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 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 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 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.

scholarly journals Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

2019 ◽  
Author(s):  
Xiu Yang ◽  
Ling Xi ◽  
Binwen Tan ◽  
Wei Zhu ◽  
Lili Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Common Wheat ◽  
Diversity Index ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Next Generation Sequencing Technology

Abstract Background Availability of information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N.Results In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content ranged from 0.1 to 0.4, with an average of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was higher as indicated by the Shannon’s information index ( I ) = 0.512, diversity index ( h ) = 0.334, observed heterozygosity ( H o ) = 0.226, and unbiased diversity index (uh) = 0.338.Conclusion The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.

scholarly journals Non-Mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (Humulus lupulus L.)

2016 ◽  
Author(s):  
Dong Zhang ◽  
Nicholi J. Pitra ◽  
Mark C. Coles ◽  
Edward S. Buckler ◽  
Paul D. Matthews
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Mendelian Inheritance ◽  
Snp Markers ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Population Structures ◽  
Wild Accessions

AbstractGenome-wide meiotic recombination structures, sex chromosomes, and candidate genes for sex determination were discovered among Humulus spp. by application of a novel, high-density molecular marker system: ~1.2M single nucleotide polymorphisms (SNPs) were profiled with genotyping-by-sequencing (GBS) among 4512 worldwide accessions, including 4396 cultivars and landraces and 116 wild accessions of hops. Pre-qualified GBS markers were validated by inferences on families, population structures and phylogeny. Candidate genes discovered for several traits, including sex and drought stress-resistance, demonstrate the quality and utility of GBS SNPs for genome-wide association studies (GWAS) and Fst analysis in hops. Most importantly, pseudo-testcross mappings in F1 families delineated non-random linkage of Mendelian and non-Mendelian markers: structures that are indicative of unusual meiotic events which may have driven the evolution and cultivation of hops.

scholarly journals Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 363
Author(s):  
Sulochana K. Wasala ◽  
Dana K. Howe ◽  
Louise-Marie Dandurand ◽  
Inga A. Zasada ◽  
Dee R. Denver
Keyword(s):  
Genetic Variation ◽  
Potato Production ◽  
Globodera Pallida ◽  
Fixation Index ◽  
Parasitic Nematodes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Field Samples ◽  
Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

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 Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

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