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Supporting Information

Extensive, clustered parental imprinting of protein-coding and non-coding RNAs in

developing maize endosperm

Mei Zhang*, Hainan Zhao*, Shaojun Xie*, Jian Chen, Yuanyuan Xu, Keke Wang, Haiming

Zhao, Haiying Guan, Xiaojiao Hu, Yinping Jiao, Weibin Song, Jinsheng Lai§

State Key Laboratory of Agrobiotechnology and National Maize Improvement Center，

Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193,

P. R. China

* These authors contributed equally.

§ Corresponding author. Email: [email protected]

Phone: 86-10-6273-1405

mailto:[email protected]

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SI Methods

Discovering SNPs and measuring allelic expression. Reads from all samples were mapped to

B73 working set genes and genome sequence by BWA (1) . SAMtools (2) were used to trim

out read for which mapping quality was less than 20. The alignments of each sample were

merged together, pileuped by SAMtools and used for calling SNPs. SNP were called if 1) a

site was covered by at least 10 reads in both B73×Mo17 and Mo17×B73, and 2) each

nucleotide of a SNP had a frequency between 20% to 80% from all merged samples. To

determine the expression of B73 and Mo17 alleles at each SNP site, reads from each sample

were mapped to the B73 working set genes and genome sequence separately. The expression

level of B73 alleles of each SNP site was determined by summary of the B73 reads that

mapped to the SNP site. To avoid mapping bias, which leads to underestimate of the

expression of Mo17 alleles, SNP sites were converted to Mo17 nucleotides and reads were

re-mapped to the SNP-masked genes, and the expression level of Mo17 alleles of each SNP

site were calculated using the sum of the Mo17-reads of the SNP site.

Identification of imprinted protein-coding genes in maize 10 DAP endosperm. To identify

the imprinted SNPs, we denominated the maternal bias Bm for maternally-biased SNPs and

the paternal bias Bp for paternally-biased SNPs in B73 X Mo17 and Mo17 X B73 of 10 DAP

endosperm. Bm represents the percentage of expression for maternal alleles out of all

expression including the maternal and paternal alleles, while Bp represents the expressional

percentage of the paternal alleles. As the endosperm has two copies of maternal alleles and

only one paternal allele, a two-tailed χ2 test was conducted at each SNP site to test parental

bias greater or less than 2:1 in both B73 X Mo17 and Mo17 X B73 (α=0.05) hybrid

endosperm. This effort allowed us to identify 450 maternally-biased SNPs and 1236

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paternally-biased SNP. To obtain high-quality imprinted genes, we employed very high

stringent standard, such that a SNP was considered to be imprinted if the expression level of

the actively expressed allele is at least five-times higher than the imprinted repressed allele.

Given that the endosperm has two doses of maternal alleles and only one dose paternal

allele, therefore the maternally preferentially expressed SNPs should have Bm value of

greater than 10/11 {Bm > 2×5 / (2×5 +1)} , while paternal preferentially expressed SNPs

should have Bp value of greater than 5/7 {Bp > 5/ (2×1 +5) }. There are 651 SNPs in 179 genes

that are satisfied this criterion and were used for further analysis.

Screening for imprinted non-coding RNAs. Candidate imprinted non-coding RNAs

contained two kinds of sequence from distinct genomic regions. One was named intergenic

non-coding RNA, while the other comes from intronic regions of protein-coding genes.

Imprinted SNPs of intergenic non-coding RNAs could come from non-gene regions, and their

transcripts should not overlap with a gene, any full length cDNA (including its up and down

10 kilobase regions) and have no homolog to any protein. Moreover, these non-coding RNAs

should be short, with the length of the ORF less than 100 amino acids, and have no

similarity with sorghum gene sequences. We screened the imprinted intronic non-coding

RNAs with the same protocol, with the only difference that we made sure one transcript

was from an intronic region by manually integrating the information of its corresponding

protein-coding gene’s ESTs, its predicted proteins and its non- or lower expression in the

seedlings transcriptome.

SNP and restriction site identification. SNPs were identified in the final 224 candidate

imprinted transcripts. In each case, potential SNPs and 25 bp to either side were analyzed

using dCAPS Finder (http://helix.wustl.edu/dcaps/dcaps.html) to select SNPs that

overlapped with a restriction site for identification of allele-specific expression.

http://helix.wustl.edu/dcaps/dcaps.html

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Allele-specific expression analysis. For each gene, primers were designed using Primer

Premier 5.0 to include an allele-specific restriction site (Table S10). Where possible, primers

were placed to span introns. To perform RT-PCR, 1ug of RNA from inbred and reciprocal

crosses between polymorphic maize strains (B73 X B73，B73 X Mo17, Mo17 X B73，or

Mo17 X Mo17) was subjected to Oligo (dT)15 (Promega) and heated to 70℃ for 5 minitues,

followed by 2 minitues on ice. First-strand cDNA synthesis was performed by adding 4 ul 5 x

reaction buffer, 1 ul RNasin, 4 ul 5 mM dNTPs and 1 ul M-MLV reverse transcriptase

(Promega). This reaction was incubated at 42℃ for 55 min, followed by 5 minitues on ice.

The cDNA was used for PCR. Standard PCR was run with Easytaq DNA polymerase

(TRANSGEN) for 35 cycles (95°C for 30 sec, 60°C for 30 sec, and 72°C for 50 sec) followed by

a final extension of 10 min at 72°C. Restriction digestions were performed by mixing 8 ul

PCR products, 2 ul 10 × reaction buffer, 1 ul allele specific restriction enzyme and 9 ul H2O,

and incubating at each enzyme’s specific temperature overnight. The digested products

were separated by electrophoresis in a TAE gel and observed by ethidium bromide staining.

Details on primers are provided in Table S10.

Gene Ontology analysis. GO annotation was performed by AgBase software (3). Then, GO

analysis was performed with WEGO (4). Pearson Chi-square test was used for statistics. GO

categories that show significant (α =0.05) enrichment than others were displayed in the

output histogram of the WEGO figure.

Clustering analysis. The distribution of the number of clusters was determined by randomly

sampling 217 endosperm-expressed genes for 10,000 times and P value was calculated from

the distribution.

Enrichment of TEs around imprinted genes. Annotated TEs were downloaded from

Maizesequence (http://maizesequence.org). Non-imprinted genes (non-IMP) should

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perfectly fit the 2:1 ratio of maternal allele to paternal allele expression in both the

reciprocal crosses. The number of TEs within 3Kb flanking regions of genes was calculated

and was used for the subsequent Fishers’ Exact test.

Homologous analysis. Imprinted genes of Arabidopsis and rice were aligned to maize

filtered-set genes. (blastp, E<=0.001). The top three genes of lower E value and higher

similarity score corresponding to mazie imprinted genes were screened out in Table S4.

Bisulfite sequencing. DNA was extracted from 10 DAP endosperm using the CTAB method,

and was sheared by sonication to fragments of 300-500 bp. Following the Illumina protocol,

after the special adapters provided by Illumina were ligated onto fragments, the

adapter-ligated fragment was treated twice with sodium bisulfate using the Qiagen EpiTect

kit, and amplified by 13 cycles of PCR using Pfu DNA polymerase (Takara). Then, the library

was sequenced using standard Illumina method.

Identification of allele-specific DMRs. The sequence reads generated were aligned to the

B73 reference genome by Bismark software (5). B73 and Mo17 reads were extracted

according to SNPs (exclude C to T and A to G loci), which were used to determine the

methylation level of each allele. We calculated the DNA methylation level of 200 bp

windows with a step size of 20 bp. Regions covered with at least 5 cytosines for both alleles

were chosen. Then, QDMR software (6) was used to get the raw aDMRs with a SD threshold

of 0.07 (Entropy threshold: 1.695). The raw aDMRs were filtered with the standard that the

methylation level of one allele should be less than 30% while the other allele is more than

70%. The overlapped DMR were merged, and turned into candidate DMRs.

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Reference

1. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler

transform. Bioinformatics (Oxford, England) 25:1754-60.

2. Li H et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics

(Oxford, England) 25:2078-9.

3. McCarthy FM et al. (2006) AgBase: a functional genomics resource for agriculture.

BMC genomics 7:229.

4. Ye J et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic acids

research 34:W293-7.

5. Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for

Bisulfite-Seq applications. Bioinformatics (Oxford, England) 27:1571-2.

6. Zhang Y et al. (2011) QDMR: a quantitative method for identification of differentially

methylated regions by entropy. Nucleic acids research 39:e58.

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Figure S1. Expression ratio between maternal allele and paternal allele at each analyzed SNP

sites. X axis represent the ratio of maternal allele compared with paternal allele (log2), while

the Y axis shows the number of SNPs corresponding to the ratio. The result of the 10 DAP

endosperm of B73×Mo17 is shown on left, while that of Mo17×B73 in right. The peaks of

expression ratio (2:1) between maternal/paternal alleles for both B73×Mo17 and Mo17×B73

are shown with red lines.

