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Table 6 Differential expression of gene transcripts associated with QTLs detected using RNA-seq

From: Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum

Gene id (v1.4) Chr Start (bp) logFC Annoatation Low N QTLs Normal N QTLs
Sb01g032875 1 55828932 6.3 Translation elongation factor EF1B qMC2-1a qMC2-1, qBY-1
Sb01g032880 1 55840286 4 SPX domain-3 qMC2-1a qMC2-1, qBY-1
Sb01g032920 1 55885605 6.84 Frigida putative expressed qMC2-1a qMC2-1, qBY-1
Sb01g033010 1 56047918 9.1 Retrotransposon protein, qMC2-1a qMC2-1, qBY-1
Sb01g033090 1 56202769 3.98 Mannose-binding lectin superfamily qMC2-1a qMC2-1, qBY-1
Sb01g033360 1 56595053 −5.2 Acetoacetyl-CoA thiolase 2 qMC2-1a qMC2-1, qBY-1
Sb01g033410 1 56731990 4.27 Cation/carnitine transporter 3 qMC2-1a qMC2-1, qBY-1
Sb01g033620 1 56944250 2.77 Metacaspase 1 qMC2-1a qMC2-1, qBY-1
Sb01g034190 1 57636134 2.49 O-Glycosyl hydrolases qMC2-1a qMC2-1, qBY-1
Sb01g035910 1 59529076 9.28 Glutathione S-transferase qMC2-1b  
Sb01g036330 1 59936853 −3.38 Ribosomal protein L16p/L10e family qTW1  
Sb01g036790 1 60395728 2.56 Late embryogenesis abundant protein 1 qTW1  
Sb01g037480 1 61031332 4.1 Nicotianamine synthase 4 qTW1  
Sb01g038720 1 62214256 −7.69 LHT1 lysine histidine transporter 1   qAD-1
Sb01g041180 1 64497962 −3.32 HSP21 Heat shock protein 21   qGY-1b
Sb01g041350 1 64653444 2.63 Subtilisin-like serine protease 2   qGY-1b
Sb01g041390 1 64692370 −2.39 Senescence associated protein   qGY-1b
Sb01g041640 1 64933485 2.04 Oxidoreductase superfamily protein   qGY-1b
Sb01g041810 1 65045823 3.75 STRUBBELIG-RECEPTOR FAMILY 7   qGY-1b
Sb01g042500 1 65775142 1.99 Caleosin-related family protein   qGY-1b
Sb01g042530 1 65792345 2.89 MA3 domain-containing protein   qGY-1b
Sb01g044230 1 67360823 2.26 Polyamine oxidase 1   qGY-1b
Sb01g044810 1 67970813 3.04 MADS-box transcription factor family   qGY-1b
Sb01g045620 1 68676107 2.29 Lectin protein kinase family protein   qGY-1b
Sb01g047250 1 70350087 2.412 Leucine-rich repeat transmembrane protein kinase   qGY-1b
Sb01g047550 1 70645925 2.215 Tetratricopeptide repeat (TPR)-like superfamily protein   qGY-1b
Sb01g047650 1 70741548 −3.156 CCT motif family protein   qGY-1b
Sb01g047780 1 70919577 −8.348 Magnesium transporter 6   qGY-1b
Sb01g048000 1 71075448 1.861 Glutathione S-transferase   qGY-1b
Sb01g048030 1 71101357 3.126 Cytochrome P450, family 78,   qGY-1b
Sb01g048100 1 71159986 −4.194 LYM2 lysm domain GPI-anchored protein 2 precursor   qGY-1b
Sb01g048640 1 71596638 6.418 Leucine-rich repeat family protein   qGY-1b
Sb06g002090 6 3921155 3.276 F-box/RNI-like/FBD-like domains-containing protein qGY-6a  
Sb06g002180 6 4089379 −2.511 UDP-glucosyltransferase qGY-6a  
Sb06g003180 6 6636307 3.018 CAP (Cysteine-rich secretory proteins qGY-6a  
Sb06g005420 6 13588101 6.889 expressed protein   
Sb06g006920 6 16373350 −2.546 purple acid phosphatase 27 qGY-6b  
Sb06g008990 6 26359064 2.375 Oxidoreductase, zinc-binding dehydrogenase family protein qGY-6b  
Sb06g010870 6 30379011 3.616 Cytochrome P450, family 71 qGY-6b  
Sb06g011767 6 32144416 6.478 auxin response factor 2 qGY-6b  
Sb06g011770 6 32145882 6.844 C2H2-like zinc finger protein qGY-6b  
Sb06g012040 6 32755618 2.708 Minichromosome maintenance (MCM2/3/5) family protein qGY-6b  
Sb06g012280 6 33774679 2.815 UDP-Glycosyltransferase superfamily qGY-6b  
Sb06g012290 6 33921889 4.708 Galactose oxidase/kelch repeat superfamily protein qGY-6b  
Sb06g014250 6 39313831 4.128 multidrug resistance-associated protein 9 qGY-6b  
Sb06g014400 6 39867816 −3.085 HSP70 Heat shock protein 70   
Sb06g015520 6 43082617 3.501 B-block binding subunit of TFIIIC qPH-6, qGY-6c  
Sb06g016160 6 44576681 2.202 seed storage 2S albumin superfamily qPH-6, qGY-6c  
Sb06g016230 6 44708205 2.164 Late embryogenesis abundant hydroxyproline-rich glycoprotein qPH-6, qGY-6c  
Sb06g016260 6 44735351 2.5 Aluminium activated malate transporter qPH-6, qGY-6c  
Sb06g019470 6 49032854 1.3 Copper transport protein family   qMC1-6a
Sb06g019600 6 49168975 4.279 Cytochrome P450 superfamily protein   qMC1-6a
Sb06g019610 6 49174004 2.452 phosphofructokinase 2   qMC1-6a
Sb06g024400 6 53535970 1.683 NUDIX family, domain containing protein qMC1-6b qMC1-6b
Sb06g024590 6 53686490 1.958 tonoplast intrinsic protein qMC1-6b qMC1-6b
Sb06g024650 6 53730735 4.367 expansin B2 qMC1-6b qMC1-6b
