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Table 1 Differentially expressed (p < 0.01) ESTs (102) between low and high digestible (dNDF) recombinant inbred lines.

From: Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population

GAa Tentative annotationb Similarityb Transcript level
    Low quality High quality
    Mean SD Mean SD
Down-regulated in lines with high dNDF content
Chaperone activity
AI948333 UP|TBB6_MAIZE Tubulin beta-6 chain 100% 0.13 0.06 0.10 0.16
Catalytic activity
AI666096 UP|SUS2_MAIZE Sucrose synthase 2 100% 0.22 0.07 0.17 0.07
AI881378 Zea mays clone Contig234 mRNA sequence   1.26 0.47 0.83 0.26
AW424679 Zea mays clone EL01N0513E01.d mRNA sequence   3.37 1.02 2.69 0.70
BG842237 UP|Q6ZL43_ORYSA Histone H2A 100% 1.63 0.55 1.25 0.48
BM073983 UP|Q9SXV0_ORYSA Cytochrome c oxidase subunit 6b-1 44% 2.96 1.06 1.92 0.68
CD970581 PIR|T02767|T02767 cinnamyl-alcohol dehydrogenase – maize {Zea mays} 100% 2.12 0.72 1.31 0.65
CD973094 UP|Q7M1Q5_ORYSA Phenylalanine ammonia-lyase 96% 1.91 0.68 1.73 0.60
CF028668 UP|Q9SLP6_MAIZE Ferredoxin 100% 3.46 1.10 2.79 0.88
Binding
AI734769 UP|Q5D1M3_POPTR Class III HD-Zip protein 4 21% 0.20 0.08 0.14 0.19
AW042324 UP|Q9XEY1_TOBAC Nt-iaa2.3 deduced protein 60% 0.34 0.12 0.24 0.08
BG841395 UP|Q8RY51_ORYSA Glucose-6-phosphate dehydrogenase 100% 1.96 0.60 1.45 0.58
BM080754 UP|O24449_MAIZE Translational initiation factor eIF-4A 100% 0.76 0.21 0.38 0.39
BM334752 UP|Q7EYM0_ORYSA Zinc finger protein family-like 98% 3.52 1.05 2.91 0.93
Unclassified
AI622221 PRF|NP_191537 expressed protein {Arabidopsis thaliana} 42% 1.00 0.33 0.68 0.20
AI622354 UP|Q8GTX9_ARATH Cell cycle control crn (Crooked neck) protein-like 17% 0.81 0.33 0.43 0.17
AI666222 UP|Q6CWV7_KLULA Kluyveromyces lactis strain NRRL Y-1140 5% 1.73 0.62 1.12 0.34
AI691363 GB|AF127565 ubiquitin-protein ligase 2 {Arabidopsis thaliana} 3% 0.37 0.14 0.23 0.08
AI692057 UP|Q6K8U3_ORYSA Leucine-rich repeat-like protein 29% 0.80 0.30 0.59 0.21
AI737226 UP|Q75GJ2_ORYSA Expressed protein (With alternative splicing) 89% 1.04 0.38 0.74 0.30
AI834139 UP|Q6J9V5_MAIZE Cf2-like protein 3% 0.28 0.12 0.16 0.07
AI834361 UP|C85A1_ORYSA Cytochrome P450 85A1 (C6-oxidase) (Dwarf protein) 10% 1.09 0.38 0.68 0.26
AI855219    0.40 0.15 0.31 0.15
AI947947 UP|Q6TY49_HYDMC Reductase 1 21% 0.57 0.18 0.46 0.23
AW018225    1.86 0.75 1.55 0.61
AW155860 UP|Q5WAM8_BACSK DNA-directed RNA polymerase 6% 1.58 0.40 1.24 0.45
AW400279 Zea mays clone EL01N0325H04.d mRNA sequence   2.18 0.69 1.88 0.48
AW400378 UP|Q9FU27_ORYSA CCCH-type zinc finger protein-like 40% 0.46 0.17 0.33 0.18
AW438085 PRF|NP_567701 expressed protein {Arabidopsis thaliana} 55% 0.98 0.47 0.41 0.27
AW787698 UP|Q94FN1_LOTJA Phosphatidylinositol transfer-like protein III 29% 3.68 1.21 2.97 0.87
BG837856 UP|Q9ZPI2_9BRAS Delta-12 desaturase 46% 2.41 0.73 1.64 0.54
