TABLE 2

Orthologous markers mapped in both Douglas fir and loblolly pine

Comparison between Douglas fir
 and loblolly pine sequences
TypeMarker mapped
 in Douglas firDouglas fir
 linkage
 groupPosition
 (cM)GenBank
 accession
 no.Orthologous marker
 mapped in loblolly pineSyntenic linkage
 group in
 loblolly pineGenBank
 accession
 no.Nucleotide identity (%)BLASTN e-value
ESTPestPpINR_RS01G05_aa127.5AL750905estPpINR_RS01G05_a in
   Pinus pinaster1AL750905NAaNAa
RFLPPtIFG_2006_ab145.1H75041H75042PtIFG_2006_A1H75041 H75042NAbNAb
ESTPestPmIFG_155H02_ac171.4CN637754estPtIFG_8537_a1AA739563891.E-107
ESTPestPmIFG_145F05_ac199.2CN637175estPtIFG_8496_a1AA739536829.E-17
ESTPestPmIFG_202H11_ac211.8CN638460estPtIFG_9022_a2AI725138931.E-160
RFLPPtIFG_2885_ab241.3NAPtIFG_2885_B2NANAbNAb
RFLPPtIFG_2356_ab3 8.3H75085PtIFG_2356_a3H75085NAbNAb
RFLPPtIFG_2988_ab337.6NAPtIFG_2988_a3NANAbNAb
RFLPPtIFG_TAM_5_ab338.2NAPtIFG_TAM_5_a3NANAbN/Ab
ESTPestPmIFG_143D03_ac365.1CN637040estPtIFG_2889_a3H75234857.E-19
ESTPestPmaLU_SB29_ad13 0.0AF051222estPmaLU_SB29_a3AF051222NSdNSd
ESTPestPtNCS_6C12F_ac1339.9AA556811estPtNCS_6C12F_a3AA55681185e3.E-30e
ESTPestPmIFG_102G09_aa4 0.0CN634675estPtNCS_2N7G_a4AA556198843.E-50
ESTPestPmIFG_200A01_ac4 6.8CN638230estPtIFG_APX4AF326783932.E-86
ESTPestPmIFG_130E12_ac427.9CN636293estPtIFG_8429_a4AA739505911.E-57
ESTPestPtIFG_6C12A_ac444.2AA556806estPtIFG_6C12A_a4AA55680693e1.E-103e
ESTPestPmIFG_137G09_ad562.6CN636731estPpINR_AN01D04_a5AL74955892f0f
RFLPPtIFG_2540_ab574.4H75131PtIFG_2540_a5H75131NAbNAb
ESTPestPmIFG_152A04_ac578.6CN637533estPtIFG_0893_a5H75118874.E-08g
ESTPestPmIFG_111F09_ac68.4CN635180estPtIFG_8531_a6AA739558823.E-57
ESTPestPmIFG_144D01_ac610.5CN637093estPt_8647_a6AA739625951.E-22
ESTPestPmIFG_014A07_aa663.8CN634509estPtIFG_8473_a6AA739526847.E-16
ESTPestPtIFG_0739_ac664.2H75167 H75168estPtIFG_0739_a6H75167 H7516892e1.E-22e
RFLPPmIFG_1545_a664.4AA701802 H75180PtIFG_1165_a6AA701802 H7518086h1.E-10h
ESTPestPmaLU_SB42_aa680.3AF051232estPmaLU_SB42_a
   in Picea abies6AF051232NAaNAa
ESTPestPmIFG_109F09_ac682.5CN635076estPtIFG_1950_a6H75126843.E-11
ESTPestPmIFG_113C11_ac696.8CN635266estPtIFG_8564_a6AA739580955.E-55
ESTPestPmIFG_101B05_ac6104.3CN634590estPtIFG_9044_a6AA739876941.E-115
ESTPestPmIFG_201D12_ac6127.8CN638348estPtFR_LP15_a6AF013803829.E-25
ESTPestPtNCS_ctg3_ac6137.0AF036095estPtNCS_CCoAOMT_a=
   estPtNCS_ctg3_a6AF03609583e2.E-26e
RFLPPtIFG_2703_a
   (=PtIFG_2707_A)b763.1H75113 H75227 H75228PtIFG_2707_A
   (=PtIFG_2703_a)b7H75113 H75227 H75228NAbNAb
STSstsPmCAS_4CL2_ac 790.5AF144507estPtIFG_4CL_a7U12012 U39405881.E-173
STSstsPmCAS_4CL1_ac 792.7AF144506 AF144508estPtIFG_4CL_a7U12012 U39405871.E-166
RFLPPtIFG_2957_ab 8 5.3NAPtIFG_2957_a8NANAbNAb
