Additional file 19GO function analysis of the enriched hypomethylated genes in YH100 vs.YH0

Locus ID / DMR location / Annotation / P-value
GRMZM2G000818 / Downstream2k / putative MYB DNA-binding domain superfamily protein / 1.86E-129
GRMZM2G006212 / Downstream2k / putative MATE efflux family protein / 0
GRMZM2G008047 / Downstream2k / pectinesterase inhibitor domain containing protein precursor / 2.52E-88
GRMZM2G033413 / Downstream2k / putative bZIP transcription factor superfamily protein / 2.96E-136
GRMZM2G048826 / Downstream2k / putative NAC domain transcription factor superfamily protein / 4.15E-165
GRMZM2G058358 / Downstream2k / subtilisin-chymotrypsin inhibitor CI-1C / 8.58E-34
GRMZM2G060583 / Downstream2k / pollen signaling protein with adenylyl cyclase activity / 0
GRMZM2G069970 / Downstream2k / protein phosphatase 2C isoform 1 / 0
GRMZM2G085948 / Downstream2k / putative RING zinc finger domain superfamily protein / 4.74E-86
GRMZM2G089050 / Downstream2k / nucleic acid binding protein / 0
GRMZM2G097768 / Downstream2k / sugar transport1 / 0
GRMZM2G099167 / Downstream2k/3’UTR / tubulin alpha-5 chain / 0
GRMZM2G100579 / Downstream2k / chloroplast outer envelope protein 86 isoform 1 / 0
GRMZM2G105954 / Downstream2k / putative cytochrome P450 superfamily protein / 0
GRMZM2G114642 / Downstream2k / glossy1 / 0
GRMZM2G118104 / Downstream2k / cleavage and polyadenylation specificity factor 5 / 4.33E-132
GRMZM2G126161 / Downstream2k/3’UTR / rab geranylgeranyl transferase like protein / 0
GRMZM2G139680 / Downstream2k / 2-cys peroxiredoxin BAS1 / 5.54E-117
GRMZM2G140754 / Downstream2k/ Upstream2k / alanyl-tRNA synthetase / 2.21E-147
GRMZM2G149520 / Downstream2k / putative DEAD-box ATP-dependent RNA helicase family protein / 0
GRMZM2G172883 / Downstream2k / histone deacetylase HDA101 / 0
GRMZM2G366411 / Downstream2k / putative S-locus-like receptor protein kinase family protein / 0
GRMZM2G403620 / Downstream2k / protein rough sheath 2 / 3.36E-113
GRMZM2G438841 / Downstream2k/CDS/Intron/3’UTR / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM5G831399 / Downstream2k / photosystem II protein H / 1.88E-34
GRMZM5G835235 / Downstream2k / putative glycogen synthase kinase family protein / 0
GRMZM5G836378 / Downstream2k / protein SUR2 / 1.96E-145
GRMZM5G861800 / Downstream2k / thioredoxin-like 2 / 5.92E-87
GRMZM5G879235 / Downstream2k / RNA polymerase alpha subunit / 0
GRMZM2G177314 / 5’UTR/ Upstream2k / ATP-binding cassette sub-family G member 2 / 0
GRMZM2G046829 / CDS / putative YABBY domain transcription factor family protein / 9.19E-99
GRMZM2G095576 / CDS/ Intron / putative cytidine/deoxycytidylate deaminase family protein / 8.85E-133
GRMZM2G125432 / CDS/ Intron / putative SET-domain containing family protein isoform 1 / 0
GRMZM2G382104 / CDS / putative protein kinase superfamily protein / 0
GRMZM2G444808 / CDS/ Intron / bcpLH protein / 0
GRMZM2G010342 / Intron / putative chromodomain helicase DNA binding protein / 0
GRMZM2G010349 / Intron / serine/threonine-protein kinase SNT7 / 0
GRMZM2G027378 / Intron / ubiquitin-conjugating enzyme spm2 / 6.93E-59
GRMZM2G033566 / Intron / anther-specific proline-rich protein APG precursor / 0
GRMZM2G044819 / Intron / 5-nucleotidase / 0
GRMZM2G046829 / Intron / putative YABBY domain transcription factor family protein / 9.19E-99
GRMZM2G052812 / Intron / putative oxidoreductase, aldo/keto reductase family protein / 0
GRMZM2G055243 / Intron / putative knotted-like transcription factor family protein / 3.43E-152
GRMZM2G063868 / Intron / transposon protein / 1.32E-129
GRMZM2G087206 / Intron / aldose reductase / 3.21E-137
GRMZM2G124455 / Intron / superoxide dismutase [Mn] 3.4, mitochondrial precursor / 9.96E-123
GRMZM2G132144 / Intron / putative eukaryotic translation initiation factor 3E subunit family protein / 0
GRMZM2G150952 / Intron / protein kinase domain containing protein / 0
GRMZM2G156861 / Intron / lipoxygenase1 / 0
GRMZM2G157034 / Intron / notchless-like protein isoform 1 / 0