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Figure S2. Expression and imprinting profile of genomic regions of three known imprinted

genes (Nrp1, ZmFie1 and Mez1) in 10 DAP endosperm transcriptome. Overall expression

level of transcribed regions is shown in light blue for both B73×Mo17 and Mo17×B73. The

relative expressional levels for specific SNP sites are shown for both B73 (orange lines) and

Mo17 (blue lines) alleles. Red rectangle, exon, black line, intron.

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Figure S3. Gene ontology analysis of identified imprinted genes. PEG and MEG represent all

paternally or maternally expressed imprinted genes, all genes represent all maize annotated

genes that have GO number. GO categories of MEGs or PEGs among molecular function and

biological process that show significant (P<0.05) enrichment than all genes were displayed.

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Figure S4. Validation of imprinting pattern in Zheng58/Chang7-2 genetic background.

RT-PCR products of GRMZM2G147226, GRMZM2G370991, GRMZM2G354579,

GRMZM2G091819 and ZmMNC-11 were digested by allele-specific enzymes using 12DAP

endosperm from the hybrids of reciprocal crosses of Zheng58 and Chang7-2. Zheng58 and

Chang7-2 inbreed were included as the control.

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Figure S5. Imprinting profile of 8 imprinted genes. The gel pictures show the RT-PCR

products digested by allele-specific enzyme. Two letters of the top represent the genotypes

(MM: Mo17 self; BB: B73 self; MB: Mo17×B73; BM: B73×Mo17), the numbers following

the letter indicate the developmental stages (2-8 DAP from kernel, 10-20 DAP from

endosperm).

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Figure S6. Expression profile of 10 imprinted genes. The gel pictures show the

semi-quantity RT-PCR products of all tested genes. Actin gene was used as a control, which

has been performed with different dilution to adjust the template concentration for PCR

among independent templates, and PCR was performed with 28 cycles. Two letters of the top

represent the genotypes (MB: Mo17×B73; BM: B73×Mo17), the numbers following the

letter indicate the developmental stages (2-8 DAP from kernel, 10-20 DAP endosperm).

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Figure S7. Expression profile of 10 imprinted genes in different tissues. The gel pictures

show the semi-quantity RT-PCR products of all tested genes. Actin gene was used as an

internal control, which has been performed with different dilution to adjust the template

concentration for PCR among independent templates, and PCR was performed with 28

cycles using samples from B73 inbred. DNA was used as control to indicate a amplification

of bigger genomic bands.

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Figure S8. Distribution of imprinted genes and clusters. Numbers around the circle specify

the 10 chromosomes in maize. Black lines on the outermost circle represent the imprinting

clusters identified in our study. Individual imprinted genes are shown in small rectangles.

Red rectangle represents MEGs, blue for PEGs, purple for MNCs, and while black for PNCs.

Black lines in the innermost circle (GD) indicate the gene densities around 10 chromosomes.

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SUPPLEMENTARY TABLES

Table S1. Transcriptome and bisulfite sequencing data used in this study.

Sample Read Number Read

Length(bp)

Amount of

Sequences

10DAP endosperm - B73×Mo17 70,791,990 reads 100 7.08Gb

10DAP endosperm - Mo17×B73 78,526,520 reads 100 7.85Gb

leaf - B73 33,477,982 reads 75 2.51Gb

leaf - Mo17 33,983,646 reads 75 2.55Gb

leaf - B73×Mo17 34,864,168 reads 75 2.61Gb

leaf - Mo17×B73 33,124,560 reads 75 2.48Gb

Total transcriptome sequences 284,768,866 reads

32.82Gb

12 DAP endoperm- B73×Mo17（BS ） 866,288,415 reads 100 86.6Gb

DAP represents Days After Pollination

BS represents Bisulfite Sequencing data

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Table S2. List of imprinted genes and associated SNPs in 10DAP endosperm.

Gene ID C

hr

SNP

relative

position

snp

norm

alized

BM_B

normali

zed

BM_M

MB_

B

M

B_

M

PvalueBM PvalueMB

Genom

ic

Region

impri

nt

type

unde

r 2:1

bias

start position end

position

par_

bias_

BM

par_

bias_

MB

imprin

t type

under

5:1

bias

Filter

GRMZM2G003909 1 889 G/T 92 0 0 19 1.18E-09 0.0020547 exon mat 350 1395 1.00 1.00 mat mat

GRMZM2G003909 1 892 C/T 88 0 0 18 2.55E-09 0.0026998 exon mat 350 1395 1.00 1.00 mat mat


GRMZM2G003909 1 1026 A/G 142 2 0 27 5.13E-13 0.0002386 exon mat 350 1395 0.98 1.00 mat mat

GRMZM2G009465 1 1573 C/T 14 0 1 27 0.0190165 0.0008355 exon mat 443 2293 1.00 0.96 mat mat

GRMZM2G009465 1 1606 A/G 15 0 1 55 0.0143059 5.50E-07 exon mat 443 2293 1.00 0.98 mat mat

GRMZM2G009465 1 1666 A/C 24 0 0 55 0.0020547 1.57E-07 exon mat 443 2293 1.00 1.00 mat mat

GRMZM2G009465 1 1696 C/T 27 0 0 63 0.0009111 1.99E-08 exon mat 443 2293 1.00 1.00 mat mat

GRMZM2G009465 1 1807 T/C 36 1 2 150 0.0004909 5.58E-17 exon mat 443 2293 0.97 0.99 mat mat



GRMZM2G010868 3 982 G/T 75 0 3 78 4.32E-08 1.54E-08 exon mat 1791 850 1.00 0.96 mat mat

GRMZM2G010868 3 1031 G/A 112 0 7 105 1.97E-11 1.20E-09 exon mat 1791 850 1.00 0.94 mat mat

GRMZM2G010868 3 1064 T/C 92 1 5 80 4.13E-09 7.93E-08 exon mat 1791 850 0.99 0.94 mat mat



GRMZM2G014119 6 290 C/A 121 1 1 157 1.16E-11 2.80E-18 exon mat 375 0 0.99 0.99 mat mat

GRMZM2G014119 6 333 T/C 107 1 0 24 1.91E-10 0.000532 exon mat 375 0 0.99 1.00 mat mat

GRMZM2G014256 6 5 T/A 19 0 1 10 0.0061699 0.0880815 exon no 0 650 1.00 0.91 mat mat

GRMZM2G014256 6 47 C/T 218 4 1 190 3.34E-19 6.65E-22 exon mat 0 650 0.98 0.99 mat mat

GRMZM2G014256 6 65 A/G 363 4 1 189 5.29E-32 8.56E-22 exon mat 0 650 0.99 0.99 mat mat

GRMZM2G014256 6 143 C/G 513 0 1 68 1.02E-46 1.93E-08 exon mat 0 650 1.00 0.99 mat mat

GRMZM2G014256 6 291 G/A 37 0 0 31 0.0001075 8.25E-05 exon mat 0 650 1.00 1.00 mat mat


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GRMZM2G050412 6 1386 G/C 39 1 0 15 0.000289 0.0061699 exon mat 1633 1075 0.97 1.00 mat mat

GRMZM2G050412 6 1399 T/C 39 1 0 19 0.000289 0.0020547 exon mat 1633 1075 0.97 1.00 mat mat

GRMZM2G050412 6 1415 T/G 41 1 0 21 0.0001704 0.0011937 exon mat 1633 1075 0.97 1.00 mat mat

GRMZM2G050412 6 1463 C/A 26 0 0 12 0.0011937 0.0143059 exon mat 1633 1075 1.00 1.00 mat mat


GRMZM2G056068 8 1969 T/A 14 0 1 12 0.0190165 0.0498602 exon mat 0 2337 1.00 0.92 mat mat




GRMZM2G062650 3 357 G/C 2558 175 26 1268 1.13E-157 2.85E-126 exon mat 449 223 0.94 0.98 mat mat








GRMZM2G063498 1 876 C/T 26 2 0 77 0.0121929 5.48E-10 exon mat 564 929 0.91 1.00 mat mat

GRMZM2G071808 7 1285 A/G 17 0 0 18 0.008151 0.0026998 exon mat 1409 1165 1.00 1.00 mat mat

GRMZM2G073700 6 186 A/G 15 1 0 14 0.0498602 0.008151 exon mat 529 0 0.92 1.00 mat no


GRMZM2G073700 6 4176 A/C 147 6 3 75 5.75E-12 3.31E-08 exon mat 4384 4071 0.96 0.96 mat mat


GRMZM2G084296 4 318 G/T 30 0 0 27 0.000532 0.0002386 exon mat 978 0 1.00 1.00 mat mat


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GRMZM2G108032 1 3248 G/C 67 0 0 13 2.03E-07 0.0107875 exon mat 2040 3428 1.00 1.00 mat mat

GRMZM2G108032 1 3326 G/T 73 1 1 12 1.96E-07 0.0498602 exon mat 2040 3428 0.98 0.92 mat mat


