Analysis of Genotyping-by-Sequencing (GBS) Data

Kagale, Sateesh; Koh, ChuShin; Clarke, Wayne E.; Bollina, Venkatesh; Parkin, Isobel A. P.; Sharpe, Andrew

doi:10.1007/978-1-4939-3167-5_15

Cited by 9 publications

(4 citation statements)

References 53 publications

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“…In this study, we used GBS technology to identify 10,619 high-quality SNPs in a collection of 50 longan accessions obtained from a community biobank. GBS can be carried out in species with or without reference genome sequences [37]. However, a high-quality reference genome sequence would greatly facilitate the discovery of high-density SNP markers.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Structure of a Longan Germplasm in Thailand Revealed by Genotyping-By-Sequencing (GBS)

et al. 2023

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Longan (Dimocarpus longan Lour.) is grown commercially in many countries, including China, Thailand, the Philippines, Malaysia, Vietnam, India, Australia, and Hawaii. Thailand is the second largest producer and largest exporter of longan in the world. Currently, there is limited information on the genetic background, population structure, and genetic relationships among longan cultivars in Thailand. In this study, a total of 50 longan accessions from a community-based germplasm collection in Thailand were analyzed using 10,619 SNPs from genotyping-by-sequencing (GBS). Based on the results of STRUCTURE analysis, 43 accessions were classified into 4 subpopulations, and the other 7 accessions were found to contain admixed genotypes. Based on UPGMA clustering analysis and PCoA analysis, the longan accessions could be divided into six major groups consistent with those identified by STRUCTURE. A relatively high degree of genetic variation was observed among the longan accessions, as quantified by the expected heterozygosity (He = 0.308). AMOVA results showed that 74% and 26% of the total variation occurred between and within populations, respectively. Obvious genetic differentiation between populations (FST = 0.25) was observed. The results of this study are useful for managing longan germplasm and may facilitate the genetic improvement of longan.

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Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Structure of a Longan Germplasm in Thailand Revealed by Genotyping-By-Sequencing (GBS)

et al. 2023

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“…A maximum-likelihood tree of the 705 samples was also reconstructed using RAxML software with 100 bootstrap replicates [71]. PCA was carried out across all vcf les using the genotype-by-sequencing (GBS) tool for population genetic analysis in R [72].…”

Section: Discussionmentioning

confidence: 99%

Exploring the zoonotic potential of Mycobacterium bovis using variant calling approaches

Banerjee¹,

Balamurugan²,

Joshi³

2020

Preprint

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BackgroundMycobacterium tuberculosis var. bovis is one of the causative agents of Tuberculosis primarily known to infect cattle and is a member of the Mycobacterium Tuberculosis Complex. M.bovis is zoonotic and infects human and other animals resulting in immense economic losses globally. M.bovis is often misdiagnosed and becomes a challenge for treatment and recovery, as M.bovis is intrinsically resistant to certain antibiotics. Hence, the need for accurate diagnostics for zoonotic tuberculosis. ResultsIn order to discern the differences which lie between M.tuberculosis and M.bovis isolates we collected a global collection of M.bovis isolates from NCBI and carried out variant identification studies keeping M.tuberculosis as the reference. Clustering approaches like Principal component analysis and distance-based UPGMA methods helped to segregate isolates into different clusters of homogeneous and heterogeneous populations, which were further analyzed for variant identification. Methods like Joint Variant Calling using population-based studies was adopted for the M.bovis strains, which helped to discern high confidence polymorphisms for each set of populations. Four different variant callers were used to predict SNPs present in their genomic regions. Based on the predicted SNPs, M.bovis samples isolated from New-Zealand were identified as a heterogeneous fast evolving population, whereas the UK samples were identified as a slow evolving homogeneous population. The core-SNP identified for each population revealed the “fixed” mutations present within the populations, whereas, the total-SNP for heterogeneous population indicated presence of clonal subpopulations. A methodology for assignment of genomic coordinates to the reference SNP cluster id of M.tuberculosis entries in dbSNP was also developed and implemented, which helped to identify the percentage of known variants in a population. ConclusionsPopulation-specific studies for global collection of M.bovis samples aided in identification of SNPs responsible for zoonosis. The core-SNP set identified across global M.bovis isolates provide a rationale for further studies to the underlying host-tropism along with aiding in as a robust genetic biomarker for distinguishing M.bovis form M.tuberculosis in addition to the already known RDs. The variation profile reported in this study can serve as potential biomarkers for identification of M.bovis isolates and provide a rationale for further studies to the underlying host-tropism.

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“…But, with GBS data, duplicated sequences are expected to be common because all sequences have the same starting point: the restriction enzyme cut site. Filtering duplicates, in this case, would reduce the read depth per loci to only one read per allele and increase the uncertainties of genotype estimation in the presence of sequencing errors [60]. Duplicates in GBS present advantages to sequencing depth.…”

Section: Radinitio Reads Simulationsmentioning

confidence: 99%

Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps

Taniguti

Amadeu

et al. 2022

Preprint

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Background: Genotyping-by-Sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by PCR duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. Results: We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK and freebayes for SNP calling and updog, polyRAD, and SuperMASSA for genotype calling, and OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. The results showed a low impact of segregation distortion in the linkage map quality, improvements in ordering markers with haplotype-based multiallelic markers, and improved maps with expected size using reliable genotype probabilities or a global error rate of 5%. Conclusions: The pipelines results in each scenario changed according to the data set used, indicating that optimal pipelines and parameters are dataset-dependent and cannot be generalized to all GBS data sets. The Reads2Map workflow can reproduce the analysis in other GBS empirical data sets where users can select the pipeline and parameters adapted to their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.

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Analysis of Genotyping-by-Sequencing (GBS) Data

Cited by 9 publications

References 53 publications

Genetic Diversity and Population Structure of a Longan Germplasm in Thailand Revealed by Genotyping-By-Sequencing (GBS)

Genetic Diversity and Population Structure of a Longan Germplasm in Thailand Revealed by Genotyping-By-Sequencing (GBS)

Exploring the zoonotic potential of Mycobacterium bovis using variant calling approaches

Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps

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