TABLE 1

Description and map location by linkage group (LG) of 18 Douglas fir candidate genes used for SNP discovery sequencing and nucleotide diversity analysis

Gene productAbbreviated gene namePotential adaptive roleExpression and position dataGene sequence coverageLGSequencesTotal sites (bp)IndelsSites excluding alignment gapsCoding sitesExonsNoncoding (introns and UTRs) sitesIntron sitesIntrons
Translation elongation factor-1, α-subunitEF1ATranslation enhancementCold induceda, colocated with QTLbPartial1271,07201,072743132900
Thiazole biosynthetic enzymeTBEDNA damage toleranceColocated with QTLcComplete1282,954152,3801,02921,6141,4301
Flavanone-3- hydroxylaseF3H1Flavonoid pathwayWater-deficit inducedd, colocated with QTLbPartial228365136426819600
Flavanone-3- hydroxylaseF3H2Flavonoid pathwayWater-deficit inducedd, colocated with QTLbPartial22864716404412206881
Formin-like protein AHF1ForminControls rearrange ments of the actin cytoskeletonColocated with QTLbPartial22833703373371000
α-tubulinAT1Microtubule cytoskeleton organization and bio genesis; cell motilityColocated and associated with wood quality related QTL and traitseComplete3282,57872,5571,35341,2041,0083
Late embryo genesis abundant type 2 dehydrin- like proteinLEA2Stress responseCold induceda, colocated with QTLbComplete4395045485249123600
Metallothionein- like proteinMT-likeDetoxification, leaf senes cence, fruit ripeningStress induced; downregulated under the water deficitd, colo cated with QTLcComplete528579256420433602022
60S ribosomal protein L31a60S-RPL31aProtein biosynthesisCold inducedafComplete528609260634022662651
Late embryo genesis abundant EMB11-like proteinLEA-EMB11Stress responsive LEA-3 proteinsStress inducedgPartial628545253226022721741
40S ribosomal protein S3a40S-RPS3aProtein biosynthesisColocated with QTLcPartial62850005001712329781
PolyubiquitinPolyUBQProtein degradation and proteolysisVirus-inducedh, colocated with QTLcComplete6278982893687120600
Early response to dehydra tion proteinERD15-likeUnknownDehydration inducedi, colocated with QTLcPartial727646164540222432031
Abscisic acid, water deficit stress and ripening- inducible proteinABA-WDSDehydrinDehydration inducedj, colocated with QTLcPartial72834403443441000
Water deficit- inducible proteinLP3-likeDehydrinDehydration inducedk, colocated with QTLcPartial738481344937211091091
4-coumarate: CoA ligase 14CL1Phenylpropa noid metabo lism, lignin and flavonoid biosynthesisDifferentially expressed in wood-forming tissuesa, colocated with wood quality- related QTLePartial11326280628566162621
4-coumarate: CoA ligase 24CL2Phenylpropanoid metabolism, lignin and flavonoid biosynthesisColocated with wood quality- related QTLePartial11386290629566163631
Ascorbate peroxidaseAPXEssential for cell protection during oxidative stressCold inducedmPartial1328867784727435733112
Mean:30843.52.7804.0478.11.7342.7221.80.9
Total:53615,1834814,4728,606316,1683,99316
  • a Thomashow (1999).

  • b Jermstad et al. (2001a,b) and Table 1 at http://dendrome.ucdavis.edu/dfgp/supplemental1.html

  • c Wheeler et al. (2005).

  • d Dubos et al. (2003).

  • e S. Brown et al. (2003, 2004b).

  • f S. B. Tyagi, A. K. Tyagi and J. P. Khurana (unpublished results; GenBank accession no. AJ272394).

  • g Dong and Dunstan (1996).

  • h Aranda et al. (1996).

  • i Kiyosue et al. (1994).

  • j Y. Pang, G. Shen, F. Tang, J. Lin, X. Sun and K. Tang (unpublished results; GenBank accession nos. AY461715 and AAR23420).

  • k Kuwabara et al. (2002).

  • l Hertzberg et al. (2001).

  • m Fowler and Thomashow (2002).