GRMZM2G169033 / Intron / putative laccase family protein / 0
GRMZM2G169073 / Intron / starch branching enzyme [Phaseolus vulgaris] / 5.74E-178
GRMZM2G178758 / Intron / putative SNF2 domain-containing protein / helicase domain-containing protein / 0
GRMZM2G382104 / Intron / putative protein kinase superfamily protein / 0
GRMZM2G428201 / Intron / putative protein kinase superfamily protein / 0
GRMZM2G452178 / Intron / homeobox protein rough sheath 1 / 5.06E-128
GRMZM2G457544 / Intron / putative RING zinc finger domain superfamily protein / 0
GRMZM5G840560 / Intron / putative glycosyl transferase family protein / 0
GRMZM2G004435 / Upstream2k / polygalacturonase / 1.96E-133
GRMZM2G008202 / Upstream2k / putative heavy metal transport/detoxification superfamily protein, partial / 1.23E-82
GRMZM2G046576 / Upstream2k / signal recognition particle protein / 3.04E-70
GRMZM2G060659 / Upstream2k / putative sucrose synthase family protein / 0
GRMZM2G069911 / Upstream2k / histone H1 / 4.82E-40
GRMZM2G086072 / Upstream2k / transcription factor Dp-1 / 3.27E-179
GRMZM2G114126 / Upstream2k / putative oxysterol binding domain family protein / 4.62E-124
GRMZM2G136918 / Upstream2k / 6-phosphogluconolactonase isoform 1 / 6.77E-161
GRMZM2G148709 / Upstream2k / arginyl-tRNA synthetase / 0
GRMZM2G149277 / Upstream2k / putative ribosomal protein S4 (RPS4A) family protein / 1.60E-51
GRMZM2G165426 / Upstream2k / CONSTANS interacting protein 6 / 0
GRMZM2G173759 / Upstream2k / probable xyloglucan glycosyltransferase 5 [Vitis vinifera] / 0
GRMZM2G302259 / Upstream2k / succinate dehydrogenase iron-sulfur protein,mitochondrial precursor / 7.65E-142
GRMZM2G370745 / Upstream2k / cytochrome P450 CYP72A28v2 / 0
GRMZM2G412296 / Upstream2k / COX VIIa-like protein, partial / 9.30E-39
GRMZM2G452996 / Upstream2k / putative HLH DNA-binding domain superfamily protein / 0
GRMZM5G850355 / Upstream2k / proteasome subunit alpha type 2 / 3.81E-128
GRMZM5G862945 / Upstream2k / ABA responsive element binding factor 1 [Sorghum bicolor] / 3.98E-107
GRMZM5G882378 / Upstream2k / 40S ribosomal protein S14 / 1.18E-65
GRMZM5G884960 / Upstream2k / cytochrome b6-f complex subunit 4 / 4.75E-98
GRMZM5G890843 / Upstream2k / putative RING zinc finger domain superfamily protein / 0

Additional file 20 GO function analysis of the enriched hypermethylated genes in YH100 vs.YH0

Locus ID / DMR location / Annotation / P-value
GRMZM2G016890 / Downstream2k / beta glucosidase1 / 0
GRMZM2G019029 / Downstream2k / phospholipase D family protein / 0
GRMZM2G023988 / Downstream2k / zinc finger, C2H2 type family protein isoform 1 / 0
GRMZM2G024993 / Downstream2k / granule-bound starch synthase precursor / 0
GRMZM2G050108 / Downstream2k / nicotianamine synthase 3 / 0
GRMZM2G062481 / Downstream2k / acyl carrier protein / 7.10E-47
GRMZM2G067489 / Downstream2k / RING-H2 finger protein ATL2B / 7.00E-101
GRMZM2G068947 / Downstream2k / 12-oxo-phytodienoic acid reductase6 / 0
GRMZM2G075051 / Downstream2k/3’UTR / ras-related protein Rab-18 / 3.51E-118
GRMZM2G075247 / Downstream2k/3’UTR / putative S-locus receptor-like protein kinase family protein / 0
GRMZM2G076705 / Downstream2k / nucleic acid binding protein / 0
GRMZM2G118409 / Downstream2k / MAC/Perforin domain containing protein / 0
GRMZM2G139463 / Downstream2k / L-asparaginase-like family protein / 8.99E-161
GRMZM2G140901 / Downstream2k / putative NAC domain transcription factor superfamily protein / 2.49E-157
GRMZM2G143335 / Downstream2k / putative proteinase inhibitor family protein / 1.29E-48
GRMZM2G149617 / Downstream2k / putative glycosyl transferase family 28 protein / 0
GRMZM2G172883 / Downstream2k / histone deacetylase HDA101 / 0
GRMZM2G181002 / Downstream2k / putative protein kinase superfamily protein / 1.35E-136
GRMZM2G338465 / Downstream2k / cytokinin-O-glucosyltransferase 3 precursor / 0
GRMZM2G340251 / Downstream2k/3’UTR / heat shock protein70-4 isoform 1 / 0
GRMZM2G428242 / Downstream2k / putative SNF2 domain-containing protein / helicase domain-containing protein isoform 1 / 0
