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Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)
Bousquet, Jean; Pavy, Nathalie; Gagnon, France; Deschênes, Astrid; Boyle, Brian; Beaulieu, Jean — 2015-09-17 Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97 075 highly reliable in silico SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2%, for in silico SNPs compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
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High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers
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Tumas, Hayley; Ilska, Joanna J.; Gérardi, Sebastien; Laroche, Jerome; A'Hara, Stuart; Boyle, Brian; Janes, Mateja; McLean, Paul; Lopez, Gustavo; Lee, Steve J.; Cottrell, Joan; Gorjanc, Gregor; Bousquet, Jean; Wolliams, John A.; Mackay, John J. — 2024-01-19 <p class="paragraph" style="line-height:150%;vertical-align:baseline;"><span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;">In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, </span><span class="normaltextrun"><span lang="EN-GB" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;">we developed a linkage map relying on 21,570 SNP makers in </span></span><span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;">Sitka spruce (<em>Picea sitchensis</em> [Bong.] Carr.)</span><span class="normaltextrun"><em><span lang="EN-GB" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;">, </span></em></span><span class="normaltextrun"><span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;">a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. </span></span><span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;">We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for <em>P. sitchensis</em> and <em>P. glauca</em> based on 27,052 makers and 11,609 gene sequences. Altogether, these two linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed herein opens new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.</span></p>
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Data from: Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs
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Cinget, Benjamin; de Lafontaine, Guillaume; Gérardi, Sébastien; Bousquet, Jean — 2015-04-09 Secondary contact between closely related taxa routinely occurs during postglacial migrations. After initial contact, the location of hybrid zones may shift geographically or remain spatially stable over time in response to various selective pressures or neutral processes. Studying the extent and direction of introgression using markers having contrasted levels of gene flow can help unravel the historical dynamics of hybrid zones. Thanks to their contrasted maternal and paternal inheritance, resulting in different levels of gene flow for mitochondrial and chloroplast DNA (mtDNA and cpDNA), the Pinaceae stand out as a relevant biological model for this purpose. The objective of the study was to assess whether the hybrid zone between Abies balsamea and Abies lasiocarpa (two largely distributed Pinaceae) has moved or remained stable over time by analysing the distribution of cytoplasmic DNA variation as well as published palaeobotanical data. Interspecific gene flow was higher for cpDNA than mtDNA markers; hence, the geographic distribution of mitotypes was more congruent with species distributions than chlorotypes. This genetic signature was contrary to expectations under a moving hybrid zone scenario, as well as empirical observations in other conifers. Genetic evidence for this rare instance of stable hybrid zone was corroborated by the colonization chronology derived from published fossil data, indicating that the two fir species initially came into contact in the area corresponding to the current sympatric zone 11 kyr ago. While an explanatory analysis suggested the putative influence of various environmental factors on the relative abundance of cytoplasmic genome combinations, further research appears necessary to assess the role of both demographic history and selective factors in driving the dynamics of hybrid zones.
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Data from: Inbreeding depression in intra-provenance crosses driven by founder relatedness in white spruce
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Doerksen, Trevor K.; Bousquet, Jean; Beaulieu, Jean — 2014-10-07 Genetic means for height growth differed between intra- and inter-provenance crosses, which we hypothesized was due partly to unidentified relatedness among intra-provenance base parents resulting in mild inbreeding and inbreeding depression among their offspring. A dense array of 5,844 single nucleotide polymorphisms was used to directly construct a genomic relationship matrix (G) that had four elements ranging from 0.17 to 0.24, between five intra-provenance base parents. Adjusting the numerator relationship matrix for this relatedness among base parents produced inbreeding coefficients of F i ≈ 0.1 in their offspring, which displayed depressed height growth. Accounting for inbreeding level as a covariate in a mixed model decreased grossly overestimated (up to 2 ×) dominance variance in models without the covariate adjustment. Height growth decreased 39 cm (∼ 6 %) for every 0.1 increase in F i .