GRMZM2G108032 1 3335 C/T 57 1 1 11 5.67E-06 0.0661926 exon no 2040 3428 0.98 0.92 mat mat







GRMZM2G116646 3 6144 C/G 26 0 0 46 0.0011937 1.62E-06 exon mat 5839 6291 1.00 1.00 mat mat




GRMZM2G118205 4 1932 A/T 96 0 0 36 5.48E-10 2.21E-05 exon mat 1985 1860 1.00 1.00 mat mat


GRMZM2G118205 4 5577 C/G 56 0 0 15 2.10E-06 0.0061699 exon mat 6006 5468 1.00 1.00 mat mat




GRMZM2G118205 4 5690 T/G 194 2 2 65 1.22E-17 1.37E-07 exon mat 6006 5468 0.99 0.97 mat mat











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GRMZM2G130580 5 885 G/A 78 4 1 21 7.01E-07 0.0041786 exon mat 1656 641 0.95 0.95 mat mat


GRMZM2G130580 5 954 C/A 91 0 0 13 1.53E-09 0.0107875 exon mat 1656 641 1.00 1.00 mat mat


GRMZM2G130580 5 1100 C/G 82 0 0 19 9.22E-09 0.0020547 exon mat 1656 641 1.00 1.00 mat mat




GRMZM2G138861 1 7614 T/C 124 11 2 113 2.80E-08 6.61E-13 exon mat 7401 8110 0.92 0.98 mat no

GRMZM2G138920 10 2469 C/T 77 1 1 43 9.03E-08 1.24E-05 intron mat 2352 2861 0.98 0.98 mat mat

GRMZM2G141136 10 1305 A/C 14 0 0 19 0.0190165 0.0020547 exon mat 1108 2406 1.00 1.00 mat mat







GRMZM2G147226 8 3909 T/A 363 16 8 143 4.77E-27 2.71E-13 exon mat 3449 4252 0.96 0.95 mat mat











GRMZM2G150134 8 1139 G/A 16 0 0 16 0.0107875 0.0046777 exon mat 886 1539 1.00 1.00 mat mat


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GRMZM2G150134 8 1210 T/G 44 0 1 33 2.87E-05 0.0001704 exon mat 886 1539 1.00 0.97 mat mat





GRMZM2G157820 6 10165 T/A 101 0 0 18 1.97E-10 0.0026998 exon mat 10214 9603 1.00 1.00 mat mat








GRMZM2G160687 3 5684 T/A 67 0 0 32 2.03E-07 6.33E-05 exon mat 5751 5156 1.00 1.00 mat mat



GRMZM2G164229 4 939 C/A 27 0 1 50 0.0009111 2.01E-06 exon mat 554 1960 1.00 0.98 mat mat




GRMZM2G169695 8 59 A/T 12 0 0 13 0.0253473 0.0107875 exon mat 256 0 1.00 1.00 mat mat












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GRMZM2G170099 3 1089 A/C 66 0 2 39 2.64E-07 0.000111 exon mat 355 1676 1.00 0.95 mat mat











GRMZM2G354579 3 277 C/G 37 0 0 12 0.0001075 0.0143059 exon mat 0 887 1.00 1.00 mat mat












GRMZM2G354579 3 1477 C/T 136 0 1 10 1.55E-13 0.0880815 exon no 1338 1575 1.00 0.91 mat mat






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GRMZM2G379898 1 1345 T/A 16 0 0 35 0.0107875 2.87E-05 exon mat 0 1607 1.00 1.00 mat mat




GRMZM2G394203 1 959 G/T 44 4 0 82 0.0008794 1.52E-10 exon mat 0 1122 0.92 1.00 mat mat






GRMZM2G424205 7 1837 T/A 26 0 0 31 0.0011937 8.25E-05 exon mat 2369 1056 1.00 1.00 mat mat



GRMZM2G445602 1 3631 G/T 17 1 0 37 0.0284597 1.70E-05 exon mat 2135 3823 0.93 1.00 mat mat






GRMZM5G843095 4 507 A/G 25 0 0 13 0.0015654 0.0107875 intron mat 36 867 1.00 1.00 mat mat







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MTU1 7 242 C/A 233 0 1 61 2.2e-16 1.168e-07 TU mat 133252446 133253607 1.00 0.98 mat mat

MTU2 7 317 A/C 65 4 0 10 1.155e-05 0.02535 TU mat 27659707 27660784 0.95 1.00 mat mat

MTU2 7 288 C/T 73 4 0 10 1.940e-06 0.02535 TU mat 27659707 27660784 0.95 1.00 mat mat

MTU2 7 362 G/A 72 6 0 12 1.901e-05 0.01431 TU mat 27659707 27660784 0.92 1.00 mat mat



MTU3 9 1422 A/G 14 1 0 25 0.06619 0.000407 TU mat 108209205 108210865 0.92 1.00 mat mat

MTU3 9 1395 C/A 15 1 1 23 0.04986 0.002437 TU mat 108209205 108210865 0.92 0.96 mat mat

MTU4 1 1264 A/C 34 0 0 18 0.0002386 0.0027 TU mat 9047305 9048729 1.00 1.00 mat mat

GRMZM5G807847 9 -5 G/A 27 0 0 10 0.0009111 0.02535 extend mat 152458871 152459700 1.00 1.00 mat mat

GRMZM2G073700 6 -19 T/A 16 1 0 14 0.03764 0.008151 extend mat 112007295 112007991 0.93 1.00 mat mat

GRMZM2G008341 4 996 G/A 27 2 0 13 0.009375 0.01079 extend mat 29922130 29923545 0.92 1.00 mat mat

GRMZM2G008341 4 998 C/T 29 2 0 13 0.00721 0.01079 extend mat 29922130 29923545 0.92 1.00 mat mat

GRMZM2G158884 2 -649 C/T 22 0 0 10 0.0027 0.02535 extend mat 190933898 190936182 1.00 1.00 mat mat

GRMZM5G832908 1 -152 C/G 20 1 0 14 0.01635 0.008151 extend mat 158473585 158475353 0.94 1.00 mat mat

GRMZM2G010669 10 4296 A/G 67 1 0 42 7.122e-07 4.593e-06 extend mat 30868152 30868699 0.98 1.00 mat mat

AC148167.6_FG001 7 2107 G/A 16 46 18 4 1.06E-09 1.41E-06 exon pat 1961 2387 0.74 0.82 pat pat

AC148167.6_FG001 7 2160 C/T 22 65 31 11 3.64E-13 2.63E-08 exon pat 1961 2387 0.74 0.74 pat pat

AC191534.3_FG003 7 101 G/A 0 20 14 0 1.54E-08 1.21E-07 exon pat 0 442 1.00 1.00 pat pat

AC191534.3_FG003 7 147 C/T 1 27 16 0 2.30E-10 1.54E-08 exon pat 0 442 0.96 1.00 pat pat

AC191534.3_FG003 7 2525 C/A 7 133 141 0 1.55E-43 2.75E-63 intron pat 2434 2644 0.95 1.00 pat pat

AC192221.3_FG001 9 25098 T/G 10 26 12 2 8.03E-06 3.22E-05 intron pat 291 54792 0.72 0.86 pat pat

AC209208.3_FG001 5 6837 A/C 0 12 10 0 7.74E-06 7.74E-06 intron pat 6982 6826 1.00 1.00 pat pat

AC209208.3_FG001 5 7514 A/T 1 27 18 0 2.30E-10 1.97E-09 intron pat 7566 7051 0.96 1.00 pat pat

AC214292.3_FG003 1 2167 C/G 0 12 27 0 7.74E-06 2.00E-13 exon pat 2315 2111 1.00 1.00 pat pat

AC214292.3_FG003 1 2168 T/A 0 12 27 0 7.74E-06 2.00E-13 exon pat 2315 2111 1.00 1.00 pat pat

AC226373.2_FG010 6 2006 A/G 0 55 12 0 6.55E-21 9.63E-07 exon pat 2108 1922 1.00 1.00 pat pat

25

GRMZM2G002100 6 4427 C/T 0 51 32 2 1.36E-19 5.54E-14 exon pat 4537 4189 1.00 0.94 pat pat


GRMZM2G006428 10 9786 T/C 1 16 14 0 2.31E-06 1.21E-07 exon pat 9599 10246 0.93 1.00 pat pat

GRMZM2G006428 10 9955 A/G 4 39 16 2 8.38E-13 5.73E-07 exon pat 9599 10246 0.91 0.89 pat pat

GRMZM2G006428 10 10002 C/G 2 32 25 1 2.36E-11 1.08E-11 exon pat 9599 10246 0.93 0.96 pat pat



GRMZM2G006732 7 1227 G/C 16 123 154 4 4.26E-35 1.45E-65 exon pat 1673 332 0.88 0.97 pat pat






GRMZM2G006732 7 1681 T/C 1 12 23 1 5.10E-05 8.29E-11 intron pat 1784 1360 0.91 0.96 pat pat

