scholarly journals Analysis of Segregation Ratio Distortion and Linkage Mapping in Two Switchgrass F1 Populations: Lowland-lowland and Lowland-upland Using Genotyping by Sequencing Data

2019 ◽  
Author(s):  
Rasyidah Razar ◽  
Katrien Devos ◽  
Ali Missaoui
Keyword(s):  
Genetic Diversity ◽  
Segregation Distortion ◽  
Biomass Yield ◽  
Genotyping By Sequencing ◽  
Segregation Ratio ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Sequencing Data ◽  
Target Number ◽  
High Genetic Diversity

Abstract Background: Switchgrass is an emerging bioenergy crop due to its perennial nature, high biomass yield, and ability to grow in marginal land. The high genetic diversity in switchgrass germplasm can be exploited to capture favorable traits that increase the range of adaptation and biomass yield. Genetic diversity can be explored using single nucleotide polymorphisms (SNPs) that next-generation sequencing has made possible for high-throughput genotyping. We used genotyping-by-sequencing (GBS) of genomic fragments resulting from two methylation sensitive restriction enzymes: PstI and MspI . Two bi-parental F1 populations were developed from crosses between lowland B6 and lowland AP13 (AB population), and lowland B6 with upland VS16 genotypes (BV population), with a target number of 298 progenies in each population. Pseudo-testcross strategy was adopted to perform linkage analysis in these populations that are segregating for winter dormancy using single dose markers (SDA): heterozygous in one parent and homozygous in the other parent. We compared the amount of polymorphisms between the two crosses and examined the pattern of segregation distortion based on the SNPs data generated. Results: Two genetic maps were generated for each population, with 2772 markers in AB and 3766 markers in BV. The higher number of markers in the BV population was expected for since the parents originated from different ecotypes and verified to have the highest genetic distance. More segregation distortion was observed in markers located in the telomeric regions where more genes reside. More markers from the AB population exhibited segregation distortion compared to the BV, and the proportion of heterozygous alleles were significantly higher than homozygous alleles in AB population. The linkage maps showed strong collinearity with P. virgatum V5.1 reference genome with a very minimal number of markers originating from different chromosomes. Conclusion: Understanding the extent of segregation distortion in switchgrass crosses is important for the correct inclusion of markers based on their segregation ratio when constructing a linkage map. Switchgrass linkage maps should be a useful resource to dissect beneficial biomass traits linked to SNP markers.

scholarly journals Accounting for Errors in Low Coverage High-Throughput Sequencing Data when Constructing Genetic Maps using Biparental Outcrossed Populations

2018 ◽  
Author(s):  
Timothy P. Bilton ◽  
Matthew R. Schofield ◽  
Michael A. Black ◽  
David Chagné ◽  
Phillip L. Wilcox ◽  
...  
Keyword(s):  
High Throughput ◽  
Genetic Linkage ◽  
High Throughput Sequencing ◽  
Diploid Species ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Sequencing Data ◽  
Genetic Linkage Maps ◽  
Low Coverage

ABSTRACTNext generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high density genetic linkage maps, which facilitate the development of non-model species’ genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sib family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sib populations of diploid species, implemented in a package called GUSMap. Our model is based on an extension of the Lander-Green hidden Markov model that accounts for errors present in sequencing data. Results show that GUSMap was able to give accurate estimates of the recombination fractions and overall map distance, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model.

scholarly journals AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

2020 ◽  
Author(s):  
Kyle Fletcher ◽  
Lin Zhang ◽  
Juliana Gil ◽  
Rongkui Han ◽  
Keri Cavanaugh ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Map ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

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 Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation

2020 ◽  
Author(s):  
Jiangbin Fan ◽  
Johannes A Jehle ◽  
Jörg T Wennmann
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Insect Pests ◽  
Consensus Sequence ◽  
Cydia Pomonella ◽  
Next Generation Sequencing Data ◽  
Snp Analysis ◽  
Sequencing Data ◽  
High Genetic Diversity ◽  
Cydia Pomonella Granulovirus

Abstract Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus–host co-evolution is of particular scientific interest and economic importance because high virulence of baculovirus products is essential and emergence of host resistance needs to be avoided as much as possible. In the present study, the population structure of twenty isolates of the Cydia pomonella granulovirus (CpGV), including twelve isolates from different geographic origins and eight commercial formulations, were studied on the basis of next-generation sequencing data and by analyzing the distribution of single nucleotide polymorphisms (SNPs). An entirely consensus sequence-free quantitative SNP analysis was applied for the identification of 753 variant SNP sites being specific for single as well as groups of CpGV isolates. Based on the quantitative SNP analysis, homogenous, heterogenous as well as mixed isolates were identified and their proportions of genotypes were deciphered, revealing a high genetic diversity of CpGV isolates from around the world. Based on hierarchical clustering on principal components (HCPC), six distinct isolate/group clusters were identified, representing the proposed main phylogenetic lineages of CpGV but comprising full genome information from virus mixtures. The relative location of different isolates in HCPC reflected the proportion of variable compositions of different genotypes. The established methods provide novel analysis tools to decipher the molecular complexity of genotype mixtures in baculovirus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than consensus based analyses.