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Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce
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Namroud, Marie-Claire; Bousquet, Jean; Doerksen, Trevor; Beaulieu, Jean — 2012-01-03 A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709 expressed genes was used to assess the potential impact of artificial selection for height growth on the genetic diversity of white spruce. Two case populations of different sizes simulating different family selection intensities (K = 13% and 5%, respectively) were delineated from the Quebec breeding program. Their genetic diversity and allele frequencies were compared with those of control populations of the same size and geographic origin to assess the effect of increasing the selection intensity. The two control populations were also compared to assess the effect of reducing the sampling size. On one hand, in all pairwise comparisons, genetic diversity parameters were comparable and no alleles were lost in the case populations compared with the control ones, except for few rare alleles in the large case population. Also, the distribution of allele frequencies did not change significantly (P ≤ 0.05) between the populations compared, but ten and nine SNPs (0.8%) exhibited significant differences in frequency (P ≤ 0.01) between case and control populations of large and small sizes, respectively. Results of association tests between breeding values for height at 15 years of age and these SNPs supported the hypothesis of a potential effect of selection on the genes harboring these SNPs. On the other hand, contrary to expectations, there was no evidence that selection induced an increase in linkage disequilibrium in genes potentially affected by selection. These results indicate that neither the reduction in the sampling size nor the increase in selection intensity was sufficient to induce a significant change in the genetic diversity of the selected populations. Apparently, no loci were under strong selection pressure, confirming that the genetic control of height growth in white spruce involves many genes with small effects. Hence, selection for height growth at the present intensities did not appear to compromise background genetic diversity but, as predicted by theory, effects were detected at a few gene SNPs harboring intermediate allele frequencies.
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Genes involved in the constitutive production of phenolic compounds in white spruce
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Gérardi, Sébastien; Laoué, Justine; Depardieu, Claire; Lamothe, Manuel; Bomal, Claude; Azaiez, Aïda; Gros-Louis, Marie-Claude; Laroche, Jerôme; Boyle, Brian; Hammerbacher, Almuth; Isabel, Nathalie; Bousquet, Jean — 2021-05-13 <p>Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (<em>Picea glauca</em>) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.</p>
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Additional file 1 of Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce
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Hung, Tin Hang; Wu, Ernest T. Y.; Zeltiņš, Pauls; Jansons, Āris; Aziz Ullah, .; Erbilgin, Nadir; Bohlmann, Joerg; Bousquet, Jean; Birol, Inanç; Clegg, Sonya M.; MacKay, John J. — 2024 Additional file 1. Supplementary Table 1. Provenances of the samples analysed in this study for P. abies and P. glauca. Supplementary Table 2. Details of the genomic regions targeted by the sequence capture bait set Picea_hung_p1.0. Supplementary Figure 1. Alignment rates of the probe set Picea_hung_p1.0 on the reference genomes of 5Picea species. Supplementary Table 3. Statistics of local genome assembly, transcriptome assembly, and gene models ofP. abies and P. glauca. Supplementary Figure 2. Syntenic relationship of 7 complete or near-complete Pgβglu-1 gene forms in P. glauca with the reference Pgβglu-1 gene model (KJ780719.1). Supplementary Figure 3. Phylogenetic tree of 139 βglu-1-like gene models in the local assemblies of P. abies (red tips) and P. glauca (blue tips) and their protein multiple sequence alignment. The bold tip labels denote the complete and near-complete gene forms ofβglu-1. Supplementary Table 4. Details of the high-confidence single-copy genes shared by P. abies andP. glauca. Supplementary Table 5. Analysis of variance (ANOVA) table of the total copy number of Paβglu-1 in P. abies. Supplementary Table 6. Analysis of variance (ANOVA) table of the total copy number of Pgβglu-1 in P. glauca. Supplementary Figure 4. (a) Standard curve of Pgβglu-1 synthetic oligomer. (b) Copy number of Pgβglu-1 in P. glauca across their provenances estimated by qPCR. The error bar shows mean± 1 standard error. Supplementary Table 7. TukeyHSD pairwise comparison table of the total copy number of Pgβglu-1 in P. glauca estimated with sequence analysis. Supplementary Table 8. TukeyHSD pairwise comparison table of the total copy number of Pgβglu-1 in P. glauca estimated with qPCR. Supplementary Table 9. Analysis of variance (ANOVA) table of the total copy number of PaUgt5b in P. abies. Supplementary Table 10. Analysis of variance (ANOVA) table of the total copy number of PgUgt5 in P. glauca. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 2 of Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce
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Hung, Tin Hang; Wu, Ernest T. Y.; Zeltiņš, Pauls; Jansons, Āris; Aziz Ullah, .; Erbilgin, Nadir; Bohlmann, Joerg; Bousquet, Jean; Birol, Inanç; Clegg, Sonya M.; MacKay, John J. — 2024 Additional file 2. Supplementary Data 1. Probe sequences of Picea_hung_p1.0. https://creativecommons.org/licenses/by/4.0/legalcode

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(auteur : Bousquet, Jean)

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