BM333894 UP|Q6SS00_ANTMA YABBY-like transcription factor GRAMINIFOLIA 23% 0.53 0.20 0.36 0.15
BM334482    2.89 0.83 2.17 0.67
BM349452 PRF|NP_850290 expressed protein {Arabidopsis thaliana} 28% 0.78 0.55 0.09 0.08
BM350803 UP|Q9PF60_XYLFA Endo-1, 4-beta-glucanase 16% 0.85 0.54 0.42 0.15
BM500212 UP|Q9LQS9_ARATH T4O12.9 39% 0.61 0.33 0.18 0.14
CB350592    0.44 0.18 0.29 0.19
CF005238 UP|Q9SBX4_MAIZE Proline-rich protein precursor 51% 3.06 1.09 2.11 0.38
CF062028 UP|UPTG_MAIZE (P80607) Alpha-1, 4-glucan-protein synthase 100% 1.13 0.47 0.97 0.48
Up-regulated in lines with high dNDF content
Motor activity
AW065585 UP|Q9FUS4_SETIT Actin 100% 0.38 0.23 0.69 0.26
Catalytic activity
AI622068 UP|Q9LLI8_MAIZE Cellulose synthase-2 10% 0.24 0.09 0.44 0.16
AI737885 UP|O60585_HUMAN Ser/Arg-related nuclear matrix protein 4% 0.94 0.31 1.85 0.77
AW927815 UP|TRXF_PEA (P29450) Thioredoxin F-type, chloroplast precursor 59% 0.24 0.11 0.48 0.20
BE050716 Zea mays clone EL01N0551B03.d mRNA sequence   0.08 0.03 0.12 0.06
BE129940 UP|PEPCK_MAIZE (Q9SLZ0) PEP carboxykinase 100% 0.42 0.15 0.92 0.37
BM334031 UP|HMT2_MAIZE (Q9FUM9) Homocysteine S-methyltransferase 2 100% 0.32 0.13 0.70 0.36
BM350652 UP|Q45W77_ARAHY Ubiquitin-conjugating enzyme 1 100% 0.68 0.28 1.40 0.60
CB617280 Zea mays clone EL01N0531D09.c mRNA sequence   0.14 0.05 0.29 0.16
CD972065 UP|Q8L7Y9_ARATH Phosphatidylglycerol specific phospholipase C 92% 0.02 0.04 0.05 0.16
CF030921 UP|Q9FNU9_DACGL Mitochondrial processing peptidase alpha-chain 100% 0.31 0.13 0.80 0.39
CF243853 UP|Q7X6T0_MAIZE Caffeoyl CoA 3-O-methyltransferase 100% 0.03 0.06 0.06 0.20
Structural molecule activity
AI691512 UP|TBA2_MAIZE Tubulin alpha-2 chain 100% 0.41 0.23 0.70 0.24
AI920382 Zea mays clone Contig900.F mRNA sequence   0.38 0.14 0.66 0.23
Transporter activity
AI621754 UP|Q9LSD4_ARATH 89% 0.68 0.49 1.38 0.42
Binding
AW400061 UP|METK_ORYSA S-adenosylmethionine synthetase 1 100% 0.16 0.06 0.43 0.19
AW438124 UP|Q8W514_MAIZE MSI type nucleosome/chromatin assembly factor C 100% 0.18 0.07 0.35 0.14
BM078288 PRF|NP_200425 KH domain-containing protein 73% 0.11 0.04 0.24 0.13
BM381996 UP|O22470_ORYSA GDP dissociation inhibitor protein OsGDI1 80% 0.07 0.03 0.15 0.08
Unclassified
AI622159 UP|O75833_HUMAN UTF1 5% 0.03 0.05 0.08 0.29
AI673886 UP|O82347_ARATH Expressed protein (At2g46220/T3F17.13) 61% 0.02 0.03 0.04 0.15
AI691788 GB|BT010134 At2g02560 {Arabidopsis thaliana} 50% 0.50 0.17 1.29 0.50
AI714870 UP|Q7XVJ6_ORYSA OJ000126_13.12 protein 89% 0.13 0.06 0.22 0.09
AI715073 UP|Q4EVD5_LISMO ATP-dependent RNA helicase DeaD 4% 0.43 0.22 1.14 0.42
AI857233 Zea mays clone EL01N0442A09.c mRNA sequence   0.06 0.02 0.12 0.10
AI881373 UP|O24293_PEA Chloroplast inner envelope protein, 110 kD precursor 32% 0.21 0.07 0.42 0.16
AI901469 UP|Q8GUG5_ARATH Threonine dehydratase/deaminase (OMR1) 27% 0.14 0.05 0.28 0.11
AI901508 UP|Q7TFG7_RHCM6 Rh175 11% 0.09 0.07 0.27 0.38