GRMZM2G008513 3 5442 C/T 4 14 8 3 0.0003298 0.005578 exon pat 5253 5497 0.79 0.73 pat pat

GRMZM2G009014 1 4387 A/C 7 19 30 4 0.0002128 1.11E-11 exon pat 4272 4796 0.71 0.88 pat pat



GRMZM2G011608 3 6077 T/C 2 30 9 1 1.78E-10 0.0001439 exon pat 6367 5853 0.92 0.90 pat pat


GRMZM2G011608 3 6188 C/G 4 11 9 1 0.0021996 0.0001439 exon pat 6367 5853 0.75 0.90 pat pat


GRMZM2G014705 6 65 A/T 724 4614 2758 567 0 0 exon pat 142 0 0.86 0.83 pat pat



GRMZM2G020302 4 276 G/A 50 789 263 21 2.87E-245 1.20E-99 exon pat 0 554 0.94 0.93 pat pat


GRMZM2G023652 2 4394 T/A 32 148 102 20 1.41E-35 4.99E-32 exon pat 3726 4474 0.82 0.84 pat pat





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GRMZM2G026301 2 4597 A/T 7 158 111 40 3.23E-52 1.15E-25 exon pat 4901 4300 0.95 0.74 pat pat

GRMZM2G028037 3 4764 T/G 2 17 14 0 4.30E-06 1.21E-07 exon pat 5349 4408 0.88 1.00 pat pat

GRMZM2G028366 5 162 G/T 1 21 15 1 3.80E-08 2.95E-07 exon pat 243 0 0.94 0.94 pat pat



GRMZM2G028366 5 4337 C/A 1 32 12 0 3.91E-12 9.63E-07 exon pat 5170 4058 0.96 1.00 pat pat

GRMZM2G028366 5 4510 G/T 0 27 9 1 3.28E-11 0.0001439 exon pat 5170 4058 1.00 0.90 pat pat





















27






GRMZM2G037553 5 2888 G/A 5 12 9 1 0.0024969 0.0001439 intron pat 15930 74 0.71 0.90 pat pat



GRMZM2G044531 8 17 G/A 5 26 11 4 7.70E-08 0.001015 exon pat 340 0 0.84 0.73 pat pat




GRMZM2G048850 10 123 A/C 2 17 9 3 4.30E-06 0.0021996 exon pat 0 1381 0.88 0.75 pat pat

GRMZM2G048850 10 128 A/G 2 20 10 3 5.73E-07 0.0008561 exon pat 0 1381 0.89 0.77 pat pat



GRMZM2G050553 8 12405 C/T 4 12 11 1 0.0008561 1.81E-05 exon pat 12351 12489 0.77 0.92 pat pat






GRMZM2G070343 4 168 G/T 4 12 19 1 0.0008561 4.91E-09 exon pat 355 0 0.77 0.95 pat pat







GRMZM2G073495 6 948 C/G 4 17 11 3 1.81E-05 0.0003298 exon pat 1124 821 0.82 0.79 pat pat


GRMZM2G088701 7 309 C/T 15 46 13 5 3.78E-10 0.0004653 exon pat 450 0 0.76 0.72 pat pat

28










GRMZM2G091819 10 2432 T/C 91 2357 159 34 0 2.32E-47 exon pat 2336 2458 0.96 0.82 pat pat

GRMZM2G091819 10 2688 C/T 78 1420 144 14 0 1.32E-53 exon pat 2632 3203 0.95 0.91 pat pat

GRMZM2G091819 10 2704 G/T 86 1597 138 16 0 1.17E-49 exon pat 2632 3203 0.95 0.90 pat pat

GRMZM2G092869 2 836 A/C 10 41 30 11 1.50E-10 6.26E-08 exon pat 1145 616 0.80 0.73 pat pat




















29





GRMZM2G107867 1 6393 T/C 6 16 16 0 0.0004653 1.54E-08 exon pat 6104 6552 0.72 1.00 pat pat




GRMZM2G108285 7 2389 T/C 4 96 27 8 7.54E-33 3.84E-08 intron pat 2387 2588 0.96 0.77 pat pat

GRMZM2G108285 7 2591 T/C 98 936 1530 205 1.12E-267 0 exon pat 2589 3174 0.90 0.88 pat pat


GRMZM2G108285 7 2882 A/G 116 371 1041 49 2.45E-72 0 exon pat 2589 3174 0.76 0.96 pat pat

GRMZM2G108285 7 2994 A/T 143 804 2118 128 5.94E-200 0 exon pat 2589 3174 0.85 0.94 pat pat

GRMZM2G108285 7 3057 T/C 392 1888 3963 349 0 0 exon pat 2589 3174 0.83 0.92 pat pat




GRMZM2G108716 5 2797 T/G 5 45 10 4 2.90E-14 0.0024969 exon pat 2445 3792 0.90 0.71 pat pat


GRMZM2G108716 5 2814 C/T 6 40 11 4 6.95E-12 0.001015 exon pat 2445 3792 0.86 0.73 pat pat









GRMZM2G121570 1 1406 G/C 4 12 9 3 0.0008561 0.0021996 exon pat 948 2050 0.77 0.75 pat pat

GRMZM2G121570 1 1411 A/G 5 14 10 3 0.001015 0.0008561 exon pat 948 2050 0.73 0.77 pat pat



30





GRMZM2G121683 3 4767 A/T 0 40 24 2 1.24E-15 1.78E-10 intron pat 4721 5071 1.00 0.92 pat pat



GRMZM2G124421 9 4260 T/C 4 10 10 2 0.005578 0.0002386 exon pat 4388 3167 0.73 0.83 pat pat

GRMZM2G127160 6 537 A/C 63 1313 1039 13 0 0 exon pat 682 398 0.95 0.99 pat pat

GRMZM2G127160 6 1555 A/C 55 1053 1071 11 0 0 exon pat 1700 1397 0.95 0.99 pat pat

GRMZM2G127160 6 1655 G/C 66 2001 1529 31 0 0 exon pat 1700 1397 0.97 0.98 pat pat









GRMZM2G134716 7 907 A/C 5 12 18 1 0.0024969 1.36E-08 intron pat 300 6335 0.71 0.95 pat pat

GRMZM2G134716 7 6406 G/A 7 19 10 0 0.0002128 7.74E-06 exon pat 6336 6496 0.71 1.00 pat pat

GRMZM2G134716 7 6815 A/G 4 15 8 2 0.000126 0.0017451 exon pat 6741 7026 0.80 0.80 pat pat











31
















GRMZM2G144219 7 1047 T/A 4 15 32 9 0.000126 1.25E-09 exon pat 807 1220 0.80 0.78 pat pat





GRMZM2G146819 1 9919 A/T 20 63 13 4 1.09E-13 0.0001613 exon pat 10043 9760 0.76 0.76 pat pat







GRMZM2G158595 9 3782 C/G 4 10 9 2 0.005578 0.0006467 exon pat 3824 3525 0.73 0.82 pat pat

GRMZM2G158595 9 6353 T/G 6 29 14 5 4.28E-08 0.0001907 exon pat 6716 6197 0.82 0.74 pat pat




32








GRMZM2G170552 8 2785 A/G 5 16 82 14 0.0001613 2.61E-27 exon pat 2893 1026 0.76 0.85 pat pat

GRMZM2G170552 8 2800 A/G 4 15 71 10 0.000126 3.36E-25 exon pat 2893 1026 0.80 0.88 pat pat

GRMZM2G170552 8 2802 T/A 4 15 70 10 0.000126 8.91E-25 exon pat 2893 1026 0.80 0.88 pat pat





GRMZM2G173852 1 9467 C/G 5 56 11 3 3.71E-18 0.0003298 exon pat 9122 9475 0.92 0.79 pat pat


















33

GRMZM2G340681 8 26506 T/A 15 46 29 10 3.78E-10 5.48E-08 intron pat 32123 356 0.76 0.74 pat pat


GRMZM2G393471 9 9701 T/A 11 30 8 3 1.58E-06 0.005578 exon pat 9854 9082 0.73 0.73 pat pat





















GRMZM2G440968 6 1900 G/T 0 39 10 2 3.43E-15 0.0002386 exon pat 1987 1216 1.00 0.83 pat pat









34















GRMZM2G467159 9 10257 G/C 2 12 13 4 0.0002386 0.0001613 exon pat 10461 10238 0.83 0.76 pat pat






GRMZM2G472052 7 5588 G/A 4 10 13 1 0.005578 2.31E-06 intron pat 5398 9555 0.73 0.93 pat pat

GRMZM2G472052 7 5589 G/A 2 10 13 1 0.0017451 2.31E-06 intron pat 5398 9555 0.80 0.93 pat pat

GRMZM2G472052 7 5590 A/G 2 11 15 1 0.0006467 2.95E-07 intron pat 5398 9555 0.82 0.94 pat pat

