Table 2.
Genes up-regulated in 7 d microspore cultures of embryogenic Westar-derived DH-2 line
| Accession no. | Genes up-regulated in Westar DH-2 | Best match to Arabidopsis | E-value | Biological process | Broad functional category |
| EE541057 | 60S ribosomal protein L32 (RPL32A) | AT4G18100.1 | 4e-71 | Ribosome biogenesis and assembly | Cell organization and biogenesis |
| CN735630 | Histone H2B, putative | AT2G37470.1 | 1e-41 | Chromosome organization and biogenesis | Cell organization and biogenesis |
| DY010080 | 60S ribosomal protein L5 (RPL5B) | AT5G39740.1 | e-123 | Ribosome biogenesis and assembly | Cell organization and biogenesis |
| EE542594 | 60S ribosomal protein L37a (RPL37aC) | AT3G60245.1 | 3e-49 | Ribosome biogenesis and assembly | Cell organization and biogenesis |
| EE541600 | MEE26 (maternal effect embryo arrest 26) | AT2G34870.1 | 4e-9 | Embryonic development ending in seed dormancy | Developmental processes |
| DY009433 | EMBRYO DEFECTIVE 2386; identical to 60S ribosomal protein L19-1 (RPL19A) | AT1G02780.1 | 1e-93 | Embryonic development ending in seed dormancy; translation | Developmental processes; protein metabolism |
| CN734060 | EMBRYO DEFECTIVE 2171; 60S ribosomal protein L23 (RPL23A) | AT3G04400.1 | 2e-76 | Embryonic development ending in seed dormancy; translation | Developmental processes; protein metabolism |
| CN727564 | EMBRYO DEFECTIVE 2171; 60S ribosomal protein L23 (RPL23A) | AT3G04400.1 | 4e-77 | Embryonic development ending in seed dormancy | Developmental processes |
| EE542973 | Histone H2A, putative | AT5G59870.1 | 8e-52 | Nucleosome assembly | DNA or RNA metabolism |
| EE550299 | NAD2B; encodes subunit of mitochondrial NAD(P)H dehydrogenase | ATMG01320.1 | 3e-23 | Electron transport | Electron transport or energy pathways |
| EE550879 | COB; mitochondrial apocytochrome b | ATMG00220.1 | e-114 | Aerobic respiration | Electron transport or energy pathways |
| DY007371 | Mitochondrial NADH dehydrogenase 5 | ATMG00665.1 | 7e-41 | Electron transport | Electron transport or energy pathways |
| CN732202 | LIPID TRANSFER PROTEIN 3 | AT5G59320.1 | 1e-52 | Response to abscisic acid stimulus | Other biological processes |
| EE548239 | Fructose-bisphosphate aldolase, putative | AT3G52930.1 | e-117 | Pentose-phosphate shunt | Other cellular processes |
| CN737059 | GLUTATHIONE S-TRANSFERASE 29, ATGSTU18 | AT1G10360.1 | 4e-72 | Toxin catabolic process | Other cellular processes |
| EE541185 | MATK; encodes a maturase located in the trnK intron in the chloroplast genome | ATCG00040.1 | 8e-70 | RNA splicing | Other cellular processes |
| CN727662 | GAPC-2; glyceraldehyde-3-phosphate dehydrogenase | AT1G13440.1 | 4e-72 | Gluconeogenesis | Other cellular processes |
| CN733306 | THI1 (THIAZOLE REQUIRING) | AT5G54770.1 | 7e-96 | Thiamine biosynthetic process | Other cellular processes |
| EE462458 | ATP synthase beta chain 2 | AT5G08690.1 | 1e-52 | ATP biosynthetic process | Other cellular processes |
| CN726197 | OLEO1 (OLEOSIN1) | AT4G25140.1 | 6e-62 | Sequestering of lipid | Other metabolic processes |
| EE548291 | TPI; ATCTIMC (CYTOSOLIC TRIOSEPHOSPHATE ISOMERASE | AT3G55440.1 | 1e-97 | Metabolic process | Other metabolic processes |
| DY010101 | Calmodulin binding/elongation factor 1-alpha/EF-1-alpha | AT5G60390.2 | e-138 | Translational elongation | Protein metabolism |
