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Jiang M, Yan S, Ren WC, Xing NN, Li HY, Zhang MQ, Liu MQ, Liu XB, Ma W. Genetic Diversity and Population Structure of Traditional Chinese Herb Radix bupleuri Resources Using Genome-Wide SNPs through Genotyping-by-Sequencing. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Hayat Z, Shahzad K, Ali H, Casini R, Naveed K, Hafeez A, El-Ansary DO, Elansary HO, Fiaz S, Abaid-Ullah M, Hafeez FY, Iqbal MS, Ullah A. 16S rRNA gene flow in Enterococcus spp. and SNP analysis: A reliable approach for specie level identification. BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Park JS, Kang MY, Shim EJ, Oh J, Seo KI, Kim KS, Sim SC, Chung SM, Park Y, Lee GP, Lee WS, Kim M, Jung JK. Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce ( Lactuca sativa L.). HORTICULTURE RESEARCH 2022; 9:uhac119. [PMID: 35928401 PMCID: PMC9343917 DOI: 10.1093/hr/uhac119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/04/2022] [Indexed: 05/08/2023]
Abstract
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation analyses based on the selected SNPs classified the lettuce cultivars into three main groups. Core sets of 192, 96, 48, and 24 markers were further selected and validated using the Fluidigm platform. Phylogenetic analyses based on all core sets of SNPs successfully discriminated individual cultivars that have been currently recognized. These core sets of SNP markers will support the construction of a DNA database of lettuce that can be useful for cultivar identification and purity testing, as well as DUS testing in the plant variety protection system. Additionally, this work will facilitate genetic research to improve breeding in lettuce.
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Affiliation(s)
- Jee-Soo Park
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Min-Young Kang
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Eun-Jo Shim
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - JongHee Oh
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyoung-In Seo
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames IA 50011, USA
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Min Chung
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Ansung 17546, South Korea
| | - Won-Sik Lee
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Minkyung Kim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
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Xiong S, Zhao Y, Chen Y, Gao M, Wu L, Wang Y. Genetic diversity and population structure of Quercus fabri Hance in China revealed by genotyping-by-sequencing. Ecol Evol 2020; 10:8949-8958. [PMID: 32884670 PMCID: PMC7452768 DOI: 10.1002/ece3.6598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 11/11/2022] Open
Abstract
Analysis of genetic diversity and population structure among Quercus fabri populations is essential for the conservation and utilization of Q. fabri resources. Here, the genetic diversity and structure of 158 individuals from 13 natural populations of Quercus fabri in China were analyzed using genotyping-by-sequencing (GBS). A total of 459,564 high-quality single nucleotide polymorphisms (SNPs) were obtained after filtration for subsequent analysis. Genetic structure analysis revealed that these individuals can be clustered into two groups and the structure can be explained mainly by the geographic barrier, showed gene introgression from coastal to inland areas and high mountains could significantly hinder the mutual introgression of genes. Genetic diversity analysis indicated that the individual differences within groups are greater than the differences between the two groups. These results will help us better understand the genetic backgrounds of Q. fabri.
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Affiliation(s)
- Shifa Xiong
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Ming Gao
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Liwen Wu
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
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Hyun DY, Sebastin R, Lee KJ, Lee GA, Shin MJ, Kim SH, Lee JR, Cho GT. Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:688. [PMID: 32625218 PMCID: PMC7311657 DOI: 10.3389/fpls.2020.00688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/30/2020] [Indexed: 05/17/2023]
Abstract
Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.
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