GRMZM2G472052 7 5637 G/A 2 44 40 3 2.68E-15 1.01E-16 intron pat 5398 9555 0.95 0.93 pat pat



GRMZM2G472052 7 5832 C/T 7 54 54 2 6.41E-16 1.30E-23 intron pat 5398 9555 0.88 0.96 pat pat






35














GRMZM2G540940 2 108 C/A 5 12 14 3 0.0024969 1.81E-05 exon pat 0 147 0.71 0.82 pat pat








PTU4 7 220 G/A 4 26 65 0 1.811e-08 2.2e-16 TU pat 86195832 86196353 0.88 1.00 pat pat

PTU4 7 205 C/T 4 19 53 0 6.795e-06 2.2e-16 TU pat 86195832 86196353 0.83 1.00 pat pat

PTU8 9 65 T/C 6 20 14 4 3.097e-05 6.334e-05 TU pat 90987183 90987346 0.76 0.78 pat pat

PTU9 1 243 T/C 0 15 18 0 9.634e-07 1.973e-09 TU pat 43392191 43392878 1.00 1.00 pat pat

GRMZM2G127739 1 5474 G/A 2 26 8 2 3.687e-09 0.001745 extend pat 165405722 165406908 0.91 0.80 pat pat

GRMZM2G127739 1 5441 G/C 9 45 13 5 2.398e-12 0.0004653 extend pat 165405722 165406908 0.84 0.72 pat pat

GRMZM2G127739 1 5371 A/C 10 34 15 3 3.84e-08 6.795e-06 extend pat 165405722 165406908 0.77 0.83 pat pat

GRMZM2G127739 1 5323 C/A 9 34 20 2 1.201e-08 1.012e-08 extend pat 165405722 165406908 0.79 0.91 pat pat

GRMZM2G127739 1 5129 G/A 16 61 44 8 2.290e-14 4.342e-15 extend pat 165405722 165406908 0.79 0.85 pat pat

GRMZM2G127739 1 5100 T/C 15 41 32 3 1.255e-08 3.079e-13 extend pat 165405722 165406908 0.73 0.91 pat pat

GRMZM2G108285 7 40196 C/G 96 255 248 9 2.2e-16 2.2e-16 extend pat 155561356 155600049 0.73 0.96 pat pat

36

GRMZM2G108285 7 3262 C/G 0 15 11 0 9.634e-07 2.727e-06 extend pat 155561356 155600049 1.00 1.00 pat pat

GRMZM2G108285 7 3225 A/T 1 46 11 4 2.2e-16 0.001015 extend pat 155561356 155600049 0.97 0.73 pat pat

GRMZM5G845175 10 7612 G/A 0 39 22 1 3.435e-15 2.298e-10 extend pat 112394066 112395932 1.00 0.96 pat pat

37

Table S3. Functional annotations of imprinted protein-coding genes.

Gene ID Annotation

GRMZM2G003909 proline-rich protein


GRMZM2G010868 lipid-transfer protein

GRMZM2G014119 ubiquitin

GRMZM2G026978 hypothetical protein

GRMZM2G044440 ubiquitin

GRMZM2G045809 germin-like protein subfamily 1

GRMZM2G050412 jasmonate-induced protein

GRMZM2G056068 cadmium tolerant 1

GRMZM2G062650 NAM-related protein 1

GRMZM2G063498 low temperature viability protein

GRMZM2G073700 RNA-binding region-containing protein 1

GRMZM2G084296 PHD-finger family protein

GRMZM2G104542 nitrate transporter

GRMZM2G108032 Glycosyl hydrolase family 10 protein


GRMZM2G116626 Glycoside hydrolase

GRMZM2G116646 YABBY2 transcription factor

GRMZM2G118205 Polycomb group protein FIE1

GRMZM2G124708 unknown

GRMZM2G129083 cold shock protein-1

GRMZM2G130580 growth-regulating factor

GRMZM2G130715 phosphofructokinase


GRMZM2G147226 regulation of nuclear pre-mRNA domain-containing

protein(RPRD)

GRMZM2G150134 peroxidase 72 precursor

GRMZM2G157820 Histone-lysine N-methyltransferase EZ1 (EC 2.1.1.43)(Enhancer

of zeste protein 1)

GRMZM2G160687 MADS-box transcription factor

GRMZM2G164229 metallothionein-like protein 1

GRMZM2G168651 histidine-rich protein

GRMZM2G169695 AT-rich element binding factor 3

GRMZM2G170044 lipid binding protein

GRMZM2G170099 PHD finger family protein

GRMZM2G354579 adhesin FhaB

GRMZM2G359952 MADS-box Transcription factor


GRMZM2G370991 ethylene signaling protein


GRMZM2G383404 anthocyanidin 3-O-glucosyltransferase

GRMZM2G384780 anther-specific proline-rich protein APG


GRMZM2G410916 glycosyltransferase

38


GRMZM2G445602 fiddlehead-like protein

GRMZM2G474194 beta-expansin 1a precursor

GRMZM2G014256 ubiquitin family protein

GRMZM2G033413 bZIP transcription factor family protein


GRMZM2G092997 legumain-like protease

GRMZM2G138861 serine/threonine-protein kinase

GRMZM2G138920 beta-tubulin

GRMZM2G177934 chemocyanin precursor

GRMZM2G401308 histone H1-like protein


GRMZM2G445613 fiddlehead-like protein

GRMZM5G845644 anther-specific proline-rich protein APG

GRMZM5G858417 Nucleobase-ascorbate transporter LPE1 (Leaf permease protein

1)

