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The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce.

ABSTRACT: BACKGROUND: The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing. RESULTS: A genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years. CONCLUSIONS: The sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree's life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers.

SUBMITTER: Prunier J

PROVIDER: S-EPMC3674900 | biostudies-other | 2013

REPOSITORIES: biostudies-other

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The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce.

Prunier Julien J Pelgas Betty B Gagnon France F Desponts Mireille M Isabel Nathalie N Beaulieu Jean J Bousquet Jean J

BMC genomics 20130601

<h4>Background</h4>The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gen ...[more]

PMID: 23724860

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Project description:BackgroundBlack spruce (Picea mariana (Mill.) BSP)-forested peatlands are widespread ecosystems in boreal North America in which peat accumulation, known as the paludification process, has been shown to induce forest growth decline. The continuously evolving environmental conditions (e.g., water table rise, increasing peat thickness) in paludified forests may require tree growth mechanism adjustments over time. In this study, we investigate tree ecophysiological mechanisms along a paludification gradient in a boreal forested peatland of eastern Canada by combining peat-based and tree-ring analyses. Carbon and oxygen stable isotopes in tree rings are used to document changes in carbon assimilation rates, stomatal conductance, and water use efficiency. In addition, paleohydrological analyses are performed to evaluate the dynamical ecophysiological adjustments of black spruce trees to site-specific water table variations.ResultsIncreasing peat accumulation considerably impacts forest growth, but no significant differences in tree water use efficiency (iWUE) are found between the study sites. Tree-ring isotopic analysis indicates no iWUE decrease over the last 100 years, but rather an important increase at each site up to the 1980s, before iWUE stabilized. Surprisingly, inferred basal area increments do not reflect such trends. Therefore, iWUE variations do not reflect tree ecophysiological adjustments required by changes in growing conditions. Local water table variations induce no changes in ecophysiological mechanisms, but a synchronous shift in iWUE is observed at all sites in the mid-1980s.ConclusionsOur study shows that paludification induces black spruce growth decline without altering tree water use efficiency in boreal forested peatlands. These findings highlight that failing to account for paludification-related carbon use and allocation could result in the overestimation of aboveground biomass production in paludified sites. Further research on carbon allocation strategies is of utmost importance to understand the carbon sink capacity of these widespread ecosystems in the context of climate change, and to make appropriate forest management decisions in the boreal biome.Supplementary informationThe online version contains supplementary material available at 10.1186/s40663-021-00307-x.

Project description:BACKGROUND: EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change. RESULTS: We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified. CONCLUSIONS: We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and ecological traits. We have also identified full-length genes and microsatellite-containing ESTs. Based on EST sequence similarities, black spruce showed close evolutionary relationships with congeneric Picea glauca and Picea sitchensis compared to other Pinaceae members and angiosperms. The EST sequences reported here provide an important resource for genome annotation, functional and comparative genomics, molecular breeding, conservation and management studies and applications in black spruce and related conifer species.

Dataset Information

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce.

Publications

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce.

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