GRMZM2G533389 / Downstream2k / putative acyl-CoA N-acyltransferases (NAT) family protein / 5.84E-108
GRMZM5G828466 / Downstream2k / putative protein kinase superfamily protein / 1.45E-159
GRMZM5G864903 / Downstream2k / putative cytochrome P450 superfamily protein / 0
GRMZM2G114126 / CDS / putative oxysterol binding domain family protein / 4.62E-124
GRMZM2G153815 / Intron / heat shock protein / 0
GRMZM2G399901 / Intron /3’UTR / putative RING zinc finger domain superfamily protein, partial / 2.44E-31
GRMZM5G829955 / Intron / WD repeat-containing protein 57 / 0
GRMZM2G007854 / Intron / ATP binding protein / 0
GRMZM2G028218 / Intron / putative dnaJ chaperone family protein / 1.13E-33
GRMZM2G034495 / Intron / acetyltransferase, GNAT family protein / 2.76E-104
GRMZM2G046601 / Intron / glutamine synthetase root isozyme 5 / 0
GRMZM2G056270 / Intron / RING finger and CHY zinc finger domain-containing protein 1 / 7.20E-171
GRMZM2G065641 / Intron/ Upstream2k / protein trpH / 9.60E-142
GRMZM2G085427 / Intron / putative MYB DNA-binding domain superfamily protein / 0
GRMZM2G114126 / Intron / putative oxysterol binding domain family protein / 4.62E-124
GRMZM2G130910 / Intron / putative histone-lysine N-methyltransferase family protein isoform 1 / 0
GRMZM2G314546 / Intron / putative homeodomain-like transcription factor superfamily protein, partial / 0
GRMZM2G428242 / Intron / putative SNF2 domain-containing protein / helicase domain-containing protein isoform 1 / 0
GRMZM2G553379 / Intron / MADS1 protein [Fargesia nitida] / 1.02E-57
GRMZM2G019029 / CDS / phospholipase D family protein / 0
GRMZM2G034495 / CDS / acetyltransferase, GNAT family protein / 2.76E-104
GRMZM2G040209 / CDS / NADH-ubiquinone oxidoreductase subunit / 0
GRMZM2G457697 / 3’UTR / enhancer of rudimentary-like protein / 1.92E-54
GRMZM2G007283 / Upstream2k / putative protein kinase superfamily protein / 7.47E-60
GRMZM2G039982 / Upstream2k / lipoic acid synthetase / 2.40E-174
GRMZM2G050641 / Upstream2k / diacylglycerol O-acyltransferase 1 / 0
GRMZM2G050800 / Upstream2k / alternative discordia1 / 8.29E-127
GRMZM2G057251 / Upstream2k / syntaxin 72 / 6.63E-149
GRMZM2G097313 / Upstream2k / putative leucine-rich repeat protein kinase family protein / 0
GRMZM2G098793 / Upstream2k / glycosyltransferase / 0
GRMZM2G102944 / Upstream2k / serine/threonine-protein kinase Haspin / 9.15E-60
GRMZM2G120302 / Upstream2k / putative acyl-peptide hydrolase / 0
GRMZM2G120329 / Upstream2k / serine/threonine-protein kinase RIO1 / 0
GRMZM2G127374 / Upstream2k / quinone oxidoreductase-like protein At1g23740 / 1.50E-162
GRMZM2G129150 / Upstream2k / putative RING zinc finger domain superfamily protein / 2.12E-119
GRMZM2G163054 / Upstream2k / putative WRKY DNA-binding domain superfamily protein / 2.85E-67
GRMZM2G322348 / Upstream2k / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM2G330684 / Upstream2k / putative RING zinc finger and VWF domain family protein / 0
GRMZM2G400655 / Upstream2k / putative SERRATE-related C2H2 zinc-finger family protein / 0
GRMZM2G459864 / Upstream2k / putative MADS-box transcription factor family protein / 3.01E-129
GRMZM5G862945 / Upstream2k / ABA responsive element binding factor 1 [Sorghum bicolor] / 3.98E-107

Additional file 21 GO function analysis of the enriched hypomethylated genes in YH200 vs.YH0

Locus ID / DMR location / Annotation / P-value
GRMZM2G016145 / Downstream2k / response regulator / 1.43E-65
GRMZM2G000818 / Downstream2k / putative MYB DNA-binding domain superfamily protein / 1.86E-129
GRMZM2G353076 / Downstream2k / ZHD9 ZF-HD type transcription factor / 8.27E-47
GRMZM2G048826 / Downstream2k / NAC domain transcription factor superfamily protein / 4.15E-165
GRMZM2G421279 / Downstream2k / Histone H4 / 1.18E-30
GRMZM2G165901 / Downstream2k / Glycine-rich RNA-binding, abscisic acid-inducible protein / 4.70E-42
GRMZM2G145758 / Downstream2k / histone H3 / 6.01E-71
GRMZM2G051528 / Downstream2k / R2R3 Myb transcription factor MYB-IF25 / 8.68E-138