The Melampsora americana population on Salix purpurea in the Great Lakes region is highly diverse with a contributory influence of clonality

2021 ◽  
Author(s):  
Chase R Crowell ◽  
Dustin G Wilkerson ◽  
Mariami Beckauri ◽  
Ali R Cala ◽  
Patrick W McMullen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Great Lakes ◽  
New York State ◽  
Genotyping By Sequencing ◽  
Resistance Breeding ◽  
Great Lakes Region ◽  
High Genetic Diversity ◽  
Shrub Willow ◽  
Growing Seasons

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons using genotyping-by-sequencing to identify single nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed for regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas with few sites showing moderate genetic differentiation. This data supports the hypothesis of sexual recombination between growing seasons as no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs, however there is also evidence of high genetic diversity of rust isolates in all settings. Together, this work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.

scholarly journals Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 283 ◽  
Author(s):  
Carla V. Filippi ◽  
Gabriela A. Merino ◽  
Juan F. Montecchia ◽  
Natalia C. Aguirre ◽  
Máximo Rivarola ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Genotyping By Sequencing ◽  
Optimal Number ◽  
Genomic Diversity ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
K 12

Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.

scholarly journals Genetic diversity of Jatropha curcas collections from different islands in Indonesia

2018 ◽  
Vol 16 (4) ◽  
pp. 334-342 ◽  
Author(s):  
Tantri Dyah Ayu Anggraeni ◽  
Dani Satyawan ◽  
Yang Jae Kang ◽  
Jungmin Ha ◽  
Moon Young Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Jatropha Curcas ◽  
De Novo ◽  
Genotyping By Sequencing ◽  
The Philippines ◽  
Snp Markers ◽  
Yield Traits ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Low Genetic Diversity

AbstractJatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic diversity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.

scholarly journals How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree

2020 ◽  
Author(s):  
Jordi Salmona ◽  
Axel Dresen ◽  
Anicet E. Ranaivoson ◽  
Sophie Manzi ◽  
Barbara Le Pors ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Forest Fragmentation ◽  
Forest Cover ◽  
Chloroplast Microsatellites ◽  
List Type ◽  
Sequencing Data ◽  
High Genetic Diversity ◽  
Vegetation Dynamic ◽  
Ancient Forest

AbstractUnderstanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exception in areas like the Loky-Manambato region (North) raises questions. This region also harbors a rich and endemic flora, whose evolutionary origin remains poorly understood.We assessed the genetic diversity of an endangered micro-endemic Malagasy olive species (Noronhia spinifolia) to better understand the vegetation dynamic in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR).Extremely high genetic diversity was revealed in the three genomic compartments (chloroplast h = 0.99, mitochondrial h = 0.85, and nuclear HO = 0.07-0.20). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is best explained by the current forest cover (R2 = 0.90), highlighting a long-standing forest fragmentation in the region. Our results further suggest a predominant role of forestdwelling organisms in mediating pollen and seed dispersals.This sustains a major and long-term role of riparian corridors in maintaining connectivity across those antique mosaic-habitats, calling for the study of organismal interactions that promote gene flow.

scholarly journals Genetic Diversity and Population Structure of Rhododendron canescens, a Native Azalea for Urban Landscaping

HortScience ◽  
2019 ◽  
Vol 54 (4) ◽  
pp. 647-651
Author(s):  
Lav K. Yadav ◽  
Edward V. McAssey ◽  
H. Dayton Wilde
Keyword(s):  
Genetic Diversity ◽  
Germplasm Collection ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Outcrossing Species ◽  
Genetic Structure And Diversity ◽  
Two Populations

Rhododendron canescens is a deciduous azalea native to the southeastern United States that is used in landscaping due to its ornamental qualities. A genotyping-by-sequencing (GBS) approach was taken to characterize the genetic structure and diversity of a R. canescens germplasm collection. Single nucleotide polymorphisms (SNPs) were identified by two software platforms, STACKS and GBS-SNP-CROP. Three distinct R. canescens populations were detected by STRUCTURE analysis with GBS-SNP-CROP data, whereas two populations were distinguished using STACKS data. Principal component analysis (PCA) with data from both SNP pipelines supported the presence of three populations. Statistical results indicated that there was low genetic differentiation between the populations, but relatively high genetic diversity within populations. The inbreeding coefficient of the R. canescens accessions was low, which would be expected with an outcrossing species. These results suggest that there may be a significant level of gene flow between populations of R. canescens.

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