Supplementary TABLE1

165 differentially expressed genes in both wild populations relative to one or more weedy populations

EST ID# / Ara_hits / Brief functional description
QHA10I23.yg.ab1 / no_hits_found
QHA11F24.yg.ab1 / no_hits_found
QHA11L02.yg.ab1 / At5g02380 / metallothionein 2b
QHA12E07.yg.ab1 / no_hits_found
QHA12O20.yg.ab1 / no_hits_found
QHA14C04.yg.ab1 / no_hits_found
QHA14P24.yg.ab1 / At2g33830 / auxin-regulated protein
QHA16C07.yg.ab1 / At4g11650 / osmotin-like protein (OSM34)
QHA17I10.yg.ab1 / At4g21960 / peroxidase, putative
QHA18A23.yg.ab1 / no_hits_found
QHA19P03.yg.ab1 / At3g51030 / thioredoxin H-type 1 (TRX-H-1)
QHA20C23.yg.ab1 / At1g20440 / dehydrin (COR47)
QHA20H10.yg.ab1 / At5g59320 / lipid transfer protein 3 (LTP 3)
QHA8E05.yg.ab1 / no_hits_found
QHA8E07.yg.ab1 / no_hits_found
QHA8E23.yg.ab1 / At1g76180 / dehydrin -related
QHB10K08.yg.ab1 / At3g17210 / expressed protein
QHB11H07.yg.ab1 / At4g30950 / omega-6 fatty acid desaturase, chloroplast (FAD6) (fadC) (delta-12 desaturase)
QHB11I13.yg.ab1 / At4g21990 / 5'-adenylylsulfate reductase (APR3)
QHB12I01.yg.ab1 / At3g28050 / nodulin MtN21 family protein
QHB12P07.yg.ab1 / no_hits_found
QHB13M17.yg.ab1 / At5g56030 / heat shock protein 81-2 (HSP81-2)
QHB13P01.yg.ab1 / At4g38040 / Exostosin family
QHB18M23.yg.ab1 / At2g02450 / No apical meristem (NAM) protein family
QHB19O09.yg.ab1 / At1g78510 / geranyl diphosphate synthase (GPPS)(dimethylallyltransferase), putative
QHB1h05.yg.ab1 / At1g75080 / expressed protein
QHB20C10.yg.ab1 / At3g09830 / protein kinase, putative
QHB21B24.yg.ab1 / At4g12130 / expressed protein
QHB23A11.yg.ab1 / no_hits_found
QHB27I17.yg.ab1 / At5g59250 / sugar transporter family
QHB27L19.yg.ab1 / At1g28330 / dormancy-associated protein -related
QHB31E20.yg.ab1 / no_hits_found
QHB34B24.yg.ab1 / no_hits_found
QHB34C08.yg.ab1 / At5g21222 / protein kinase family
QHB34C17.yg.ab1 / At3g48280 / cytochrome P450 71A25
QHB34L10.yg.ab1 / At1g20630 / catalase 1
QHB36O22.yg.ab1 / At5g51260 / acid phosphatase
QHB3g08.yg.ab1 / no_hits_found
QHB41M10.yg.ab1 / At4g30960 / CBL-interacting protein kinase 6
QHB5B05.yg.ab1 / At3g09980 / expressed protein
QHB9E01.yg.ab1 / At3g22120 / protease inhibitor/seed storage/lipid transfer protein (LTP) family
QHC3h09.yg.ab1 / no_hits_found
QHC4g04.yg.ab1 / At3g26740 / light regulated protein -related
QHE12K16.yg.ab1 / At4g02920 / expressed protein
QHE12P12.yg.ab1 / no_hits_found
QHE12P20.yg.ab1 / At1g74470 / geranylgeranyl reductase
QHE16B05.yg.ab1 / no_hits_found
QHE16E14.yg.ab1 / no_hits_found
QHE17A09.yg.ab1 / no_hits_found
QHE1a04.yg.ab1 / At5g02140 / thaumatin-like protein, putative