GRMZM2G040278 / Downstream2k / F-box protein GID2 / 3.63E-40
GRMZM2G006080 / Downstream2k / putative receptor-like protein kinase family protein / 0
GRMZM2G060583 / Downstream2k / pollen signaling protein with adenylyl cyclase activity / 0
GRMZM2G066734 / Downstream2k / putative bZIP transcription factor superfamily protein / 2.41E-31
GRMZM2G090869 / Downstream2k / putative DEAD-box ATP-dependent RNA helicase family protein / 0
GRMZM2G100976 / Downstream2k / photosystemI1 / 8.25E-113
GRMZM2G130332 / Downstream2k / diaminopimelate epimerase isoform 1 / 0
GRMZM2G133029 / Downstream2k / aspartic proteinase nepenthesin-2 / 0
GRMZM2G141774 / Downstream2k / putative protein kinase superfamily protein / 9.44E-98
GRMZM2G155021 / Downstream2k / outer plastidial membrane protein porin / 3.94E-154
GRMZM2G394450 / Downstream2k / invertase1 / 0
GRMZM2G426125 / Downstream2k / zinc finger protein 7 / 4.50E-78
GRMZM2G438840 / Downstream2k / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM2G442658 / Downstream2k/3’UTR / alcohol dehydrogenase 1 / 0
GRMZM5G837822 / Downstream2k / hevamine-A / 2.69E-158
GRMZM5G861800 / Downstream2k / thioredoxin-like 2 / 5.92E-87
GRMZM2G097768 / Downstream2k / sugar transport1 / 0
GRMZM2G155021 / Downstream2k / outer plastidial membrane protein porin / 3.94E-154
GRMZM5G861800 / Downstream2k / thioredoxin-like 2 / 5.92E-87
GRMZM2G177314 / 5’UTR/ Upstream2k / ATP-binding cassette sub-family G member 2 / 0
GRMZM2G012052 / 5’UTR/ Upstream2k / ubiquitin-conjugating enzyme protein E2 / 1.19E-77
GRMZM2G403007 / 5’UTR/ Upstream2k / nonspecific lipid-transfer protein precursor / 1.45E-30
GRMZM2G060540 / CDS/ Intron / arginine/serine-rich splicing factor SR45_1 / 1.13E-71
GRMZM2G137380 / CDS/ Intron / putative HLH DNA-binding domain superfamily protein / 0
GRMZM2G324643 / CDS/ Intron/ Upstream2k / calmodulin / 1.14E-85
GRMZM2G010342 / Intron / putative chromodomain helicase DNA binding protein / 0
GRMZM2G010349 / Intron / serine/threonine-protein kinase SNT7 / 0
GRMZM2G010779 / Intron / vacuolar cation/proton exchanger 2 / 0
GRMZM2G027378 / Intron / ubiquitin-conjugating enzyme spm2 / 6.93E-59
GRMZM2G030915 / Intron/ Upstream2k / 40S ribosomal protein S3a / 0
GRMZM2G033566 / Intron / anther-specific proline-rich protein APG precursor / 0
GRMZM2G048243 / Intron / protein kinase domain superfamily protein / 0
GRMZM2G052812 / Intron / putative oxidoreductase, aldo/keto reductase family protein / 0
GRMZM2G055243 / Intron / putative knotted-like transcription factor family protein / 3.43E-152
GRMZM2G056988 / Intron / putative dnaJ chaperone family protein / 0
GRMZM2G063868 / Intron / transposon protein / 1.32E-129
GRMZM2G107309 / Intron / histone deacetylase / 0
GRMZM2G109354 / Intron / squamosa promoter-binding protein-like (SBP domain) transcription factor family protein / 0
GRMZM2G124455 / Intron / superoxide dismutase mitochondrial precursor / 9.96E-123
GRMZM2G126832 / Intron/ Upstream2k / putative protein phosphatase 2C family protein / 5.57E-61
GRMZM2G135691 / Intron / prefoldin subunit 1 / 3.57E-65
GRMZM2G136712 / Intron / homoserine dehydrogenase / 0
GRMZM2G139024 / Intron / E2F-DP transcription factor / 1.33E-141
GRMZM2G140590 / Intron / putative protein kinase superfamily protein / 0
GRMZM2G154839 / Intron / regulator of telomere elongation helicase 1 / 2.23E-74
GRMZM2G156861 / Intron / lipoxygenase / 0
GRMZM2G169033 / Intron / putative laccase family protein / 0
GRMZM2G169073 / Intron / starch branching enzyme [Phaseolus vulgaris] / 5.74E-178
GRMZM2G178758 / Intron / putative SNF2 domain-containing protein / helicase domain-containing protein / 0
GRMZM2G343218 / Intron / putative 1-phosphatidylinositol-4-phosphate 5-kinase/ zincion binding family / 0
GRMZM2G428035 / Intron / putative protein kinase superfamily protein
GRMZM2G448104 / Intron / putative MYB DNA-binding domain superfamily protein / 0
GRMZM2G457544 / Intron / putative RING zinc finger domain superfamily protein / 0