RFLPPtIFG_2553_ab 842.9H75210PtIFG_2553_a8H75210NAbNAb
ESTPestPtIFG_8732_ac 847.3AA739680estPtIFG_8732_a8AA73968090e7.E-19e
ESTPestPaTUM_PA0053_aa 870.5AJ132535estPaTUM_PA0053_a
   in Picea abies8AJ132535NAaNAa
STSstsPmCAS_CAD_ac 922.7AF145985AF145986estPtNCS_ptCadA_a9Z37991902.E-92
ESTPestPmIFG_136B01_ac 949.4CN636620estPtIFG_500_a9H75151862.E-51
ESTPestPmIFG_141H03_ac11 0.0CN636962PtIFG_2899_a9H75245952.E-71
ESTPestPtIFG_2290_ba1128.8H75067estPtIFG_2290_a9H75067NAaNAa
ESTPestPmIFG_202A06_ac1072.8CN638390estPtIFG_8436_a10AA739508932.E-87
RFLPPtIFG_2025_ab1088.8H75045H75046PtIFG_2025_a10H75045H75046NAbNAb
ESTPestPmaLU_SB21_ad10103.0AF051216estPmaLU_SB21_a
   in Picea abies10AF051216NSdNSd
ESTPestPmIFG_115B07_ac10118.2CN635370estPtIFG_4CH-2_a10AF096998893.E-52
ESTPestPmIFG_128D06_ac10131.1CN636156estPtIFG_8580_a10AA739590871.E-22
  • a Direct sequencing of the PCR product was not applicable (NA) to these markers because their PCR pattern included additional background bands amplified. Those additional bands were mostly light, but they usually interfere with sequencing and produce unreadable sequence runs. However, all of these markers were mapped also as orthologs in several other species, supporting their orthology in Douglas fir.

  • b Nucleotide identity and e-values were not available (NA) for the RFLP markers because Douglas fir genomic DNA, which hybridized with the loblolly pine cDNA probes, was not sequenced.

  • c The identity of the ESTP marker to the corresponding EST sequence, which was used to design primers, was confirmed by sequencing the PCR product amplified in Douglas fir.

  • d The PCR product, which was amplified in Douglas fir for these markers, was not sequenced (NS), but all of these markers were mapped also as orthologs in several other species, supporting their orthology in Douglas fir.

  • e The values are based on comparison between the sequence of the PCR product amplified in Douglas fir and the EST sequence of the ESTP marker mapped in loblolly pine using the same PCR primers.

  • f Comparison was done between the maritime pine (Pinus pinaster) cDNA clone AN01D04 sequence and the Douglas fir contig sequence that included the EST sequence of the cDNA clone 137G09.

  • g The e-value was unsatisfactory because the Douglas fir EST sequence was very short and contained only partial coding sequence. However, the similarity between this partial coding region and loblolly pine counterpart was relatively high at the amino acid level (93%) and qualified this ESTP marker as a potential ortholog.

  • h Based on comparison between PmIFG_1545 (AA701802) and PtIFG_1165 (H75180) cDNA orthologous sequences.