed that this collection is comprised of multiple sub-groups, each including 1-13 closely related cultivars. Parentage analysis of cultivars with known pedigree information proved the efficacy of using these SNP markers for parentage verification. A subset of 96 SNPs with high information index was selected for future downstream application including gene bank management, verification of pedigrees in breeding programs, quality control for propagation of planting materials and support of the traceability and authentication of jujube products.

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Genetic diversity and ancestry of cacao (Theobroma cacao L.) in Dominica revealed by single nucleotide polymorphism markers

Genome ◽

10.1139/gen-2019-0214 ◽

2020 ◽

Vol 63 (12) ◽

pp. 583-595

Author(s):

David Gopaulchan ◽

Lambert A. Motilal ◽

Rena K. Kalloo ◽

Amrita Mahabir ◽

Marissa Moses ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Theobroma Cacao ◽

Gene Diversity ◽

Germplasm Collection ◽

Snp Markers ◽

Regional Differentiation ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Geographical Regions ◽

Theobroma Cacao L

Cacao (Theobroma cacao L.), an introduced tree crop in Dominica, is important for foreign exchange earnings from fine or flavour cocoa. The genetic structure of farmed cacao in Dominica was examined to identify varieties for conservation, breeding, and propagation to improve their cocoa industry. Cacao trees (156) from 73 sites over seven geographical regions were genotyped at 192 single nucleotide polymorphism (SNP) markers. Identity, regional differentiation, phylogenetic, multi-variate, ancestry, and core collection analyses were performed. Farmed cacao germplasm had moderate gene diversity (He = 0.320 ± 0.005) from generally unique trees, but cocoa growing regions were genetically similar. Synonymous matching (16.3%) showed that some clonal material was supplied to farmers. Cacao trees were mainly mixed from Amelonado, Criollo, Iquitos, Contamana, and Marañon ancestries, with predominantly Amelonado–Criollo hybrids. Criollo ancestry, linked to fine or flavour cocoa, was found at more than 30% in 28 unique trees. Forty-five trees, containing the SNP diversity of cacao in Dominica, are recommended as a core germplasm collection. This study identifies promising trees for improving cocoa quality; provides genetic evidence that community, regional, or country-wide pooling would not compromise the exclusive fine or flavour cocoa industry; and discusses other implications towards improving the Dominican cocoa industry.

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Isolation and characterization of 91 single nucleotide polymorphism (SNP) markers for the blue swimming crab (Portunus pelagicus)

Conservation Genetics Resources ◽

10.1007/s12686-017-0720-6 ◽

2017 ◽

Vol 9 (4) ◽

pp. 549-556 ◽

Cited By ~ 1

Author(s):

Guidong Miao ◽

Hongyu Ma ◽

Xiaolong Yang ◽

Shuqi Wang ◽

Qingyang Wu ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Snp Markers ◽

Swimming Crab ◽

Nucleotide Polymorphism ◽

Portunus Pelagicus ◽

Single Nucleotide ◽

Isolation And Characterization

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Detecting strawberry cultivar misidentification in the Philippines using single nucleotide polymorphism markers from the anthocyanin reductase gene

10.1101/2020.02.02.922369 ◽

2020 ◽

Author(s):

Nadine Adellia Ledesma ◽

John Mark Matulac ◽

Jesus Emmanuel Sevilleja ◽

Maria Luisa Enriquez

Keyword(s):

Single Nucleotide Polymorphism ◽

Germplasm Collection ◽

Optimal Growth ◽

Molecular Classification ◽

The Philippines ◽

Snp Markers ◽

Germplasm Management ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Small Holder Farmers

ABSTRACTBACKGROUNDCommercial strawberry production in the Philippines is done by small-holder farmers in La Trinidad, Benguet, where the climate is conducive for optimal growth of this temperate crop. However, these farmers are not cognizant of the importance of proper cultivar identification, particularly during runner propagation, distribution, and transplanting. Thus, there is a high likelihood that misidentification of commonly grown cultivars has taken place.OBJECTIVEThe study aimed to develop single nucleotide polymorphism markers and use them to detect possible misidentification among strawberry cultivars.METHODSLeaf samples from several cultivars were obtained from farmers and the germplasm collection of a local university in La Trinidad, Benguet, Philippines. Expressed sequence tags from the ANR gene were screened for putative SNPs. Eleven SNP markers were developed and used to discriminate among the collected samples.RESULTSThe SNP markers grouped the cultivars into five genotypic clusters with seven distinct genotypic identities. Clustering analysis revealed inconsistencies between the farmers’ identification and the molecular classification. ‘Sweet Charlie’ samples were assigned to four genotypic clusters and ‘Strawberry Festival’ samples were grouped into three separate clusters.CONCLUSIONThere is a high probability that cultivar misidentification has indeed occurred. The molecular markers developed in this study could assist in future cultivar verification efforts, germplasm management, and breeding programs.

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