GRMZM2G469061 / Intron / putative ribosomal protein S4 (RPS4A) family protein / 1.21E-92
GRMZM2G054136 / Intron / ribosomal proteinS6
GRMZM2G072997 / Intron / putative MADS-box transcription factor family protein
GRMZM2G156861 / Intron / lipoxygenase1 / 0
GRMZM2G001524 / Upstream2k / putative nucleoside diphosphate kinase family protein
GRMZM2G004435 / Upstream2k / polygalacturonase
GRMZM2G008712 / Upstream2k / zinc finger protein 7 / 2.38E-96
GRMZM2G014672 / Upstream2k / transmembrane BAX inhibitor motif protein-containing protein 4
GRMZM2G025387 / Upstream2k / calcium-dependent protein kinase, isoform 2 / 0
GRMZM2G028313 / Upstream2k / putative translation elongation/initiation factor family protein / 0
GRMZM2G032049 / Upstream2k / glutaminyl-tRNA synthetase / 0
GRMZM2G060659 / Upstream2k / putative sucrose synthase family protein / 0
GRMZM2G069911 / Upstream2k / histone H1 / 4.82E-40
GRMZM2G122479 / Upstream2k / malic enzyme / 0
GRMZM2G131853 / Upstream2k / putative glycogen synthase kinase family protein / 0
GRMZM2G143886 / Upstream2k / putative alcohol dehydrogenase superfamily protein / 0
GRMZM2G153991 / Upstream2k / FK506-binding protein 2-1 precursor / 2.94E-70
GRMZM2G157458 / Upstream2k / ferredoxin-thioredoxin reductase, variable chain / 2.34E-42
GRMZM2G161696 / Upstream2k / lysosomal protective protein / 0
GRMZM2G368799 / Upstream2k / inositol hexaphosphate kinase
GRMZM2G400156 / Upstream2k / SAUR33-auxin-responsive SAUR family member / 2.48E-52
GRMZM2G403813 / Upstream2k / putative protein kinase superfamily protein / 0
GRMZM2G417089 / Upstream2k / putative jumonji-like transcription factor family protein / 0
GRMZM2G429940 / Upstream2k / CBL-interacting serine/threonine-protein kinase 15 / 0
GRMZM5G846811 / Upstream2k / Rho-related protein from plants2 / 8.15E-99
GRMZM2G014672 / Upstream2k / transmembrane BAX inhibitor motif protein-containing protein 4 / 4.58E-113
GRMZM2G157458 / Upstream2k / ferredoxin-thioredoxin reductase, variable chain / 2.34E-42

Additional file 22 GO function analysis of the enriched hypermethylated genes in YH200 vs.YH0

Locus ID / DMR location / Annotation / P-value
GRMZM2G000278 / Downstream2k/3’UTR / putative snRK/SAPK family protein kinase / 1.38E-103
GRMZM2G011526 / Downstream2k / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM2G014672 / Downstream2k / transmembrane BAX inhibitor motif protein-containing protein 4 / 4.58E-113
GRMZM2G028218 / Downstream2k/Intron / putative dnaJ chaperone family protein / 1.13E-33
GRMZM2G028928 / Downstream2k/CDS/Intron/3’UTR / putative translation elongation factor family protein / 0
GRMZM2G029292 / Downstream2k/ Intron / putative WRKY DNA-binding domain superfamily protein / 2.05E-37
GRMZM2G052067 / Downstream2k / putative CBL-interacting protein kinase family protein / 0
GRMZM2G058220 / Downstream2k / putative D-mannose binding lectin receptor-like protein kinase family protein / 0
GRMZM2G062481 / Downstream2k / acyl carrier protein / 7.10E-47
GRMZM2G067489 / Downstream2k / RING-H2 finger protein ATL2B / 7.00E-101
GRMZM2G072868 / Downstream2k / putative leucine-rich repat protein kinase family protein / 0
GRMZM2G075247 / Downstream2k / putative S-locus receptor-like protein kinase family protein / 0
GRMZM2G115773 / Downstream2k / putative subtilase family protein / 0
GRMZM2G116563 / Downstream2k / N6-adenosine-methyltransferase MT-A70-like protein / 0
GRMZM2G116952 / Downstream2k / putative RING zinc finger domain superfamily protein isoform 1 / 0
GRMZM2G134687 / Downstream2k / putative NAC domain transcription factor superfamily protein / 4.60E-165
GRMZM2G142873 / Downstream2k / opaque endosperm5 / 0
GRMZM2G143335 / Downstream2k / putative proteinase inhibitor family protein / 1.29E-48
GRMZM2G148693 / Downstream2k/3’UTR / zea apetala-like protein / 8.83E-124
GRMZM2G150608 / Downstream2k / protein Kinase-associated protein phosphatase / 0
GRMZM2G156517 / Downstream2k / putative ubiquitin-conjugating enzyme family / 3.23E-69
GRMZM2G159171 / Downstream2k / glutamate carboxypeptidase 2 / 0