QHE1d06.yg.ab1 / no_hits_found
QHE1e12.yg.ab1 / At1g71880 / sucrose transport protein
QHE1f07.yg.ab1 / At1g43710 / histidine decarboxylase -related
QHE20F20.yg.ab1 / At5g23150 / PWWP domain protein
QHE20I12.yg.ab1 / At2g05070 / light-harvesting chlorophyll a/b binding protein
QHE26C09.yg.ab1 / At2g36830 / major intrinsic protein (MIP) family]
QHE26I22.yg.ab1 / no_hits_found
QHE27M04.yg.ab1 / no_hits_found
QHE29L11.yg.ab1 / At3g04120 / glyceraldehyde-3-phosphate dehydrogenase C subunit (GapC)
QHE2h08.yg.ab1 / no_hits_found
QHE30J18.yg.ab1 / At2g45910 / protein kinase family [ F4I18.11 NP_182115.2 30690163 CDS forward ]
QHE3d04.yg.ab1 / no_hits_found
QHE5O02.yg.ab1 / no_hits_found
QHE9M14.yg.ab1 / no_hits_found
QHE9O24.yg.ab1 / At5g37820 / major intrinsic protein (MIP) family
QHF12E13.yg.ab1 / At3g53260 / phenylalanine ammonia-lyase (PAL2)
QHF1g12.yg.ab1 / At1g80930 / eukaryotic initiation factor 4 (eIF4) family protein
QHF4g09.yg.ab1 / no_hits_found
QHF9B21.yg.ab1 / At5g62680 / peptide transporter
QHG12O20.yg.ab1 / no_hits_found
QHG17C01.yg.ab1 / no_hits_found
QHG17D10.yg.ab1 / At1g05010 / 1-aminocyclopropane-1-carboxylate oxidase (ACC oxidase) (ethylene-forming enzyme) (EFE)
QHG17I02.yg.ab1 / no_hits_found
QHG1e02.yg.ab1 / no_hits_found
QHG5I24.yg.ab1 / At2g21660 / glycine-rich RNA-binding protein (AtGRP7)
QHG7I09.yg.ab1 / no_hits_found
QHG7P13.yg.ab1 / At5g43060 / cysteine proteinase RD21A
QHG9D09.yg.ab1 / At4g32940 / gamma-VPE (vacuolar processing enzyme)
QHG9H16.yg.ab1 / At3g30775 / osmotic stress-induced proline dehydrogenase (pro1)
QHH5D23.yg.ab1 / no_hits_found
QHI11E12.yg.ab1 / At3g12630 / expressed protein
QHI11F24.yg.ab1 / no_hits_found
QHI11K12.yg.ab1 / At1g17030 / expressed protein
QHI11N07.yg.ab1 / At5g03860 / malate synthase, putative
QHI15E11.yg.ab1 / At4g29120 / expressed protein
QHI21I06.yg.ab1 / no_hits_found
QHI21K21.yg.ab1 / At4g25620 / proline-rich protein family
QHI23L24.yg.ab1 / At3g02470 / S-adenosylmethionine decarboxylase
QHI7N03.yg.ab1 / At5g59300 / ubiquitin-conjugating enzyme 7 (UBC7)
QHJ16H14.yg.ab1 / no_hits_found
QHJ18D20.yg.ab1 / no_hits_found
QHJ8N13.yg.ab1 / no_hits_found
QHJ9L09.yg.ab1 / At2g01080 / expressed protein
QHL10B02.yg.ab1 / At3g16240 / delta tonoplast integral protein (delta-TIP)
QHL10L02.yg.ab1 / At2g16850 / putative plasma membrane intrinsic protein
QHL11K09.yg.ab1 / At2g45180 / protease inhibitor/seed storage/lipid transfer protein (LTP) family
QHL12L20.yg.ab1 / At5g55190 / GTP-binding protein atran3, putative
QHL13O20.yg.ab1 / At4g04640 / ATP synthase gamma chain 1, chloroplast (H(+)-transporting two-sector ATPase