GRMZM5G898444 nonspecific lipid-transfer protein 4 precursor

GRMZM5G898755 nonspecific lipid-transfer protein 4 precursor


MTU1 hypothetical protein

MTU2 unknown

MTU3 unknown

MTU4 unknown

GRMZM2G008341 alpha-zein protein


GRMZM5G832908 GAUT13

GRMZM2G010669 putative MADS-domain transcription factor

AC148167.6_FG001 seed specific protein Bn15D14A

AC209208.3_FG001 ATP binding protein

GRMZM2G002100 ABA stimulation MAP kinase

GRMZM2G006428 zinc finger protein-related

GRMZM2G006732 F-box domain containing protein



GRMZM2G011608 nucleotidyltransferase family protein

GRMZM2G012964 pumilio/Mpt5 family RNA-binding protein

GRMZM2G014705 early nodulin 93 protein

GRMZM2G018837 calmodulin binding protein


GRMZM2G023652 lymphoid organ expressed yellow head virus receptor protein


GRMZM2G025409 pentatricopeptide repeat protein (PPR) family

GRMZM2G025703 PHD finger family protein

GRMZM2G026301 putative protein kinase

GRMZM2G028037 putative serine/threonine protein kinase

GRMZM2G028366 eukaryotic initiation factor 4A


39

GRMZM2G044531 Putative uncharacterized protein

GRMZM2G047104 unknown protein

GRMZM2G048850 GATA type transcription factor


GRMZM2G057436 putative ubiquitin-protein ligase

GRMZM2G068117 protein kinase

GRMZM2G070343 Thioredoxin-like protein

GRMZM2G073495 50s ribosomal protein

GRMZM2G086489 NADPH-cytochrome P450 reductase

GRMZM2G091819 disulfide oxidoreductase monooxygenase oxidoreductase


GRMZM2G093316 ATP binding protein

GRMZM2G096153 glutathione s-transferase

GRMZM2G097207 glycosyl hydrolase family 17 protein

GRMZM2G102745 mitochondrial carrier protein

GRMZM2G103909 fiber protein Fb2


GRMZM2G104866 AP2/ERF domain transcription factors

GRMZM2G106141 protein phosphatase 2A regulatory subunit B

GRMZM2G106222 Ubiquitin carboxyl-terminal hydrolase

GRMZM2G107867 SNF1-related protein kinase

GRMZM2G108285 isopentenyl pyrophosphate isomerase

GRMZM2G108716 transcription elongation factor

GRMZM2G121570 MYB family transcription factor-like


GRMZM2G124421 CBF/NF-Y family transcription factor

GRMZM2G127160 tryptophan aminotransferase

GRMZM2G127739 extra-large GTP-binding protein

GRMZM2G128663 PAPA-1-like family protein

GRMZM2G132184 serine threonine protein kinase


GRMZM2G136067 histone deacetylase

GRMZM2G136465 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1

GRMZM2G136868 anaphase-promoting complex

GRMZM2G138245 calcium dependent protein kinase1

GRMZM2G138382 anthranilate synthase alpha 1 subunit

GRMZM2G138511 putative heat shock protein

GRMZM2G145968 nucleosome/chromatin assembly factor D

GRMZM2G146819 metal ion binding protein

GRMZM2G158595 putative selenoprotein O

GRMZM2G161680 CBF/NF-Y family transcription factor

GRMZM2G164663 cysteine-type peptidase

GRMZM2G170552 CBL-interacting protein kinase

GRMZM2G171383 anthranilate synthase component II

GRMZM2G173852 acetyltransferase

GRMZM2G181251 SEU3A protein

GRMZM2G324131 GATA type transcription factor

40


GRMZM2G339820 VIN3 like protein


GRMZM2G393471 nuclear receptor binding set domain containing protein 1


GRMZM2G440949 Dr1-associated corepressor

GRMZM2G447406 pherophorin-dz1 protein-like



GRMZM2G472052 KH domain nucleic acid binding protein

GRMZM2G477503 glycosyl transferase




AC191534.3_FG003 putative zinc finger protein/VARIANT IN METHYLATION-like

protein

AC192221.3_FG001 unknown protein

AC214292.3_FG003 trimeric autotransporter adhesin

AC226373.2_FG010 zinc finger C-x8-C-x5-C-x3-H type family protein







GRMZM2G144219 unknnown


GRMZM2G152526 RNA recognition motif (RRM)-containing protein-like





GRMZM2G440968 cysteine proteinase inhibitor

GRMZM2G457001 putative cytidine deaminase




GRMZM5G830365 ethylene-responsive factor-like transcription factor erfl2b

GRMZM5G854045 PAPA-1-like family protein


GRMZM5G881380 Zinc finger CCCH domain-containing protein

PTU4 hypothetical protein

PTU8 rRNA intron-encoded homing endonuclease

PTU9 protein kinase APK1B

GRMZM5G845175 SNF4

http://www.ncbi.nlm.nih.gov/protein/13171103?report=genbank&log$=prottop&blast_rank=2&RID=VK6GW7XX01S

41

Table S4. Imprinted genes homologous to known imprinted genes in Arabidopsis.

Gene ID _maize Imprinting

Type_maize Gene ID _At/rice

Imprinting

Type_At/rice similarity E value Annotation

AC191534.3 pat AT1G57800 pat 60.73 7.00E-150 VIM5 (VARIANT IN METHYLATION 5); protein binding / zinc

ion binding

GRMZM2G091819 pat AT1G48910 pat 49.1 2.00E-106 YUC10; FAD binding / monooxygenase/ oxidoreductase

GRMZM2G103909 pat AT3G05700 mat 31.69 5.00E-18 Drought induced 19/drought-responsive family protein

GRMZM2G157820 mat AT1G02580 mat 50.75 2.00E-14 MEA (MEDEA); sequence-specific DNA binding /

transcription factor

GRMZM2G370991 mat AT5G03280 mat 41.94 2.00E-25 EIN2 (ETHYLENE INSENSITIVE 2); transporter

GRMZM5G832908 mat AT5G15470 mat 64.48 2.00E-59 GAUT14 (Galacturonosyltransferase 14);

GRMZM2G003909 mat LOC_Os10g05750.1 mat 71.74 2.40E-31 POEI3 - Pollen Ole e I allergen and extensin family protein

precursor, expressed

GRMZM2G028366 pat LOC_Os02g12840.1 pat 65.81 7.30E-54 DEAD-box ATP-dependent RNA helicase, putative, expressed

GRMZM2G045809 mat LOC_Os08g08960.1 mat 76.13 5.20E-63 Cupin domain containing protein, expressed

GRMZM2G073700 mat LOC_Os06g11730.1 mat 92.63 6.90E-46 RNA recognition motif containing protein, putative,

expressed

GRMZM2G091819 pat LOC_Os12g08780.1 pat 67.93 5.50E-69 flavin monooxygenase, putative, expressed

GRMZM2G114356 mat LOC_Os10g05750.1 mat 74.47 1.80E-31 POEI3 - Pollen Ole e I allergen and extensin family protein


GRMZM2G118205 mat LOC_Os08g04290.1 mat 72.59 2.40E-118 WD domain, G-beta repeat domain containing protein,

expressed

GRMZM2G146819 pat LOC_Os03g38970.1 pat 90.8 0.00E+00 metal ion binding protein, putative, expressed

GRMZM2G147226 mat LOC_Os01g70060.1 pat 71.82 5.00E-40

regulation of nuclear pre-mRNA domain-containing

protein(RPRD)/ protein of unknown function, DUF618

domain containing protein, expressed

GRMZM2G158884 mat LOC_Os06g23460.1 pat 63.64 5.00E-04 KH domain containing protein, putative, expressed

GRMZM2G170099 mat LOC_Os01g18810.1 mat 76.92 1.10E-05 PHD finger family protein / hypothetical protein

42

GRMZM2G379898 mat LOC_Os03g01320.1 mat 81.63 7.30E-71 LTPL116 - Protease inhibitor/seed storage/LTP family protein


GRMZM2G447406 pat LOC_Os01g70060.1 pat 74.19 3.30E-05 pherophorin-dz1 protein-like/protein of unknown function,

DUF618 domain containing protein, expressed

GRMZM2G472052 pat LOC_Os07g12490.1 pat 91.7 3.10E-150 KH domain containing protein, putative, expressed

GRMZM5G845175 pat LOC_Os04g32880.1 pat 90.12 8.60E-40 SNF4/CBS domain containing membrane protein, putative,

expressed

43

Table S5. List of imprinted non-coding transcripts identified in our study.

Gene ID Chromosome

Transcript Start

Position(bp)

Transcript

End

Position(bp)

Estimated

Transcript

Length(bp)

Details

non-coding

Transcripts

Imprinting

Type

Associated Gene

ID

Associated

Gene

Imprinting

Status

MNC-1 1 51041955 51042289 335 intergenic maternal - -

MNC-2 1 1789 1965 177 intronic maternal GRMZM2G128663 paternal

MNC-3 1 29232 29621 390 intronic maternal GRMZM2G072939 no

MNC-4 2 2143 2431 289 intronic maternal GRMZM5G859691 unknown


















MNC-22 9 intronic maternal GRMZM2G415192 unknown




44

PNC-1 2 1350 1428 79 intronic paternal GRMZM2G033962 unknown



PNC-4 3 4731 4999 269 intronic paternal GRMZM2G121683 paternal


PNC-6 5 202930577 202932226 1650 intergenic paternal - -


PNC-8 6 691 934 244 intronic paternal GRMZM2G127160 paternal






45

Table S6. List of imprinted non-coding transcripts and associated SNPs.

Gene

Name

Chr SNP

Position

SNP normalized

BM_B

normali

zed

BM_M

MB

_B

MB_

M

pvalue_B

M

Pvalue_MB Imprint

Status

under

2:1

Genomic

Structure

Start

position

End

position

Parent

_bias_

BM

Parent_

bias_M

B

Imprint

Status

under

5:1

MNC-3 1 29394 C/G 52 5 1 56 0.000393 4.25E-07 mat intron 29232 29621 0.91 0.98 mat

MNC-17 7 1422 G/A 98 7 1 15 2.77E-07 0.02155627 mat intron 922 1651 0.93 0.94 mat

MNC-20 9 2852 T/C 34 0 1 48 0.000239 3.37E-06 mat intron 2606 3057 1.00 0.98 mat

MNC-10 5 1026 G/A 36 0 0 13 0.00014 0.01078745 mat intron 857 1270 1.00 1.00 mat


MNC-10 5 1117 T/C 31 2 1 22 0.004267 0.0031897 mat intron 857 1270 0.93 0.96 mat

MNC-10 5 1121 C/T 29 2 1 22 0.00721 0.0031897 mat intron 857 1270 0.92 0.96 mat

MNC-10 5 1145 C/A 31 1 0 20 0.001425 0.0015654 mat intron 857 1270 0.96 1.00 mat



MNC-6 4 3027 T/C 175 1 1 48 1.61E-16 3.37E-06 mat intron 2930 3369 0.99 0.98 mat

MNC-6 4 3073 G/A 136 0 2 41 1.55E-13 6.61E-05 mat intron 2930 3369 1.00 0.95 mat

MNC-6 4 3298 A/G 773 9 8 189 9.26E-66 2.89E-18 mat intron 2930 3369 0.99 0.96 mat

MNC-25 10 4779 C/T 132 7 1 129 3.37E-10 3.37E-15 mat intron 4485 5117 0.95 0.99 mat




MNC-19 9 2319 T/G 14 0 0 26 0.019016 0.00031149 mat intron 1880 2512 1.00 1.00 mat


MNC-15 7 5408 A/G 76 7 3 128 2.31E-05 4.80E-14 mat intron 5022 5536 0.91 0.98 mat

MNC-15 7 5460 A/G 62 6 0 74 0.000137 1.18E-09 mat intron 5022 5536 0.91 1.00 mat

MNC-21 9 3164 T/C 31 0 1 15 0.000407 0.02155627 mat intron 2979 3306 1.00 0.94 mat

MNC-21 9 3207 G/C 29 0 0 17 0.000696 0.00355147 mat intron 2979 3306 1.00 1.00 mat

46

MNC-4 2 2215 A/T 50 5 0 14 0.000647 0.00815097 mat intron 2143 2431 0.91 1.00 mat