GRMZM2G179802 / Downstream2k / heat shock transcription factor like protein / 0
GRMZM2G300133 / Downstream2k/3’UTR / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM2G375002 / Downstream2k / rac-like GTP-binding protein 5 / 1.17E-90
GRMZM2G415327 / Downstream2k / Rho-related protein from plants 1 / 7.29E-12
GRMZM2G011526 / Downstream2k / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM2G028218 / Downstream2k/ CDS / putative dnaJ chaperone family protein / 1.13E-33
GRMZM2G052067 / Downstream2k / putative CBL-interacting protein kinase family protein / 0
GRMZM2G058220 / Downstream2k / putative D-mannose binding lectin receptor-like protein kinase family protein / 0
GRMZM2G067489 / Downstream2k / RING-H2 finger protein ATL2B / 7.00E-101
GRMZM2G075247 / Downstream2k / putative S-locus receptor-like protein kinase family protein / 0
GRMZM2G132632 / Downstream2k / putative RING zinc finger domain superfamily protein / 5.12E-115
GRMZM2G143335 / Downstream2k / putative proteinase inhibitor family protein / 1.29E-48
GRMZM2G156517 / Downstream2k / putative ubiquitin-conjugating enzyme family / 3.23E-69
GRMZM2G181002 / Downstream2k / putative protein kinase superfamily protein / 1.35E-136
GRMZM2G300133 / Downstream2k / putative leucine-rich repeat receptor-like protein kinase family protein / 0
GRMZM2G415327 / Downstream2k / Rho-related protein from plants 1 / 7.29E-12
GRMZM2G422581 / 5’UTR/ CDS/ Intron / putative NADH-cytochrome B5 reductase family protein / 1.06E-85
GRMZM2G017982 / 5’UTR/ CDS/ Upstream2k / putative serine/threonine protein phosphatase superfamily protein / 3.38E-171
GRMZM2G044744 / 5’UTR/ Upstream2k / starch synthase IV / 0
GRMZM2G140590 / CDS/ Intron / putative protein kinase superfamily protein / 0
GRMZM2G127181 / CDS/Intron / putative protein kinase superfamily protein / 0
GRMZM2G399901 / CDS/3’UTR / putative RING zinc finger domain superfamily protein, partial / 2.44E-31
GRMZM2G409224 / CDS/ Intron / putative trithorax-like family protein / 0
GRMZM2G019515 / Intron / disulfide oxidoreductase/ monooxygenase/ oxidoreductase / 0
GRMZM2G052812 / Intron / putative oxidoreductase, aldo/keto reductase family protein / 0
GRMZM2G056524 / Intron / putative RING zinc finger domain superfamily protein / 0
GRMZM2G099231 / Intron / poly [ADP-ribose] polymerase 2(NAD(+) ADP-ribosyltransferase 2) / 0
GRMZM2G320549 / Intron / putative MADS-box transcription factor family protein / 8.23E-38
GRMZM2G448104 / Intron / putative MYB DNA-binding domain superfamily protein / 0
GRMZM2G448213 / Intron / protein kinase domain superfamily protein / 0
GRMZM2G448258 / Intron / cell division cycle 2-related protein kinase 7 / 0
GRMZM2G477829 / Intron / putative protein kinase superfamily protein / 0
GRMZM2G700188 / Intron / putative cinnamyl-alcohol dehydrogenase family protein / 2.08E-159
GRMZM2G033820 / Upstream2k / phospholipase A2 / 1.23E-61
GRMZM2G039396 / Upstream2k / protoporphyrinogen IX oxidase (plastidic)1 / 0
GRMZM2G053767 / Upstream2k / 40S ribosomal protein S4-like protein isoform 1 / 2.45E-100
GRMZM2G055549 / Upstream2k / blue copper protein precursor / 1.59E-76
GRMZM2G064473 / Upstream2k / plastidic ATP/ADP-transporter / 0
GRMZM2G073826 / Upstream2k / putative MYB DNA-binding domain superfamily protein / 2.43E-156
GRMZM2G153666 / Upstream2k / polygalacturonase precursor / 0
GRMZM2G177934 / Upstream2k / chemocyanin precursor / 8.49E-53
GRMZM2G179454 / Upstream2k / chorismate mutase / 1.14E-118
GRMZM2G343218 / Upstream2k / putative 1-phosphatidylinositol-4-phosphate 5-kinase/ zinc ion binding family / 0
GRMZM2G347226 / Upstream2k / putative calcium-dependent protein kinase family protein isoform 1 / 0
GRMZM2G366434 / Upstream2k / putative AP2/EREBP transcription factor superfamily protein / 0
GRMZM2G366659 / Upstream2k / putative trehalose phosphatase/synthase family protein / 0
GRMZM2G426847 / Upstream2k / putative DNA polymerase epsilon catalytic subunit family protein / 4.61E-175
