scholarly journals Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3582 ◽  
Author(s):  
Jes Johannesen ◽  
Armin G. Fabritzek ◽  
Bettina Ebner ◽  
Sven-Ernö Bikar
Keyword(s):  
Genotyping By Sequencing ◽  
Extraction Methods ◽  
Snp Markers ◽  
Small Scale ◽  
Sequencing Data ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
Genome Wide ◽  
Western Palearctic ◽  
Dna Extraction Methods

Phylogeographic analyses of the gall fly Urophora cardui have in earlier studies based on allozymes and mtDNA identified small-scale, parapatrically diverged populations within an expanding Western Palearctic population. However, the low polymorphism of these markers prohibited an accurate delimitation of the evolutionary origin of the parapatric divergence. Urophora cardui from the Western Palearctic have been introduced into Canada as biological control agents of the host plant Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-, penta- and tetra-nucleotide repeat motifs and report a genotyping-by-sequencing SNP protocol. We test the markers for genetic variation among three parapatric U. cardui populations. Microsatellite variability (N = 59 individuals) was high: expected heterozygosity/locus/population (0.60–0.90), allele number/locus/population (5–21). One locus was alternatively sex-linked in males or females. Cross-species amplification in the sister species U. stylata was successful or partially successful for seven loci. For genotyping-by-sequencing (N = 18 individuals), different DNA extraction methods did not affect data quality. Depending on sequence sorting criteria, 1,177–2,347 unlinked SNPs and 1,750–4,469 parsimony informative sites were found in 3,514–5,767 loci recovered after paralog filtering. Both marker systems quantified the same population partitions with high probabilities. Many and highly differentiated loci in both marker systems indicate genome-wide diversification and genetically distinct populations.

PSVIII-31 Genome-wide estimation of linkage disequilibrium using American mink genotyping-by-sequencing data

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 267-267
Author(s):  
Karim Karimi ◽  
A Hossain Farid ◽  
Mehdi Sargolzaei ◽  
Sean Myles ◽  
Younes Miar
Keyword(s):  
Linkage Disequilibrium ◽  
Association Studies ◽  
Average Distance ◽  
American Mink ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genome Wide Association Studies ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genome Wide

Abstract Linkage disequilibrium (LD) has been defined as the correlation between alleles at different loci in the genome. The LD levels can be influenced by the evolutionary processes and historical events in populations. The main objective of this study was to estimate the LD levels at different distances of American mink genome using genotyping-by-sequencing (GBS) data. A total of 285 American mink (Neovison vison) were sequenced based on GBS libraries prepared by digesting the genomic DNA with the restriction enzyme ApeKI. After quality control, 13,321 single nucleotide polymorphism (SNP) markers located on 46 Scaffolds were used to determine the extension of LD in the genome. The average r2 was computed for all syntenic SNP pairwise at inter-marker distances from 0 up to 1 Mb. The average r2 between adjacent SNPs was 0.29, ranged from 0.18 to 0.53 across all scaffolds. In addition, the average distance between adjacent markers was 51 kb. The average r2 above 0.3 was observed in less than 1 kb distances and declined with increase in distances between markers. The average r2 was estimated to be less than 0.2 for markers more than 10 kb apart. Furthermore, the average LD level was decreased to 0.08 for inter-marker distances between 0.9 and 1 Mb. The results of this study can be used to determine the optimum maker density required for obtaining enough accuracy and power in both genomic selection and genome-wide association studies.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals Development of an SNP Marker Set for Marker-Assisted Backcrossing Using Genotyping-By-Sequencing in Tetraploid Perilla

2021 ◽  
Author(s):  
Yun-Joo Kang ◽  
Bo-Mi Lee ◽  
Jangmi Kim ◽  
Moon Nam ◽  
Myoung-Hee Lee ◽  
...  
Keyword(s):  
Recurrent Selection ◽  
Diploid Species ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genome Wide ◽  
A Genome ◽  
Marker Assisted Backcrossing

Abstract High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2,326 and 2,454 SNP markers that spanned a total genetic distance of 2,133 cM across 16 linkage groups and 2,169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1,123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

scholarly journals Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines

2020 ◽  
Author(s):  
Jing Li ◽  
Delin Li ◽  
Cristian Zavala Espinosa ◽  
Viridiana Trejo Pastor ◽  
Awais Rasheed ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Snp Markers ◽  
Phenotypic Variance ◽  
Genome Wide ◽  
Gradual Loss ◽  
Modern Maize ◽  
Culinary Uses ◽  
Maize Kernels