Sb06g025220 6 54190773 −2.114 calcium-dependent protein kinase 29 qMC1-6b qMC1-6b
Sb06g025250 6 54207289 2.782 Prolyl oligopeptidase family protein qMC1-6b qMC1-6b
Sb06g025330 6 54262137 2.362 expressed protein qMC1-6b qMC1-6b
Sb06g028210 6 57045616 2.252 Terpenoid cyclases/Protein prenyltransferases superfamily protein   qMC2-6
Sb06g028480 6 57260405 2.019 unknown   qMC2-6
Sb06g028760 6 57496434 1.729 Leucine-rich receptor-like protein kinase   qMC2-6
Sb07g022670 7 57311597 2.956 Glutamate decarboxylase qChl3-7, qBY-7  
Sb07g022800 7 57514740 2.625 aspartyl protease family protein qChl3-7, qBY-7  
Sb07g023140 7 57977647 4.794 Gibberellin receptor GID1L2 qChl3-7, qBY-7  
Sb07g023220 7 58087984 −3.707 phospholipase A qChl3-7  
Sb07g023300 7 58178273 2.495 expressed protein qChl3-7  
Sb07g023770 7 58722654 11.097 rotamase qChl3-7  
Sb07g024200 7 59189842 −7.492 Ribosomal protein L1p/L10e family qChl3-7  
Sb07g025190 7 60212195 4.048 MATE efflux family protein qChl3-7  
Sb07g025240 7 60280418 −2.248 hydroxymethylglutaryl-CoA synthase qChl3-7  
Sb07g025843 7 60959427 2.544 ethylene-responsive transcription factor ERF114, putative, expressed qChl1-7  
Sb08g000550 8 482761 −2.111 ferritin-1, chloroplast precursor   qGS-8
Sb08g002590 8 2673615 −2.004 WRKY DNA-binding protein 55   qGS-8
Sb08g002660 8 2779571 2.726 Protease inhibitor/seed storage/LTP   qGS-8
Sb08g003170 8 3513569 3.001 Chalcone and stilbene synthase family   qGS-8
Sb08g003820 8 4423015 −3.008 zinc finger superfamily protein   qGS-8
Sb08g004500 8 5410066 −2.127 fructose-bisphosphate aldolase 2   qGS-8
Sb09g018440 9 46098300 6.288 methyl esterase 3 qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g020000 9 49032969 8.222 inosine-uridine preferring nucleoside hydrolase family protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g020240 9 49471823 3.041 Major facilitator superfamily protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g021016 9 50446536 3.241 ethylene-responsive transcription factor qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g021250 9 50714173 2.158 alpha/beta-Hydrolases superfamily protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g021490 9 50944384 4.533 Subtilase family protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g021720 9 51194456 −1.869 histone deacetylase 8 qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g022390 9 52044973 8.308 Ribosomal protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g023150 9 52794183 2.46 ribonuclease P family protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g023320 9 52948577 6.593 Major facilitator superfamily protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g024840 9 54319624 −2.168 ferredoxin--nitrite reductase qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g025530 9 55006797 2.719 O-methyltransferase family protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g025540 9 55018768 2.155 O-methyltransferase family protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g025730 9 55141225 3.406 non-symbiotic hemoglobin 2 qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g025900 9 55284480 −2.24 HSP101 Heat shock protein 101 qAD-9a, qChl2-9b qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g026590 9 55803666 1.86 RING/U-box superfamily protein qAD-9a, qChl2-9b qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g027380 9 56449825 −2.508 serine/threonine-protein kinase SNT7, chloroplast precursor qAD-9a, qChl2-9b qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g027470 9 56561299 7.612 Disease resistance protein qAD-9a, qChl2-9b qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g027590 9 56662520 2.783 seed storage 2S albumin superfamily qAD-9a, qChl2-9b qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g028890 9 57684814 2.326 Iron-sulfur cluster, SufE/NifU family protein qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g028960 9 57721281 3.573 ribosomal protein L13 qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
Sb09g029540 9 58186320 5.903 AMP-dependent synthetase qAD-9a qGY-9, qChl2-9a, qBY-9, qChl3-9, qPH-9
  1. Chr, chromosome number; log2 ratio; number of folds the gene transcript is differentially expressed in RNA-seq. Log2 ratio >0 indicates, positive values indicates gene transcript expressed high in CK60. ns, indicate the transcript is not differentially expressed between CK60 and china17