GRMZM2G438871 / Upstream2k / putative lectin-like receptor protein kinase family protein / 0
GRMZM2G452935 / Upstream2k / presenilin / 1.60E-139
GRMZM5G861800 / Upstream2k / thioredoxin-like 2 / 5.92E-87
GRMZM5G862945 / Upstream2k / ABA responsive element binding factor 1 / 3.98E-107

Additional file 23 GO function analysis of the enriched hypomethylated genes in YH250 vs.YH0

Locus ID / DMR location / Annotation / P-value
GRMZM2G000818 / Downstream2k / putative MYB DNA-binding domain superfamily protein / 1.86E-129
GRMZM2G006212 / Downstream2k / putative MATE efflux family protein / 0
GRMZM2G038791 / Downstream2k / EC synthetase / 0
GRMZM2G076212 / Downstream2k / putative protein kinase superfamily protein / 0
GRMZM2G085089 / Downstream2k / selenium-binding protein / 0
GRMZM2G085948 / Downstream2k / putative RING zinc finger domain superfamily protein / 4.74E-86
GRMZM2G098764 / Downstream2k /3’UTR / DNA-directed RNA polymerase III subunit polypeptide / 1.02E-137
GRMZM2G105869 / Downstream2k / histone-lysine N-methyltransferase SUVR3 / 3.03E-151
GRMZM2G114642 / Downstream2k / glossy1 / 0
GRMZM2G128929 / Downstream2k / lactate dehydrogenase A / 0
GRMZM2G414805 / Downstream2k / squamosa promoter-binding protein-like (SBP domain) transcription factor family protein / 1.05E-88
GRMZM2G461569 / Downstream2k / urease / 0
GRMZM5G899366 / Downstream2k / RNA polymerase beta' subunit / 0
GRMZM2G002531 / 5’UTR / ATP binding protein / 0
GRMZM2G004703 / 5’UTR/ Upstream2k / calmodulin1 / 6.20E-80
GRMZM2G177314 / 5’UTR / ATP-binding cassette sub-family G member 2 / 0
GRMZM2G444808 / CDS/ Intron / bcpLH protein / 0
GRMZM2G033566 / Intron / anther-specific proline-rich protein APG precursor / 0
GRMZM2G063868 / Intron / transposon protein / 1.32E-129
GRMZM2G065612 / Intron / ubiquitin-protein ligase / 0
GRMZM2G079850 / Intron / structural constituent of ribosome / 4.16E-53
GRMZM2G109354 / Intron / squamosa promoter-binding protein-like (SBP domain) transcription factor family protein / 0
GRMZM2G132144 / Intron / putative eukaryotic translation initiation factor 3E subunit family protein / 0
GRMZM2G135691 / Intron / prefoldin subunit 1 / 3.57E-65
GRMZM2G156861 / Intron / lipoxygenase1 / 0
GRMZM2G169033 / Intron / putative laccase family protein / 0
GRMZM2G169073 / Intron / starch branching enzyme [Phaseolus vulgaris] / 5.74E-178
GRMZM2G343218 / Intron / putative 1-phosphatidylinositol-4-phosphate 5-kinase/ zinc ion binding family / 0
GRMZM2G393002 / Intron / putative alpha-L-arabinofuranosidase family protein / 0
GRMZM2G428035 / Intron / putative protein kinase superfamily protein / 1.81E-155
GRMZM2G443953 / Intron / putative coatomer beta subunit family protein / 0
GRMZM2G469061 / Intron / putative ribosomal protein S4 (RPS4A) family protein / 1.21E-92
GRMZM2G002531 / Upstream2k / ATP binding protein / 0
GRMZM2G011893 / Upstream2k / glutamine cyclotransferase / 9.07E-166
GRMZM2G038108 / Upstream2k / activator of heat shock protein ATPase / 0
GRMZM2G044947 / Upstream2k / esterase isoform 1 / 0
GRMZM2G058310 / Upstream2k / beta-amylase / 8.11E-89
GRMZM2G069911 / Upstream2k / histone H1 / 4.82E-40
GRMZM2G086088 / Upstream2k / ubiquitin-conjugating enzyme E2-17 kDa 9 / 1.24E-78
GRMZM2G097030 / Upstream2k / UDP-glucosyltransferase / 0
GRMZM2G110511 / Upstream2k / Full=Cis-zeatin O-glucosyltransferase 2; Short=cisZOG2 / 0
GRMZM2G114126 / Upstream2k / putative oxysterol binding domain family protein / 4.62E-124
GRMZM2G118770 / Upstream2k / malic enzyme Precursor / 0
GRMZM2G124051 / Upstream2k / CCR4-NOT transcription complex subunit 6 / 0
GRMZM2G136918 / Upstream2k / 6-phosphogluconolactonase isoform 1 / 6.77E-161
GRMZM2G147210 / Upstream2k / putative protein disulfide isomerase family protein / 0
GRMZM2G148709 / Upstream2k / arginyl-tRNA synthetase / 0
GRMZM2G173759 / Upstream2k / probable xyloglucan glycosyltransferase 5 [Vitis vinifera] / 0
GRMZM2G177314 / Upstream2k / ATP-binding cassette sub-family G member 2 / 0