Abstract Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte–to–modern maize.

scholarly journals A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes

2020 ◽  
Author(s):  
Lindsay V. Clark ◽  
Wittney Mays ◽  
Alexander E. Lipka ◽  
Erik J. Sacks
Keyword(s):  
Genotyping By Sequencing ◽  
Population Level ◽  
Read Depth ◽  
Multiple Alignment ◽  
Sequencing Data ◽  
Genotype Calling ◽  
Expected Heterozygosity ◽  
Level Statistic ◽  
Alignment Errors ◽  
Environmental Importance

AbstractGiven the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for accurate genotyping methodology that distinguishes paralogs in order to yield Mendelian markers. Methods such as comparing observed and expected heterozygosity are frequently used for identifying collapsed paralogs, but have limitations in genotyping-by-sequencing datasets, in which observed heterozygosity is difficult to estimate due to undersampling of alleles. These limitations are especially pronounced when the species is highly heterozygous or the expected inheritance is polysomic. We introduce a novel statistic, Hind/HE, that uses the probability of sampling reads of two different alleles at a sample*locus, instead of observed heterozygosity. The expected value of Hind/HE is the same across all loci in a dataset, regardless of read depth or allele frequency. In contrast to methods based on observed heterozygosity, it can be estimated and used for filtering loci prior to genotype calling. We also introduce an algorithm that can choose among multiple alignment locations for a given sequence tag in order to optimize the value of Hind/HE for each locus, correcting alignment errors that frequently occur in highly duplicated genomes. Our methodology is implemented in polyRAD v1.2, available at https://github.com/lvclark/polyRAD.

scholarly journals Whole Genome Variation of Transposable Element Insertions in a Maize Diversity Panel

2021 ◽  
Author(s):  
Yinjie Qiu ◽  
Christine H O’Connor ◽  
Rafael Della Coletta ◽  
Jonathan S Renk ◽  
Patrick J Monnahan ◽  
...  
Keyword(s):  
Association Studies ◽  
Repetitive Sequences ◽  
Snp Markers ◽  
Valuable Insight ◽  
Maize Genome ◽  
Sequencing Data ◽  
Frequency Distributions ◽  
Maize Diversity ◽  
Genome Wide ◽  
Genome Assemblies

Abstract Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 non-redundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e. LTRs, Helitrons, TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 &lt; 0.5) that potentially represent information that has not been well captured in previous SNP based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize, and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.

scholarly journals Impact of bead-beating intensity on microbiome recovery in mouse and human stool: Optimization of DNA extraction

2020 ◽  
Author(s):  
Bo Zhang ◽  
Matthew Brock ◽  
Carlos Arana ◽  
Chaitanya Dende ◽  
Lora Hooper ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Extraction Methods ◽  
Dna Integrity ◽  
Sequencing Data ◽  
16S Sequencing ◽  
Bead Beating ◽  
Dna Yield ◽  
Dna Extraction Methods ◽  
The Impact ◽  
Human Stool

AbstractDNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data in microbiome studies. In this study, we assessed the impact of bead-beating intensity during DNA extraction on microbiome recovery in mouse and human stool. We observed a higher DNA yield, better DNA integrity, higher Shannon’s entropy and Simpson’s index in samples beaten for 4 and 9 minutes as compared to unbeaten samples. 16S sequencing data showed that bead beating has a statistically-significant (p<0.05) impact on the recovery of many clinically relevant microbes that live in the mouse and human gut, including Bifidobacterium, Sutterella and Veillonella. It was observed that 4 minutes of bead beating promotes recovery of about 70% of OTUs in mouse and human stool, while the remaining 30% requires longer bead beating. In conclusion, our study indicates adjustments in bead beating treatment based on the composition of the specimen and the targeted bacteria.

scholarly journals Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

2021 ◽  
Vol 22 (13) ◽  
pp. 6722
Author(s):  
Do Yoon Hyun ◽  
Raveendar Sebastin ◽  
Gi-An Lee ◽  
Kyung Jun Lee ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Cucumis Melo ◽  
Systematic Approach ◽  
Genome Wide Association Study ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Cucumis Melo L

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

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