玉米雌穗发育杂种优势相关miRNA的研究

doi:10.3724/SP.J.1006.2018.00796

Abstract

Abstract:

Heterosis has been utilized widely in maize breeding; it plays an important role in increasing yield, improving quality and enhancing stresses resistance. However, the molecular mechanism of heterosis is far from clear. MicroRNAs (miRNAs) act as key regulating factors of gene expression in post-transcriptional level. To investigate whether miRNA-dependent gene regulation is responsible for heterosis during maize ear development, we performed an illumine miRNA deep-sequencing on the most widely-planted elite hybrid Zhengdan 958 and its parental inbred lines (Chang 7-2 and Zheng 58) in China. The ear samples at the developmental stages of inflorescence meristem (IM) producing spikelet pair meristems (SPM), resulting in spikelet meristems (SMs), and floral meristems (FM) were collected for RNA library construction. As a result, 81 conserved miRNAs belonging to 16 miRNA families were identified which were non-additively expressed. At the three stages, 80.30%, 56.06%, and 48.10% of these non-additively expressed miRNAs were repressed ever dominantly or over-dominantly. A total of 82 target transcripts from 42 genes of conserved miRNAs among Zhengdan 958 and its parents were detected via whole genome degradome sequencing. Additionally, eight novel maize miRNAs belonging to seven miRNA families were identified using stringent criteria. Global repression of miRNAs in hybrid ears at the early stage might lead to the up-regulated expressing of their target genes. Moreover, the in-step de-repression of given miRNA family members may be the reason of enhanced repression of their target genes. These results revealed, at least in part, the involvement of maize miRNAs in hybrids leads to higher ear developing vigor compared with its parental lines.

Key words: ear development, heterosis, miRNA, degradome, Zea mays L.

Qi-Yue WANG, Shu-Jun MENG, Ke ZHANG, Zhan-Hui ZHANG, Ji-Hua TANG, Dong DING. Investigation of Maize miRNA Involved in Developing-ear Heterosis[J].Acta Agronomica Sinica, 2018, 44(6): 796-813.

Figures/Tables 11

Table 1

Stem-loop RT and PCR primer sequences for ear development heterosis associated miRNAs and their target genes"

引物 Primer	引物序列 Primer sequence (5°-3°)
zma-miR159a/b RT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACCAGAGC
zma-miR159a/b PCR	CGACCTTTGGATTGAAGGGA
zma-miR160a-e,gRT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACTGGCAT
zma-miR160a-e,gPCR	GTAAGTGCCTGGCTCCCTGT
zma-miR167a-dRT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACTAGATC
zma-miR167a-dPCR	TCTAGTGAAGCTGCCAGCAT
zma-miR168a/b RT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACGTCCCG
zma-miR168a/b PCR	CATAGTCGCTTGGTGCAGAT
zma-miR169a/b RT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACTCGGCA
zma-miR169a/b PCR	CGTAGCAGCCAAGGATGACT
zma-miR172a-dRT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACTGCAGC
zma-miR172a-dPCR	GCGCCAGAATCTTGATGAT
zma-miR172eRT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACATGCAG
zma-miR172ePCR	CCGTCGGAATCTTGATGATG
zma-miR390a/b RT	F: GTCGTATCCAGTGCAGGGTCCGAGG; R: TATTCGCACTGGATACGACGGCGCT
zma-miR390a/b PCR	GCATCAAGCTCAGGAGGGAT
Universal Reverse	ATTCATGAAAGGCGGATGGC
Y-tubulin-A	TGTCGTCCAACCTTACAACTCACT
Y-tubulin-S	TCTCCAGGGTCCTCCATTCC
T159a/b(GRMZM2G423833_T01)-A	TGGTCTGGCTGACTGTTGTT
T159a/b(GRMZM2G423833_T01)-S	CTTGTGAGCGTGATGGAAAT
T160a-e,g(AC207656.3_FGT002)-A	AACCGAAACTGCCGAACC
T160a-e,g(AC207656.3_FGT002)-S	TGACCATACTGACGGACGAGA
T167a-d(GRMZM2G078274_T03)-A	CAGGGATGGATACATAGGAAAG
T167a-d(GRMZM2G078274_T03)-S	GAATCAACCGCAGGAGAAAG
^#T168a/b(GRMZM2G361518_T01)-A	ACAACAGCAGCAATGGAAGG
^#T168a/b(GRMZM2G361518_T01)-S	AAGGTCGGAGGAAGGAACAC
T169a/b(GRMZM2G000686_T01)-A	TATGATATGGCGAAGGACTG
T169p(GRMZM2G000686_T01)-S	CATCAAGAAGCGTCTGGAAT
T172a-d(GRMZM5G862109_T01)-A	GCGATAAATAGCGTGGTGGG
T172a-d(GRMZM5G862109_T01)-S	CTTCTCGTCCTCGGTCCTCC
T172e(GRMZM2G700665_T02)-A	CGTTGTTGCGGTACATTTAGGC
T172e(GRMZM2G700665_T02)-S	GTGCAGGATGGTCGTCAGGG
T390a/b(GRMZM2G084821_T02)-A	CCCGGTGGCATAATAACTGC
T390a/b(GRMZM2G084821_T02)-S	TGGAGCCGAATAATGGAAGC