QHL15H22.yg.ab1 / At2g15970 / stress-regulated protein SAP1 [Xerophyta viscosa]
QHL16D19.yg.ab1 / At3g12580 / heat shock protein hsp70
QHL17H05.yg.ab1 / At1g06680 / photosystem II oxygen-evolving complex 23 (OEC23)
QHL17H12.yg.ab1 / At4g33410 / expressed protein
QHL18E09.yg.ab1 / At4g23400 / major intrinsic protein (MIP) family
QHL18K18.yg.ab1 / At5g56360 / Calmodulin-binding protein
QHL19K02.yg.ab1 / At4g33950 / protein kinase, putative
QHL1A16.yg.ab1 / At4g00430 / transmembrane protein (MIP family)
QHL2A20.yg.ab1 / At1g29150 / 26S proteasome regulatory subunit (RPN6), putative
QHL2H09.yg.ab1 / At3g63410 / chloroplast inner envelope membrane protein, putative
QHL3P14.yg.ab1 / no_hits_found
QHL5E01.yg.ab1 / no_hits_found
QHL5L03.yg.ab1 / At1g77120 / alcohol dehydrogenase (EC 1.1.1.1)
QHL7O22.yg.ab1 / At3g02230 / reversibly glycosylated polypeptide-1
QHL8C05.yg.ab1 / At3g12610 / DNA-damage-repair/toleration protein, putative (DRT100)
QHN10E13.yg.ab1 / At4g16190 / cysteine proteinase
QHN10H11.yg.ab1 / At3g47950 / ATPase, plasma membrane-type (proton pump), putative
QHN11A06.yg.ab1 / At2g38540 / nonspecific lipid transfer protein 1 (LTP 1)
QHN11C12.yg.ab1 / At5g14040 / mitochondrial phosphate transporter
QHN11E23.yg.ab1 / At1g22710 / sucrose transporter SUC2 (sucrose-proton symporter)
QHN12H17.yg.ab1 / At3g22840 / early light-induced protein
QHN13F21.yg.ab1 / At1g21065 / expressed protein
QHN14B11.yg.ab1 / lipid transfer protein SDi-9, drought-induced - common sunflower
QHN15N12.yg.ab1 / At1g48370 / expressed protein
QHN16B16.yg.ab1 / At3g45140 / lipoxygenase (LOX2)
QHN16O01.yg.ab1 / At1g09740 / ER6 protein -related
QHN17E20.yg.ab1 / At1g55020 / probable lipoxygenase (EC 1.13.11.12) CPRD46, drought-inducible - cowpea
QHN17I20.yg.ab1 / At4g02380 / late embryogenesis abundant protein family
QHN17P23.yg.ab1 / At5g47530 / auxin-induced protein, putative
QHN18P03.yg.ab1 / At1g01620 / plasma membrane intrinsic protein 1c
QHN19D17.yg.ab1 / At1g19910 / H+-pumping ATPase 16 kDa proteolipid, vacuolar (avap2)
QHN19I09.yg.ab1 / At5g10230 / annexin -related protein
QHN19I15.yg.ab1 / no_hits_found
QHN19J12.yg.ab1 / At2g39780 / S-like ribonuclease RNS2
QHN19O06.yg.ab1 / At4g35180 / amino acid transporter family
QHN1K05.yg.ab1 / At2g10940 / protease inhibitor/seed storage/lipid transfer protein (LTP) family
QHN20N11.yg.ab1 / At5g03340 / transitional endoplasmic reticulum ATPase -related
QHN21M08.yg.ab1 / At5g14610 / DEAD box RNA helicase, putative
QHN22J20.yg.ab1 / At4g27960 / ubiquitin-conjugating enzyme 9 (UBC9)
QHN23M12.yg.ab1 / At3g03620 / MATE efflux protein family
