Double-digest RAD-sequencing: do wet and dry protocol parameters impact biological results?

Cumer, Tristan; Pouchon, Charles; Boyer, Frédéric; Yannic, Glenn; Rioux, Delphine; Bonin, Aurélie; Capblancq, Thibaut

doi:10.1101/445122

Cited by 8 publications

(7 citation statements)

References 58 publications

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“…Using the ProcessMyRAD scripts (https://github.com/cumtr/PmR, Cumer et al, 2018), we also produced graphical outputs at the filtering step of the treatment, which allowed an evaluation of the experimental success for each individual. This method provides the proportion of retained reads after the first step of filtering, the number of reads by individuals, the quality of the sequencing and the proportion of the different nucleotides along the reads.…”

Section: Methodsmentioning

confidence: 99%

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Capblancq

Morin

Guéguen

et al. 2020

J of Evolutionary Biology

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Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could impede the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a double‐digest restriction‐site‐associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)‐derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north‐western and south‐eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for F. sylvatica in the Alps, which could be helpful for future management plans.

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Section: Methodsmentioning

confidence: 99%

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Capblancq

Morin

Guéguen

et al. 2020

J of Evolutionary Biology

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“…Using the ProcessMyRAD scripts (https://github.com/cumtr/PmR, Cumer et al . 2018), we also produced graphical outputs at the filtering step of the treatment, which allowed an evaluation of the experimental success for each library and individual.…”

Section: Methodsmentioning

confidence: 99%

Climate associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Capblancq

Morin

Guéguen

et al. 2019

Preprint

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1 Local adaptation patterns have been found in many plants and animals, 2 highlighting the genetic heterogeneity of species along their range of distribution. 3 In the next decades, global warming must induce a change in the selective 4 pressures that drive this adaptive variation, forcing a reshuffling of the 5 underlying adaptive allele distributions. For species with low dispersion capacity 6 and long generation time such as trees, the rapidity of the change could imped the 7 migration of beneficial alleles and lower their capacity to track the changing 8 environment. Identifying the main selective pressures driving the adaptive 9 genetic variation is thus necessary when investigating species capacity to 10 respond to global warming. In this study, we investigate the adaptive landscape 11 of Fagus sylvatica along a gradient of populations in the French Alps. Using a 12 ddRAD-seq approach, we identified 7,000 SNPs from 570 individuals across 36 13 different sites. An RDA-derived method allowed us to identify several SNPs that 14 were strongly associated with climatic gradients; moreover, we defined the 15 primary selective gradients along the natural populations of F. sylvatica in the 16 Alps. Strong effects of elevation and humidity, which contrast north-western and 17 south-eastern site, were found and were believed to be important drivers of 18 genetic adaptation. Finally, simulations of future genetic landscapes that used 19 these findings predicted a severe range contraction and a shift towards higher 20 altitudes for F. sylvatica in the Alps and allowed to identify populations at risk, 21 which could be helpful for future management plans. 22 23

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“…NGS is particularly sensitive to low DNA quality, and vulnerable to errors which can emerge during the library preparation [71,72]. Our results suggest that laboratory errors can lead to genomic region/marker dropout, as in the case of our RADseq dataset, despite a satisfying number of reads per sample.…”

Section: Discussionmentioning

confidence: 75%

Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Ulaszewski

Meger

Burczyk

2021

Forests

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Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

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Double-digest RAD-sequencing: do wet and dry protocol parameters impact biological results?

Cited by 8 publications

References 58 publications

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Climate associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

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