QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments
department or school: Forest Sciences, Department of
department or school: Forestry, Faculty of
department or school: Non UBC
data provider: DSpace
identifier citation: BMC Genomics. 2011 Mar 10;12(1):145
rights copyright: Betty et al; licensee BioMed Central Ltd.
creator: Pelgas, Betty
creator: Bousquet, Jean
creator: Meirmans, Patrick G
creator: Ritland, Kermit
creator: Isabel, Nathalie
issued: 2016-01-28T22:48:46Z
issued: 2011-03-10
description: Background: The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results: Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions: This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/56770
note: RESEARCH ARTICLE Open AccessQTL mapping in white spruce: gene maps andgenomic regions underlying adaptive traits acrosspedigrees, years and environmentsBetty Pelgas1,2*, Jean Bousquet2, Patrick G Meirmans1,3, Kermit Ritland4, Nathalie Isabel1,2AbstractBackground: The genomic architecture of bud phenology and height growth remains poorly known in mostforest trees. In non model species, QTL studies have shown limited application because most often QTL data couldnot be validated from one experiment to another. The aim of our study was to overcome this limitation by basingQTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs acrosspedigrees, years, and environments.Results: Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtainedusing a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers.For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 forbud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11,13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealedspatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted,indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were alsounderlined by recent genome scans or expression profile studies.Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance couldbe accounted for by QTLs for bud flush or bud set, and up to 59% for height growth.Conclusions: This study…
has type: Article
is shown at: 10.14288/1.0228122
language: eng
peer review status: Reviewed
provider: Vancouver : University of British Columbia Library
publisher: BioMed Central
publisher DOI: 10.1186/1471-2164-12-145
rights: Attribution 4.0 International (CC BY 4.0)
rights URI: http://creativecommons.org/licenses/by/4.0/
scholar level: Faculty
type: Text
identifier URI: http://hdl.handle.net/2429/56770