A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

Isabel, Nathalie; Lamothe, Manuel; Thompson, Stacey Lee

doi:10.1007/s11295-012-0569-5

Cited by 28 publications

(24 citation statements)

References 21 publications

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“…In poplar, SNPs are mostly species‐specific (Isabel et al . ) and thus the already available Populus trichocarpa genome sequence could not be used directly as a reference to detect SNPs in P. nigra . Nevertheless, we were able to use it as a template to map the short reads from P. nigra to obtain a black poplar genome reference sequence.…”

Section: Discussionmentioning

confidence: 99%

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Faivre-Rampant

Zaina

Jorge

et al. 2016

Molecular Ecology Resources

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Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.

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Section: Discussionmentioning

confidence: 99%

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Faivre-Rampant

Zaina

Jorge

et al. 2016

Molecular Ecology Resources

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“…We typed each sample using an array of 36 diagnostic SNP markers (Isabel et al 2013). This SNP array allowed simultaneous detection of eight poplar species: P. angustifolia James, P. balsamifera , P. deltoides , P. fremontii Watson, P. laurifolia Ledeb., P. maximowiczii Henry, P. nigra L., and P. trichocarpa Torr.…”

Section: Methodsmentioning

confidence: 99%

Fitness dynamics within a poplar hybrid zone: I.Prezygotic and postzygotic barriers impacting a native poplar hybrid stand

Roe

MacQuarrie

Gros‐Louis

et al. 2014

Ecology and Evolution

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Hybridization and introgression are pervasive evolutionary phenomena that provide insight into the selective forces that maintain species boundaries, permit gene flow, and control the direction of evolutionary change. Poplar trees (Populus L.) are well known for their ability to form viable hybrids and maintain their distinct species boundaries despite this interspecific gene flow. We sought to quantify the hybridization dynamics and postzygotic fitness within a hybrid stand of balsam poplar (Populus balsamifera L.), eastern cottonwood (P. deltoides Marsh.), and their natural hybrids to gain insight into the barriers maintaining this stable hybrid zone. We observed asymmetrical hybrid formation with P. deltoides acting as the seed parent, but with subsequent introgression biased toward P. balsamifera. Native hybrids expressed fitness traits intermediate to the parental species and were not universally unfit. That said, native hybrid seedlings were absent from the seedling population, which may indicate additional selective pressures controlling their recruitment. It is imperative that we understand the selective forces maintaining this native hybrid zone in order to quantify the impact of exotic poplar hybrids on this native system.

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“…Nuclear SNP markers were developed from DNA sequences obtained for 14 provenances/individuals covering the natural species range of Populus balsamifera from New Brunswick to Alaska (Isabel et al, 2013). For cross-validation and to make sure that primers would work in both species, three individuals of P. trichocarpa were also included.…”

Section: Nuclear Snp Developmentmentioning

confidence: 99%

“…Libraries were then sequenced 2 9 100 bp on three lanes of an Illumina Genome Analyzer II (GAII) using the Solexa clonal single molecule array (CSMA) technology according to their internal protocols. The species designation of the included individuals was previously validated with an assay of 36 interspecific SNPs (Isabel et al, 2013). DNA concentration of the individual extractions used in pools was evaluated on a NanoDrop 8000 (Thermo Scientific, Wilmington, DE, USA).…”

Section: Chloroplast Snp Developmentmentioning

confidence: 99%

History rather than hybridization determines population structure and adaptation in Populus balsamifera

Meirmans

Godbout

Lamothe

et al. 2017

J of Evolutionary Biology

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Hybridization between species is known to greatly affect their genetic diversity and, therefore, their evolution. Also, within species, there may be genetic clusters between which gene flow is limited, which may impact natural selection. However, few studies have looked simultaneously at the influence of among-species and within-species gene flow. Here, we study the influence of hybridization between Populus balsamifera and Populus trichocarpa on population structure and adaptation in P. balsamifera. We did this by sampling a total of 1517 individuals from across the ranges of these two species, and by genotyping them using a combination of 93 nuclear and 17 cpDNA SNPs. We found that hybridization is mostly limited to the contact zone where the species' distributions overlap. Within P. balsamifera, we found multiple levels of population structure. Interestingly, the border between the Eastern and Central clusters is very sharp, whereas the border between the Central and Western clusters is diffuse. Outlier analysis revealed that three loci associated with the sharp border were also associated with climate. We hypothesize that the observed clusters derive from three refugia during the Pleistocene ice ages. Between the Central and Western clusters, post-glacial long-distance gene flow has led to the diffusion of their border. In the Eastern cluster, we hypothesize that endogenous genomic barriers have developed, leading to the sharp border and a spurious climate association. We conclude that the large-scale genetic structure of P. balsamifera is mostly shaped by historical factors and the influence of interspecific hybridization is limited.

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A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

Cited by 28 publications

References 21 publications

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Fitness dynamics within a poplar hybrid zone: I.Prezygotic and postzygotic barriers impacting a native poplar hybrid stand

History rather than hybridization determines population structure and adaptation in Populus balsamifera

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