GRMZM5G862945 / Upstream2k / ABA responsive element binding factor 1 [Sorghum bicolor] / 3.98E-107

Additional file 24GO function analysis of the enriched hypermethylated genes in YH250 vs.YH0

Locus ID / DMR location / Annotation / P-value
GRMZM2G013794 / Downstream2k / putative trithorax-like family protein isoform 1 / 0
GRMZM2G028218 / Downstream2k/Intron / putative dnaJ chaperone family protein / 1.13E-33
GRMZM2G029486 / Downstream2k / Ras protein Rab11A / 1.45E-107
GRMZM2G058173 / Downstream2k / undecaprenyl pyrophosphate synthetase / 6.88E-154
GRMZM2G074094 / Downstream2k / putative histone-lysine N-methyltransferase family protein / 2.30E-166
GRMZM2G081955 / Downstream2k / tab2 protein / 9.13E-166
GRMZM2G098179 / Downstream2k/3’UTR / myb transcription factor MYB30 / 8.63E-141
GRMZM2G118037 / Downstream2k/3’UTR / Pi starvation-induced protein / 8.73E-42
GRMZM2G118409 / Downstream2k/3’UTR / MAC/Perforin domain containing protein / 0
GRMZM2G129761 / Downstream2k / 1-Cys peroxiredoxin PER1 / 6.69E-134
GRMZM2G141216 / Downstream2k / putative RING zinc finger domain superfamily protein / 0
GRMZM2G141299 / Downstream2k / putative WRKY DNA-binding domain superfamily protein / 2.94E-97
GRMZM2G143335 / Downstream2k / putative proteinase inhibitor family protein / 1.29E-48
GRMZM2G148693 / Downstream2k/CDS/3’UTR / zea apetala-like protein / 8.83E-124
GRMZM2G165137 / Downstream2k / cell wall integrity protein scw1 / 3.98E-141
GRMZM2G172883 / Downstream2k / histone deacetylase HDA101 / 0
GRMZM2G178517 / Downstream2k / nitrilase 1 / 6.20E-179
GRMZM2G366434 / Downstream2k / putative AP2/EREBP transcription factor superfamily protein / 0
GRMZM2G429759 / Downstream2k / putative leucine-rich repeat receptor-like protein kinase family protein / 2.10E-169
GRMZM2G430600 / Downstream2k / calmodulin / 0
GRMZM2G576752 / Downstream2k / putative WAK family receptor-like protein kinase / 0
GRMZM5G828466 / Downstream2k / putative protein kinase superfamily protein / 1.45E-159
GRMZM5G862955 / Downstream2k/3’UTR / putative cytochrome C oxidase subunit II family protein / 0
GRMZM2G057535 / 5’UTR/Upstream2k / elongation factor 1-alpha / 0
GRMZM2G059285 / 5’UTR/ Upstream2k / putative oxidoreductase, aldo/keto reductase family protein / 0
GRMZM2G399901 / 5’UTR/CDS/Intron/3’UTR / putative RING zinc finger domain superfamily protein, partial / 2.44E-31
GRMZM2G422581 / 5’UTR/CDS/Intron/Upstream2k / putative NADH-cytochrome B5 reductase family protein / 1.06E-85
GRMZM5G862945 / 5’UTR / ABA responsive element binding factor 1 [Sorghum bicolor] / 3.98E-107
GRMZM2G028218 / CDS / putative dnaJ chaperone family protein / 1.13E-33
GRMZM2G126161 / CDS/Intron / rab geranylgeranyl transferase like protein / 0
GRMZM2G149617 / CDS/Intron / putative glycosyl transferase family 28 protein / 0
GRMZM2G153815 / CDS / heat shock protein / 0
GRMZM2G162388 / CDS/3’UTR / putative peptidyl-prolyl cis-trans isomerase family protein / 6.58E-88
GRMZM2G171604 / CDS/Intron / 26S protease regulatory subunit S10B / 0
GRMZM5G890843 / CDS/Intron / putative RING zinc finger domain superfamily protein / 0
GRMZM2G029107 / Intron / calmodulin / 1.74E-79
GRMZM2G041561 / Intron / putative RING zinc finger domain superfamily protein / 0
GRMZM2G046601 / Intron / glutamine synthetase root isozyme 5 / 0
GRMZM2G050405 / Intron / putative cytidine/deoxycytidylate deaminase family protein / 2.76E-51
GRMZM2G058276 / Intron / putative TCP-1/cpn60 chaperonin family protein / 0
GRMZM2G067853 / Intron / ATPase cadmium transporter / 0
GRMZM2G085427 / Intron / putative MYB DNA-binding domain superfamily protein, partial / 0
GRMZM2G119717 / Intron / putative leucine-rich repeat receptor-like protein kinase family protein / 1.75E-171
GRMZM2G128114 / Intron / succinate semialdehyde dehydrogenase / 0
GRMZM2G130910 / Intron / putative histone-lysine N-methyltransferase family protein isoform 1 / 0
GRMZM2G139463 / Intron / L-asparaginase-like family protein / 8.99E-161
GRMZM2G448104 / Intron / putative MYB DNA-binding domain superfamily protein / 0