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Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology
Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, POB 7043, S-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, POB 7043, S-75007 Uppsala, Sweden..
Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, POB 7043, S-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, POB 7043, S-75007 Uppsala, Sweden..
Rothamsted Res, Computat & Syst Biol Dept, Harpenden AL5 2JQ, Herts, England..
Rothamsted Res, AgroEcol Dept, Harpenden AL5 2JQ, Herts, England..
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2016 (English)In: Global Change Biology Bioenergy, ISSN 1757-1693, E-ISSN 1757-1707, Vol. 8, no 3, 670-685 p.Article in journal (Refereed) PublishedText
Abstract [en]

Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnas, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (GxE) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR<0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small estimates and to considerable GxE interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).

Place, publisher, year, edition, pages
2016. Vol. 8, no 3, 670-685 p.
Keyword [en]
adaptation, association mapping, candidate gene, growth, marker-assisted selection, phenology, Salix, short-rotation coppice, willow
National Category
Wood Science Bioenergy
URN: urn:nbn:se:uu:diva-300297DOI: 10.1111/gcbb.12280ISI: 000374060500013OAI: oai:DiVA.org:uu-300297DiVA: diva2:951319
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Energy Agency, 31468-1;30599-2
Available from: 2016-08-08 Created: 2016-08-08 Last updated: 2016-08-08Bibliographically approved

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Lagercrantz, Ulf
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