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Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China.

ABSTRACT: Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7943628 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:IntroductionCigars are a popular tobacco product of choice for youth and young adults. Despite growing interest in cigar research, there are gaps in the available literature limiting an ability to set evidence-based policies. Too small research samples, the heterogeneity of types of cigars when asking a single question about use, makes analyzing data difficult. Given the Food and Drug Administration's (FDA's) authority granted in 2016 to regulate cigars, and its popularity, data to better understand use and preference for cigars will help FDA set appropriate regulatory policies.MethodsWe harmonized cigar survey data previously collected by five independent tobacco regulatory science survey research projects. Data supplying participants included three Tobacco Centers of Regulatory Science, one Center for Tobacco Products grantee, and data from Population Assessment of Tobacco and Health (PATH) study's public use dataset.ResultsAnalyzing 92 data variables from across five studies, and applying a rigorous data harmonization protocol, we report findings on 24 key cigar use variables. The step by step protocol for harmonizing is presented. Selected findings showing strict reproducibility across all five studies reveal youth 17-19 years at highest risk for cigar initiation; relative reproducibility shows males more likely to try cigars than females but with significant differences in magnitude across studies; and areas of inconsistent reproducibility are revealed when evaluating brand preferences.ConclusionHarmonizing data from multiple sources fosters a broader view of the robustness and generalizability of survey data than that from a single source. These observations raise awareness to look for the highest degree of reproducibility among and across data sources to inform policy.ImplicationsHarmonizing data from discrete datasets provides insights into cigar initiation and use and is presented showing opportunities, challenges, and solutions. Comparing observational data from PATH and four independent research studies provides a best-practices approach and example of data synthesis for the tobacco research community. The dataset of five studies offers a look at the degree of confidence in analyzing harmonized survey results. Variable conclusions raise the need to strive for the highest degree of reproducibility, to best understand the behaviors of cigar users, and allow for the future development of the most effective interventions to alter tobacco use patterns.

Dataset Information

Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China.

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