scholarly journals Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1185
Author(s):  
Helena Eklöf ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Picea Abies ◽  
Norway Spruce ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Complexity Reduction ◽  
Exome Capture ◽  
Genome Wide ◽  
Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation inNothofagus dombeyi(Mirb.) Oerst. in Chile

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Rodrigo Hasbún ◽  
Jorge González ◽  
Carolina Iturra ◽  
Glenda Fuentes ◽  
Diego Alarcón ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Woody Species ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Diversity Studies ◽  
Nothofagus Dombeyi

Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation.Nothofagus dombeyi(Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories inNothofagus dombeyirequires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species.

scholarly journals Population-level genome-wide STR typing in Plasmodium species reveals higher resolution population structure and genetic diversity relative to SNP typing

2021 ◽  
Author(s):  
Jiru Han ◽  
Jacob E Munro ◽  
Anthony Kocoski ◽  
Alyssa E Barry ◽  
Melanie Bahlo
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Tandem Repeats ◽  
Plasmodium Species ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Wide ◽  
Field Samples

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been made available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

2018 ◽  
Author(s):  
Marco A. Escalante ◽  
Charles Perrier ◽  
Francisco J. García-De León ◽  
Arturo Ruiz-Luna ◽  
Enrique Ortega-Abboud ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Local Adaptation ◽  
Population Genomics ◽  
Landscape Heterogeneity ◽  
Genotyping By Sequencing ◽  
Anthropogenic Factors ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Potential

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

scholarly journals Genetic differentiation of Norway spruce (Picea abies (L.) Karst.) trees with diferent crown types from the mountain Golija

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 849-861 ◽  
Author(s):  
Vladislava Galovic ◽  
Mirjana Sijacic-Nikolic ◽  
Robert Safhauzer ◽  
Dijana Cortan ◽  
Sasa Orlovic
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Picea Abies ◽  
Genetic Differentiation ◽  
Norway Spruce ◽  
Plant Species ◽  
Genetic Characterization ◽  
Similarity Matrix ◽  
Primer Sets

The knowledge of genetic diversity degree of given species is of great importance for the successful process of breeding and genetic conservation. The aim of conducted research was to determine the genetic differentiation of Norway spruce (Picea abies (L.) Karst) genotypes with very specific narrow pyramidal and normal crown type, which grows at different altitude of the mountain Golija. For assessment of genetic similarities or differences between studied genotypes co-dominant microsatellite system had been used. This system has proven to be reliable and efficient in the genetic characterization of plant species. In total 22 primer sets have been tested, while 16 (73%) of them resulted in the successful yield of the amplified product. The analysis show that studied individuals had in total 130 alleles, in average 8.125 polymorphic alleles per each locus. The lowest polymorphism was detected in the locus EATC1D10, EATC1F03B and EATC2G09, while the highest level of polymorphism was detected in EATC2G08. Based on microsatellite date and similarity matrix, cluster analysis dendrogram indicates existence of the vertical differentiation of studied genotypes, which is consistent with results of previous Norway spruce studies.

scholarly journals Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1511
Author(s):  
Xue Gong ◽  
Aihong Yang ◽  
Zhaoxiang Wu ◽  
Caihui Chen ◽  
Huihu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Japanese Population ◽  
Eastern China ◽  
Genotyping By Sequencing ◽  
Central China ◽  
Western China ◽  
Cinnamomum Camphora ◽  
Ecological Value ◽  
Genome Wide

Cinnamomum camphora (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of C. camphora trees have resulted in the shrinking of wild population sizes and rare germplasm resources. In this study, we characterized 171 C. camphora trees from 39 natural populations distributed throughout the whole of China and one Japanese population. We investigated genetic diversity and population structure using genome-wide single-nucleotide polymorphism (SNP) identified by genotyping by sequencing (GBS) technology. The results showed the genetic diversity of the C. camphora populations from western China > central China > eastern China. Moreover, the Japanese population showed the highest diversity among all populations. The molecular variance analysis showed 92.03% of the genetic variation within populations. The average pairwise FST was 0.099, and gene flow Nm was 2.718, suggesting a low genetic differentiation among populations. Based on the genetic clustering analysis, the 40 C. camphora populations clustered into three major groups: Western China, Central China, and Eastern China + Japan. Eastern China’s population had the closest genetic relationship with the Japanese population, suggesting possible gene exchange between the two adjacent areas. This study furthers our understanding of the genetic diversity and genetic structure of C. camphora in East Asia and provides genetic tools for developing strategies of C. camphora germplasm utilization.

scholarly journals Comparative analysis of genetic diversity in Norway spruce (Picea abies) clonal seed orchards and seed stands

2021 ◽  
Vol 49 (4) ◽  
pp. 12575
Author(s):  
Elena CIOCÎRLAN ◽  
Neculae ȘOFLETEA ◽  
Georgeta MIHAI ◽  
Maria TEODOSIU ◽  
Alexandru L. CURTU
Keyword(s):  
Genetic Diversity ◽  
Comparative Analysis ◽  
Picea Abies ◽  
Norway Spruce ◽  
Allelic Richness ◽  
Conifer Species ◽  
Seed Orchards ◽  
Eastern Carpathians ◽  
Nuclear Microsatellite ◽  
Planted Tree

Norway spruce, Picea abies (L.) Karst. is the most important conifer species in Romania and the most planted tree species in the Carpathian Mountains. Here we compare the genetic diversity of four Norway spruce clonal seed orchards and two seed stands located in the Eastern Carpathians. A set of highly polymorphic nuclear microsatellite markers was used. The analysis of genotypic identity of ramets for each Norway spruce clone in all seed orchards indicated that nearly all sampled ramets (97%) were genetically identical. The genetic diversity in seed orchards (He=0.700) was slightly smaller compared to the seed stands (He=0.718). Allelic richness was higher in seed stands (10.874), compared to clonal seed orchards (8.941). The Bayesian analysis indicated a genetic structure with two clusters, one corresponding to the clonal seed orchards and a second one consisting of the two seed stands. Our results provide valuable information for the management of Norway spruce seed orchards in Romania.

scholarly journals Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

2021 ◽  
Author(s):  
Dong Cao ◽  
Dongxia Wang ◽  
Shiming Li ◽  
Yun Li ◽  
Ming Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Energy Crop ◽  
Hexaploid Triticale ◽  
Genome Wide ◽  
Genetic Mechanisms

Abstract Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

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