Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology

A - Papers appearing in refereed journals

Hallingbäck, H. R., Fogelqvist, J., Powers, S. J., Turrion-Gomez, J., Rossiter, R., Amey, J., Martin, T., Weih, M., Gyllenstrand, N., Karp, A., Lagercrantz, U., Hanley, S. J., Berlin, S. and Rönnberg-Wästljung, A-C. 2016. Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology. GCB Bioenergy. 8 (3), pp. 670-685.

AuthorsHallingbäck, H. R., Fogelqvist, J., Powers, S. J., Turrion-Gomez, J., Rossiter, R., Amey, J., Martin, T., Weih, M., Gyllenstrand, N., Karp, A., Lagercrantz, U., Hanley, S. J., Berlin, S. and Rönnberg-Wästljung, A-C.
Abstract

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).

KeywordsAgronomy; Biotechnology & Applied Microbiology; Energy & Fuels
Year of Publication2016
JournalGCB Bioenergy
Journal citation8 (3), pp. 670-685
Digital Object Identifier (DOI)doi:10.1111/gcbb.12280
PubMed ID27547245
PubMed Central IDPMC4973673
Open accessPublished as ‘gold’ (paid) open access
FunderSwedish Research Council (VR)
Knut and Alice Wallenberg foundation
Swedish Energy Agency - EPA Sweden
SAMBA2 grant from the Swedish Energy Agency
NL faculty at the Swedish University of Agricultural Sciences
Biotechnology and Biological Sciences Research Council
Funder project or codeTowards targeted breeding of a European SRC willow crop for diverse environments and future climates (BREDNET-SRC)
Publisher's version
Output statusPublished
Publication dates
Online25 Apr 2015
Publication process dates
Accepted14 Mar 2015
Copyright licenseCC BY
PublisherWiley
ISSN1757-1693

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