AI920330 UP|Q6I683_ORYSA UDP-glucuronic acid decarboxylase 91% 0.59 0.22 0.89 0.36
AI948303    0.96 0.31 1.67 0.61
AI964683 UP|NRTN_HUMAN (Q99748) Neurturin precursor 7% 0.59 0.16 0.94 0.37
AW065798 UP|RL10_MAIZE 60S ribosomal protein L10 39% 0.26 0.07 0.38 0.13
AW091349 UP|Q4NPG7_9DELT PE-PGRS family protein 3% 1.09 0.31 1.47 0.49
AW120445 UP|Q5U1M6_ORYSA Class III peroxidase 67 precursor 53% 2.06 0.73 3.42 1.15
AW146725 PRF|NP_192621 expressed protein {Arabidopsis thaliana} 60% 0.31 0.09 0.48 0.17
AW330680 UP|Q8L7U7_ARATH AT4g39670/T19P19_60 76% 0.17 0.05 0.36 0.16
AW331016    0.36 0.12 0.78 0.33
AW331105 PRF|NP_189346 expressed protein {Arabidopsis thaliana} 77% 0.19 0.08 0.47 0.32
AW331480 UP|Q6ILL4_DROME HDC09080 8% 0.15 0.07 0.29 0.12
AW400073 UP|Q9FRX0_MAIZE Bundle sheath cell specific protein 1 100% 0.14 0.04 0.27 0.12
AW438246 PRF|NP_197590 expressed protein {Arabidopsis thaliana} 20% 0.26 0.13 0.45 0.20
BE051493 UP|Q9M0X9_ARATH 4-coumarate-CoA ligase-like protein 34% 0.29 0.12 0.70 0.32
BE129888 UP|Q6K702_ORYSA MATE efflux protein-like 56% 0.03 0.05 0.10 0.27
BF728781 UP|Q9XEI4_MAIZE Unconventional myosin heavy chain 10% 0.31 0.12 0.70 0.31
BG321060 PRF|NP_567470 expressed protein {Arabidopsis thaliana} 23% 0.08 0.05 0.16 0.09
BG842356 UP|Q8L6I1_ORYSA Plasma membrane H+ ATPase 47% 0.09 0.06 0.23 0.13
BG842835 PRF|NP_195843 haloacid dehalogenase-like hydrolase family protein 91% 0.12 0.04 0.30 0.15
BM073617 UP|Q56WY6_ARATH Serine protease like protein 65% 0.48 0.22 1.12 0.43
BM080336 UP|Q9FZ91_ARATH F3H9.17 protein (Sulfotransferase family protein) 7% 0.38 0.18 0.64 0.30
BM080577 PRF|NP_193327 nodulin MtN3 family protein {Arabidopsis thaliana} 70% 0.74 0.22 1.52 0.55
BM350621 UP|Q4SGI8_TETNG Chromosome 3 SCAF14593 5% 0.29 0.09 0.78 0.36
BM382642 UP|PSBQ1_MAIZE (Q41048) Oxygen-evolving enhancer protein 3–1 100% 0.23 0.08 0.39 0.22
BQ279795 Zea mays clone Contig815.F mRNA sequence   0.33 0.15 0.78 0.35
BU093700 PRF|NP_680116 transcription factor jumonji family protein 7% 0.44 0.14 0.87 0.40
CB605303 UP|Q56WY6_ARATH Serine protease like protein 65% 0.17 0.07 0.35 0.16
CB815513 PRF|NP_850290 expressed protein {Arabidopsis thaliana} 28% 0.11 0.04 0.25 0.11
CD446744 Zea mays clone EL01T0206E01.c mRNA sequence   0.15 0.06 0.27 0.12
CD972441 UP|Q9XE75_SORBI Patatin-like protein 100% 0.24 0.10 0.42 0.19
CD984112 PRF|NP_174335 SIT4 phosphatase-associated family protein 9% 0.36 0.15 0.68 0.42
CD986361 GB|AP003561 ankyrin-like protein {Oryza sativa} 76% 0.10 0.03 0.29 0.13
CD990067 UP|C98A1_SORBI (O48956) Cytochrome P450 98A1 100% 0.21 0.07 0.43 0.17
CF031839 Zea mays clone Contig483.F mRNA sequence   0.17 0.07 0.30 0.12
CF062473 UP|Q8LBV7_ARATH plastid ribosomal protein L19 33% 0.15 0.07 0.29 0.17
  1. a GenBank accession number.
  2. b Annotation of each gene sequence was taken from the TIGR Maize Gene Index [12].
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