| No Acc. No. | Elongation factor 1-alpha/EF-1-alpha | AT1G07920 | Translational elongation | Protein metabolism | |
| EE551198 | RPS3; ribosomal protein S3 | ATMG00090.1 | e-127 | Translation | Protein metabolism |
| EE461044 | RPS3; encodes a chloroplast ribosomal protein S3 | ATCG00800.1 | 4e-68 | Translation | Protein metabolism |
| EE439665 | Elongation factor 1-alpha/EF-1-alpha | AT5G60390.1 | 7e-94 | Translational elongation | Protein metabolism |
| EE542027 | Elongation factor 1-alpha/EF-1-alpha | AT5G60390.1 | e-133 | Translational elongation | Protein metabolism |
| EE550930 | CLPP1; encodes the only ClpP (caseinolytic protease) encoded within the plastid genome | ATCG00670.1 | 2e-38 | Proteolysis | Protein metabolism |
| CN725880 | Cysteine proteinase, putative | AT3G54940.3 | 3e-85 | Proteolysis | Protein metabolism |
| CN730121 | 40S ribosomal protein S4 (RPS4B) | AT5G07090.1 | e-114 | Translation | Protein metabolism |
| EE543924 | RPS7, RPS7.1; encodes a chloroplast ribosomal protein S7 | ATCG00900.1 | 1e-82 | Translation | Protein metabolism |
| EE542577 | 60S ribosomal protein L36 (RPL36B) | AT3G53740.4 | 7e-50 | Translation | Protein metabolism |
| EE550742 | RPS6 (RIBOSOMAL PROTEIN S6) | AT4G31700.1 | 4e-95 | Translation | Protein metabolism |
| CN737473 | RPS15 (RIBOSOMAL PROTEIN S15) | AT1G04270.1 | 3e-82 | Translation | Protein metabolism |
| CX270671 | RPL2.2; encodes a chloroplast ribosomal protein L2 | ATCG01310.1 | 1e-67 | Translation | Protein metabolism |
| CN726155 | 60S ribosomal protein L10A (RPL10aB) | AT2G27530.2 | e-102 | Translation | Protein metabolism |
| EE542556 | 60S ribosomal protein L4/L1 (RPL4A) | AT3G09630.1 | 5e-89 | Translation | Protein metabolism |
| CN737233 | 60S ribosomal protein L29 (RPL29B) | AT3G06680.1 | 7e-31 | Translation | Protein metabolism |
| EE551248 | RPL14; encodes a chloroplast ribosomal protein L14 | ATCG00780.1 | 4e-43 | Translation | Protein metabolism |
| EE543194 | CCB452; cytochrome c biogenesis orf452 | ATMG00180.1 | 5e-61 | Translation | Protein metabolism |
| DY009980 | RPL2.2; encodes a chloroplast ribosomal protein L2 | ATCG01310.1 | e-102 | Translation | Protein metabolism |
| CN731939 | 60S acidic ribosomal protein P1 | AT4G00810.2 | 2e-29 | Translational elongation | Protein metabolism |
| EE541984 | RPS11-BETA (putative ribosomal protein S11-beta) | AT5G23740.1 | 6e-75 | Translation | Protein metabolism |
| EE541830 | 60S ribosomal protein L10 (RPL10C) | AT1G66580.1 | e-125 | Translation | Protein metabolism |
| CN735269 | Eukaryotic translation initiation factor 5A, putative/eIF-5A, putative | AT1G26630.1 | 3e-70 | Translational initiation | Protein metabolism |
| EE569706 | ATP1; ATPase subunit 1 | ATMG01190.1 | e-142 | Response to oxidative stress | Response to stress |
| EE462567 | CRT1 (CALRETICULIN 1); calcium ion binding | AT1G56340.2 | e-132 | Response to oxidative stress | Response to stress |
| DY013565 | HSP70-1, HEAT SHOCK COGNATE 70 KDA PROTEIN 1 | AT5G02500.1 | e-116 | Response to cold | Response to stress |
| CN730192 | AT1G56075.1, LOS1 (low expression of osmotically responsive genes 1) | AT1G56070.1 | 7e-52 | Response to cold | Response to stress |