MNC-8 5 11101 C/A 123 0 2 21 1.98E-12 0.01219285 mat intron 10958 11541 1.00 0.91 mat



MNC-24 10 2864 T/G 32 0 0 11 0.000311 0.01901647 mat intron 2708 3081 1.00 1.00 mat

MNC-18 8 1690 A/G 36 0 0 11 0.00014 0.01901647 mat intron 1523 1782 1.00 1.00 mat

MNC-9 5 1869 T/C 52 0 2 22 4.59E-06 0.00937477 mat intron 1720 2347 1.00 0.92 mat

MNC-9 5 1927 G/A 44 0 0 15 2.87E-05 0.0061699 mat intron 1720 2347 1.00 1.00 mat

MNC-22 9 6241 C/A 20 0 1 65 0.004678 4.17E-08 mat intron 6142 6403 1.00 0.98 mat

MNC-22 9 6264 C/T 24 0 1 70 0.002055 1.15E-08 mat intron 6142 6403 1.00 0.99 mat

PNC-4 3 4767 A/T 0 40 24 2 1.24E-15 1.78E-10 pat intron 4731 4999 1.00 0.92 pat

PNC-8 6 719 C/T 2 29 10 0 4.89E-10 7.74E-06 pat intron 691 934 0.92 1.00 pat

PNC-8 6 745 T/C 0 29 10 0 1.18E-11 7.74E-06 pat intron 691 934 1.00 1.00 pat

PNC-1 2 1354 A/G 1 55 52 1 4.70E-20 1.46E-23 pat intron 1350 1428 0.98 0.98 pat

PNC-1 2 1373 G/T 1 66 60 1 5.32E-24 4.58E-27 pat intron 1350 1428 0.98 0.98 pat



PNC-7 6 530 A/T 5 12 46 17 0.002497 2.36E-11 pat intron 441 762 0.71 0.73 pat

PNC-5 4 19046 G/A 4 31 8 2 3.37E-10 0.00174512 pat intron 18977 19086 0.89 0.80 pat

PNC-11 8 5427 G/A 0 20 58 0 1.54E-08 4.75E-27 pat intron 5311 5460 1.00 1.00 pat

PNC-13 10 606 T/C 4 19 13 3 6.80E-06 4.79E-05 pat intron 492 880 0.83 0.81 pat

PNC-3 2 6736 G/A 12 51 50 1 1.01E-12 1.10E-22 pat intron 6483 6876 0.80 0.98 pat


PNC-2 2 31095 G/T 2 11 11 1 0.000647 1.81E-05 pat intron 31070 31314 0.82 0.92 pat


MNC-1 1 236 T/C 19 1 0 10 0.02156 0.02535 mat intergenic 51041955 51042289 0.94 1.00 mat

MNC-23 10 114 C/T 15 1 0 43 0.04986 3.54E-06 mat intergenic 1.28E+08 127854008 0.92 1.00 mat


MNC-7 5 463 C/T 39 0 2 43 8.25E-05 3.94E-05 mat intergenic 18696083 18696868 1.00 0.96 mat

MNC-7 5 412 T/C 41 0 2 45 4.87E-05 2.35E-05 mat intergenic 18696083 18696868 1.00 0.96 mat

47

MNC-11 6 600 G/A 147 1 0 90 5.51E-14 1.97E-11 mat intergenic 79477512 79478438 0.99 1.00 mat

MNC-11 6 621 A/C 200 2 1 180 2.20E-16 2.20E-16 mat intergenic 79477512 79478438 0.99 0.99 mat

MNC-11 6 666 C/T 264 1 0 173 2.20E-16 2.20E-16 mat intergenic 79477512 79478438 1.00 1.00 mat

MNC-11 6 693 G/A 258 0 0 163 2.20E-16 2.20E-16 mat intergenic 79477512 79478438 1.00 1.00 mat



MNC-11 6 762 A/G 182 1 3 99 2.20E-16 7.45E-11 mat intergenic 79477512 79478438 0.99 0.97 mat


MNC-14 7 147 T/C 39 0 0 10 8.25E-05 0.02535 mat intergenic 28354008 28354474 1.00 1.00 mat

MNC-14 7 129 C/T 35 1 0 18 0.00064 0.0027 mat intergenic 28354008 28354474 0.97 1.00 mat

PNC-12 10 437 T/C 37 108 105 30 2.20E-16 2.20E-16 pat intergenic 23382213 23382890 0.74 0.78 pat

PNC-6 5 1146 C/G 0 29 24 0 1.18E-11 4.26E-12 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1157 G/A 0 27 20 0 3.28E-11 2.54E-10 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1169 T/G 0 25 17 0 2.54E-10 5.51E-09 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1314 T/G 0 24 32 0 7.07E-10 1.24E-15 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1328 T/A 0 25 35 0 2.54E-10 2.20E-16 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1425 A/G 0 56 50 0 2.20E-16 2.20E-16 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1191 T/C 0 20 18 0 1.54E-08 1.97E-09 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1449 A/C 0 71 56 0 2.20E-16 2.20E-16 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-6 5 1203 A/C 0 19 17 0 4.32E-08 5.51E-09 pat intergenic 2.03E+08 202932226 1.00 1.00 pat

PNC-10 7 106 A/G 2 42 42 1 7.36E-15 2.20E-16 pat intergenic 1.28E+08 127720048 0.94 0.98 pat

48

Table S7. Clusters of Imprinted genes.

Cluster ID Chr Cluster Start

Position(bp)

Cluster End

Position(bp)

Cluster

Range(bp)

Number

of

Genes

Gene ID Gene Start

Position(bp)

Gene End

Position(bp)

Imprinting

Type

Gene

Number

Order

cluster1 1 1665098 1878455 213357 2 GRMZM2G474194 1665098 1666489 MEG 513

GRMZM2G379898 1876848 1878455 MEG 539

cluster2 1 7768664 8519625 750961 3 GRMZM2G136868 7768664 7770577 PEG 985

GRMZM2G096153 7866607 7868253 PEG 994

GRMZM2G009014 8514829 8519625 PEG 1058


GRMZM2G445613 16822906 16826454 MEG 1639

cluster4 1 43392191 44373917 981726 2 PTU9 43392191 43392878 PEG

GRMZM2G107867 44367365 44373917 PEG 3271


MNC-1 51041955 51042289 MNC


GRMZM2G114356 119998869 120000361 MEG 6897

GRMZM2G009465 120192918 120195211 MEG 6904


MNC-2 291927853 291928029 MNC


GRMZM2G158884 190934769 190939263 MEG 26466


PNC-4 23431930 23432198 PNC


GRMZM2G011608 230653193 230659560 PEG 41549


49

GRMZM2G118205 35757180 35763186 MEG 43908


GRMZM5G845644 171633150 171634739 MEG 49709


GRMZM2G108716 2792233 2796025 PEG 54487


MNC-9 3089080 3089707 MNC


GRMZM2G136465 202416165 202420768 PEG 64572


GRMZM2G073495 3052152 3054637 PEG 66134


MNC-11 79477512 79478438 MNC


GRMZM2G014256 95841312 95843445 MEG 70085


GRMZM2G092895 99884497 99890846 PEG 70359


PNC-8 123434933 123435176 PNC

cluster21 6 155654630 156419381 764751 4 MNC-12 155654630 155655030 MNC

GRMZM2G440949 155661607 155667746 PEG 73983

GRMZM2G440968 155666553 155668540 PEG 73984

AC226373.2_FG010 156415329 156419381 PEG 74040


AC148167.6_FG001 11665296 11671232 PEG 76044

cluster23 7 27659707 28354474 694767 3 MTU2 27659707 27660784 MEG

AC191534.3_FG003 27669317 27671990 PEG 76821

MNC-14 28354008 28354474 MNC

50

cluster24 7 133252446 133361750 109304 2 MTU1 133252446 133253607 MEG

MNC-16 133361548 133361750 MNC


MNC-18 13782690 13782949 MNC


GRMZM2G447406 160604534 160610434 PEG 92132


GRMZM5G830365 97020918 97021679 PEG 98406

GRMZM2G104866 97035492 97037054 PEG 98409


MNC-19 117958560 117959192 MNC


GRMZM5G898755 4243325 4244555 MEG 102643

GRMZM5G898444 4243825 4244497 MEG 102644


GRMZM2G324131 9530641 9532659 PEG 103009


GRMZM2G091819 16517475 16520678 PEG 103360


MNC-23 127853717 127854008 MNC


MNC-24 148301715 148302088 MNC

GRMZM2G138920 148323855 148327356 MEG 109873

51

Table S8. Detailed information for our identified allele-specific DMRs for the

imprinted genes.