QHN23P02.yg.ab1 / At1g72180 / leucine-rich repeat transmembrane protein kinase, putative]
QHN24F23.yg.ab1 / NP24 protein precursor (Pathogenesis-related protein PR P23) (Salt-induced protein)
QHN24J03.yg.ab1 / miraculin homolog, root-knot nematode-induced - tomato
QHN24J09.yg.ab1 / hairy root 4 [Nicotiana tabacum]
QHN24L21.yg.ab1 / probable cell wall-plasma membrane linker protein PRP precursor - rape
QHN24N01.yg.ab1 / root-specific protein RCc3 - rice
QHN24O05.yg.ab1 / protein kinase MMK4 (EC 2.7.1.-), cold- and drought-induced - alfalfa
QHN24P03.yg.ab1 / ESTs gb|R64994, gb|AI994832, gb|Z47674 come from this gene. [Arabidopsis thaliana]
QHN2A20.yg.ab1 / At4g39090 / cysteine proteinase RD19A
QHN2C12.yg.ab1 / At1g07650 / leucine-rich repeat transmembrane protein kinase, putative [
QHN2E10.yg.ab1 / At3g14930 / uroporphyrinogen decarboxylase (UPD)
QHN2H12.yg.ab1 / At1g16180 / expressed protein
QHN2N03.yg.ab1 / At5g48230 / acetyl-CoA C-acetyltransferase (acetoacetyl-coenzyme A thiolase)
QHN2P06.yg.ab1 / At4g24220 / expressed protein
QHN3G08.yg.ab1 / At5g66400 / dehydrin RAB18-related protein
QHN3H02.yg.ab1 / At1g64720 / membrane related protein CP5 -related
QHN3K19.yg.ab1 / At3g06170 / expressed protein
QHN5A13.yg.ab1 / At3g21180 / potential calcium-transporting ATPase 9
QHN6B23.yg.ab1 / At3g59140 / ABC transporter family protein
QHN6F16.yg.ab1 / At5g20650 / expressed protein
QHN7D11.yg.ab1 / At1g30510 / ferredoxin--NADP(+) reductase (adrenodoxin reductase)
QHN7E20.yg.ab1 / no_hits_found
QHN7K16.yg.ab1 / At4g27400 / expressed protein
QHN8F11.yg.ab1 / At5g43010 / 26S proteasome AAA-ATPase subunit RPT4a
QHN8G11.yg.ab1 / At4g11650 / osmotin-like protein, Pathogenesis-related protein in H.annuus
QHN8N18.yg.ab1 / no_hits_found
QHN9G17.yg.ab1 / At5g35160 / endomembrane protein 70, putative

Supplementary TABLE 2

Primers used for Q-PCR

EST Name / Forward primer / Reverse primer / Product length
QHN14D03 / TTGTGGACGGATTCAATGTG / TGTACACGGTGCAAGGGTTA / 147 bp
QHF6K23 / ATTGTTCGCCGTTGATTCTC / TGGGGCTATGTAGCCGTAAG / 167 bp
QHA14C04 / GCGTCAAGTTGAGACAAGAGC / ATCACGGTGGAATGAAGAGG / 152 bp
QHG18P13 / ATTCTCGTGTGGCGAAAAAT / GGAAACACCCAACCGTAAAA / 163 bp
QHA16C07 / CTTCTGGTGGGTGCCATAAC / CACCAGGGCATGTAAATGTG / 168 bp
QHE6N16 / CTATCGATGCCCAAGAGTCC / CAGTGGGAGATTTGGTGGTT / 172 bp
QHE1e12 / AAACATCATATGCGGGAATCA / CGGCGTTAATAAGTGGCCTA / 185 bp
QHN2P06 / AGGTGTTGGCTGAGCAATTC / ATGCTGCAACCTCTTCCAGT / 159 bp
QHL5L13 / TCCTTCGGTTGTCGAAAAGT / ATGCAACGAAGACCTTCACC / 129 bp
actin / CTCGGGGTCTACTGTGGAGA / ATCAGCAATACCCGGAAACA / 241 bp
ribosomal protein / CGGCATGAAGAAGAAAGGAG / TATCAGCTCCAGCACACGAC / 221 bp