| EE439511 | AT1G56075.1, LOS1 (low expression of osmotically responsive genes 1) | AT1G56070.1 | e-144 | Response to cold | Response to stress |
| CN737456 | 60S ribosomal protein L26 (RPL26A) | AT3G49910.1 | 4e-58 | Response to cold | Response to stress |
| EE541625 | ATCYP1, ROC5 (ROTAMASE CYP 5) | AT4G34870.1 | 5e-68 | Aignal transduction | Signal transduction |
| EE541128 | Protease inhibitor/seed storage/lipid transfer protein (LTP) family protein | AT5G38195.1 | 2e-32 | Lipid transport | Transport |
| EE541584 | LTP12 (LIPID TRANSFER PROTEIN 12) | AT3G51590.1 | 3e-51 | Lipid transport | Transport |
| DY003849 | 2S seed storage protein 1 | AT4G27140.1 | 1e-46 | Lipid transport | Transport |
| DY013108 | LTP2 (LIPID TRANSFER PROTEIN 2). | AT2G38530.1 | 2e-45 | Phospholipid transfer to membrane | Transport |
| CN735143 | LTP5 (LIPID TRANSFER PROTEIN 5) | AT3G51600.1 | 2e-52 | Lipid transport | Transport |
| EE543261 | Protease inhibitor/seed storage/lipid transfer protein (LTP) family protein | AT1G55260.1 | 2e-73 | Lipid transport | Transport |
| CN728941 | AAC2 (ADP/ATP CARRIER 2) | AT5G13490.2 | 1e-67 | Transport | Transport |
| EE550070 | Unknown protein | AT1G49310.1 | 3e-23 | Biological process unknown | Unknown biological processes |
| EE541862 | Unknown protein | AT1G49310.1 | 9e-7 | Biological process unknown | Unknown biological processes |
| EE543031 | BURP domain-containing protein | AT1G49320.1 | e-101 | Biological process unknown | Unknown biological processes |
| EE548292 | Glycine-rich protein | AT3G24250.1 | 9e-8 | Biological process unknown | Unknown biological processes |
| CX271266 | BURP domain-containing protein | AT1G49320.1 | 5e-21 | Biological process unknown | Unknown biological processes |
| ES265407 | Unknown protein | AT1G75870.1 | 4e-29 | Biological process unknown | Unknown biological processes |
| EE549026 | Glycine-rich protein | AT2G30560.1 | 2e-10 | Biological process unknown | Unknown biological processes |
| EE542023 | UInknown protein | AT3G06090.1 | 2e-7 | Biological process unknown | Unknown biological processes |
| EE550161 | Similar to unknown protein (Arabidopsis thaliana) | AT1G49290.1 | 3e-9 | Biological process unknown | Unknown biological processes |
| EE548723 | No hits found | ||||
| EE569070 | No hits found | ||||
| EE569674 | No hits found | ||||
| CN735696 | No hits found | ||||
| CN730585 | No hits found | ||||
| EE544345 | No hits found | ||||
| CN726406 | No hits found | ||||
| DY011515 | No hits found | ||||
| EE569173 | No hits found |
Locus identifiers for the best gene match in Arabidopsis are based on BlastX against the TAIR7_pep database. Biological process is taken from the Gene Ontology (GO) annotation on TAIR for each locus identifier (http://www.arabidopsis.org/tools/bulk/go/index.jsp). GenBank accession numbers identify the longest EST sequence for each gene from the collection of ESTs (∼67 000 ESTs) examined to construct this cDNA array (see Xiang et al., 2008), and these are included in the GAL file as descriptors for each reporter (Brassica gene) on the microarray (http://www.brassicagenomics.ca/cdnaarray.html).
Genes listed in bold were identified previously, based on EST abundance, as up-regulated during early stages of microspore embryogenesis in B. napus Topas DH4079 (Malik et al., 2007).
Organellar-derived genes are underlined.