Gene ID

Imprinting

Type

DMR

Start

DMR

End

DMR

Length

Methyl %

of B73

allele

Methyl%

of Mo17

allele

Genomic

Region of

DMR

GRMZM2G009465 MEG -1716 -1417 300 37.89 96.67 upstream

GRMZM2G130580 MEG 8 367 360 1.30 87.92 last_exon


GRMZM2G044440 MEG 2393 2812 420 21.29 91.01 downstream



GRMZM2G424205 MEG 1600 1979 380 25.82 91.67 first_exon

MTU2 MEG 495 914 420 2.98 83.89 intragenic

MTU4 MEG -823 -484 340 9.58 100.00 intergenic

GRMZM2G107867 PEG 1277 1736 460 20.92 100.00 first_intron

GRMZM2G020302 PEG 6337 6676 340 14.84 100.00 first_intron

GRMZM2G018837 PEG 7818 8197 380 4.74 100.00 last_exon


GRMZM2G011608 PEG 541 900 360 9.42 90.00 internal_intron




MNC-3 MNC -699 -240 460 13.60 95.28 intronic

MNC-7 MNC 1459 1838 380 14.20 95.83 intergenic

MNC-13 MNC -331 -112 220 18.65 82.14 intronic

MNC-24 MNC -154 385 540 5.48 97.14 intronic

MTU, maternally expressed transcription unit.

Minus sign, represents the extension length for certain genes’ genomic region.

52

Table S9. Transposible element enrichment around imprinted genes.

NO. of TEs located in proximity to genes Fisher's Exact test

TE Type MEG(64) PEG(108) non-IMP(2955) P value_MEG P value_PEG

CACTA 26 24 416 3.46E-05 0.06

Helitron 4 5 77 0.10 0.22

MITE 47 109 3368 0.03 0.41

Mutator 5 23 553 0.06 0.54

PIF/Harbinger 4 20 319 0.40 0.03

hAT 9 20 893 0.03 0.05

LINE 24 53 1635 0.12 0.50

SINE 1 9 390 0.01 0.24

Ty1/copia 148 235 6954 0.94 0.51

Ty3/gypsy 152 254 7335 0.76 0.64

Total 420 752 21940 0.36 0.52

The numbers in brackets show the gene numbers that used for analysis.

53

Table S10. Primers and corresponding enzymes used for imprinting validation.

Gene Name

Primer

Name

SNP

Posit

ion

Allele-

specific

Enzyme Primers Sequence(5'→3')

Usage / Purpose

GRMZM2G091819 1819-f 2085 AluI AGTACATCACGAGGGAGCAGTT Validate imprinted

expression/Expression

1819-r

ATCCTCGAACTCCACTGTGTTT

GRMZM2G127160 7160-f 1584 KpnI CCCGACTATGTACGAGGAGTTC Validate imprinted


7160-r

TTGGCTTGTTTTACCAGAGGAT

GRMZM2G449489 489-f 4650 BglII GCATCATCGTCTGAGTTGGATA Validate imprinted


489-r

TTGGTTTGATCCTGAGTTGTTG

GRMZM2G138382 382-f 591 NheI TGAGGGAGGAGGAGTCCAGGT Validate imprinted


382-r

CTGTCAGCAATCTGCGGGTTC

GRMZM2G447406 406-f 5222 NarI AAGAGCACACTTCTGGTAACAAGAG Validate imprinted


406-r

GTGTTCTCGGATGATCTAGCGA

AC208539.3_FG002 539-f 1070 NlaIII AGCCCTATCTATCCAGTCCTATAGC Validate imprinted


539-r

CATGCCCAATACTTGACAAATAAAC

GRMZM2G354579 579-f 487 TaiI CAGACACAACAAAGCCCAAG Validate imprinted


579-r

TGCCAACATGCATTTCAAAT

GRMZM2G028366 366-f 6885 DdeI GATCAAGCGCCCAAGGTGA Validate imprinted


366-r

TGCCAAGTCGGGTGTCGGT

GRMZM2G147226 226-f 3682 KpnI GGGTATCTTTGCTGTACCTTGC Validate imprinted


226-r

AACTTCACGACAATTTGCACAC

GRMZM2G160687 687-f 5463 RsaI TGAGAAAGGCATCTCTAAGATCAGG Validate imprinted


687-r

CACACACAAAAGGCAACAACAATA

GRMZM2G370991 0991-f

1027

2 NlaIII AGAGGCGGGTATGACGAGAAG Validate imprinted


0991-r

CACAGCTTCCACGCTGATACG

GRMZM2G097059 059-f

1111

3 EarI CCCGTAGTGGACTATGATGAGACC Validate imprinted


059-r

GCATCGCATCTTTATTTATTCCC

GRMZM2G084703 703-f -155 NlaII ACATAGAGAAAGCAAACACCACACC Validate imprinted


703-r

CAAACATCAGCTAGAACAATCCTGA

GRMZM2G027937 937-f 585 RsaI GCCTTTTGTGTGTGATTCTCCGT Validate imprinted


937-r

ACATGATGTCCTGATCACAGCCT

ZmMNC-24 MNC24-f 2864 HinfI CGGTCAGCCAGAATGACCAG Validate imprinted


MNC24-r

GCCCTTTGAACACCGCCT

GRMZM2G406553 553-f 9913 NcoI GCATTTTGCTGCTGCTATTCC Validate imprinted


553-r

ATGACAAAGGGAGGTACTCAGAAGA

ZmMNC-18 MNC18-f 1690 BceAI GCTGAGTTGATTAGGTGGTCTGAGT Validate imprinted


MNC18-r

TAAGAATACATTCTCACGCAGATCG

GRMZM2G477503 503-f 5818 TatI TGCCATCGGAGTCAGAAACG Validate imprinted


503-r

CCACACCAATCACAGTCCAATAC

ZmMNC-11 MNC11-f 176 HhaI AGCCATCAATCAAAAAGTTACAATC Validate imprinted


MNC11-r

GCATAGAGGATAGTGAACTAGCAAG

54

ZmPNC-10 PNC10-f 107 MboII ACCATCAGAGAGAGAGAGAGAAACG Validate imprinted


PNC10-r －－ TGTACTAGCTAGAGAGCTGGAGCCT

GRMZM2G477503 GSP1-13 －－ GCAGATCGAGAAAACCCATGTCCCAC for whole length of

ZmMNC-18 GRMZM2G477503 NGSP1-12 －－ CGGACCTTAGACCTGTGATTTGGTGTGA

GRMZM2G477503 GSP2-12 －－ CCAAATCACAGGTCTAAGGTCCGGTCA for whole length of

ZmMNC-18 GRMZM2G477503 NGSP2-12 －－ TGTGTATGGGTGGGACATGGGTTTTCTC

GRMZM2G477503 503-1-f －－ GCCTACAAAGTTCTCACCCCAG for whole length of

GRMZM2G477503 GRMZM2G477503 503 -1-r －－ GCAACCTCCGAAATGATCCTAG

GRMZM2G477503 503-2-f －－ TTTCGCTGGCACTCAGTCCTA for whole length of

GRMZM2G477503 GRMZM2G477503 503 -2-R －－ AGCGTTTCTGACTCCGATGG

GRMZM2G477503 503-3-F －－ CATGCCATCGGAGTCAGAAAC for whole length of

GRMZM2G477503 GRMZM2G477503 503 -3-R －－ GTAATCGATGGAATTGCCACAC

GRMZM2G406553 553-T2-f －－ ATGCGTCCAATGTGAACTGC for whole length of

GRMZM2G406553 GRMZM2G406553 553-T2-r －－ GCGACACCATAGAGGATGAAGC

GRMZM2G406553 553-T3-f －－ TTGGAGACATTTGAGTTGATTGGAT for whole length of

GRMZM2G406553 GRMZM2G406553 553-T3-r －－ CACCATAGAGGATGAAGCGGAC

GRMZM2G406553 553-T4-f －－ AAATAGAATGCAAACATGGAGAACA for whole length of

GRMZM2G406553 GRMZM2G406553 553-T4-r －－ GAGTAAGGCGACCTGGATGC

ZmMNC-24 553-T-2R －－ CGTGGCTCTCCTTCCTCCTG for whole length of

ZmMNC-24 ZmMNC-24 553-t-2r －－ CACGCCCTTTGAACACCG

ZmMNC-24 mnc24-1-f －－ GTTATCGGGGGAGATTGGGCTGCTA for whole length of

ZmMNC-24 ZmMNC-24 mnc24-1-r －－ CGATGCCTTGACTTGCGATTGGTGTA

ZmMNC-24 mnc24-2-f －－ TTGAGTTGATTGGATCTACAGGACCTGAGG for whole length of

ZmMNC-24 ZmMNC-24 mnc24-2-r －－ TTACTCCGTAGCCTAAGGCGTCCGC

ZmMNC-24 mnc24-3-f －－ AGCAGATGAAGTTACTGAGGGCAGCTCC for whole length of


ZmMNC-24 mnc24-4-f －－ GGTTCTTGTCACCGGAGGAGAGGATCAT for whole length of


ZmMNC-24 mnc24-5-f －－ CAGGGCGACACCATAGAGGATGAAGC for 3' RACE of

ZmMNC-24

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