Table 1

Fig. 1

Table 2

Co-detected conserved miRNA expression trends"

miRNA	IM to SPM	SPM to SM		FM		miRNA			IM to SPM		SPM to SM	FM
zma-miR156a-5p	- -	- -		-		zma-miR166m-3p			- -		+ -	+ +
zma-miR156b-5p	- -	- -		- -		zma-miR166n-3p			- -		+	- -
zma-miR156c	- -	- -		-		zma-miR167a-5p			+ -		- -	- -
zma-miR156d-5p	- -	- -		- -		zma-miR167b-5p			+ -		- -	- -
zma-miR156f-5p	- -	- -		- -		zma-miR167c-5p			+ -		- -	- -
zma-miR156g-5p	- -	- -		- -		zma-miR167d-5p			+ -		- -	- -
zma-miR156j-5p	+ +	+		- -		zma-miR167e-5p			+ -		- -	- -
zma-miR156k-5p	- -	- -		- -		zma-miR167f-5p			+ -		- -	- -
zma-miR159a-3p	- -	-		+ +		zma-miR167g-5p			+ -		- -	- -
zma-miR159b-3p	- -	-		+ +		zma-miR167h-5p			+ -		- -	- -
zma-miR159f-3p	- -	-		+ +		zma-miR167i-5p			+ -		- -	- -
zma-miR159j-3p	- -	-		+ +		zma-miR167j-5p			+ -		- -	- -
zma-miR159k-3p	- -	-		+ +		zma-miR168a-5p			+ -		+ +	+ +
zma-miR160a-5p	- -	+ +		+ +		zma-miR168b-5p			+ -		+ +	+ +
zma-miR160b-5p	- -	+ +		+ +		zma-miR169a-5p			- -		+ +	+ +
zma-miR160c-5p	- -	+ +		+ +		zma-miR169b-5p			- -		+ +	+ +
zma-miR160d-5p	- -	+ +		+ +		zma-miR169c-5p			- -		+ +	+
zma-miR160e	- -	+ +		+ +		zma-miR169r-5p			- -		+ +	+
zma-miR160f-5p	- -	+ +		+ +		zma-miR171d-3p			- -		-	- -
zma-miR160g-5p	- -	+ +		+ +		zma-miR171e-3p			- -		-	- -
zma-miR162-3p	- -	- -		+ -		zma-miR171i-3p			- -		-	- -
zma-miR164a-5p	+	- -		+ +		zma-miR171j-3p			- -		-	- -
zma-miR164b-5p	+	- -		+ +		zma-miR171l-3p			+ -		- -	+ +
zma-miR164c-5p	+	- -		+ +		zma-miR171m-3p			+ -		- -	+ +
zma-miR164d-5p	+	- -		+ +		zma-miR172a			- -		+ +	- -
zma-miR164e-5p	+	+ +		- -		zma-miR172b-3p			- -		+ +	- -
miRNA	IM to SPM	SPM to SM		FM			miRNA		IM to SPM		SPM to SM	FM
zma-miR164f-5p	+		- -		+ +		zma-miR172c-3p	- -		+ +		- -
zma-miR164g-5p	+		- -		+ +		zma-miR172d-3p	- -		+ +		- -
zma-miR164h-5p	+		- -		+ +		zma-miR172e	- -		+		- -
zma-miR166a-3p	- -		+ -		+ +		zma-miR319a-3p	- -		+		- -
zma-miR166b-3p	- -		+ -		+ +		zma-miR319b-3p	- -		+		- -
zma-miR166c-3p	- -		+ -		+ +		zma-miR319c-3p	- -		+		- -
zma-miR166d-3p	- -		+ -		+ +		zma-miR319d-3p	- -		+		- -
zma-miR166e	- -		+ -		+ +		zma-miR390a-5p	+		+		+ +
zma-miR166f	- -		+ -		+ +		zma-miR390b-5p	+		+		+ +
zma-miR166g-3p	- -		+ -		+ +		zma-miR444a	- -		+ -		- -
zma-miR166h-3p	- -		+ -		+ +		zma-miR444b	- -		+ -		- -
zma-miR166i-3p	- -		+ -		+ +		zma-miR528a-5p	+ +		+ -		+ -
zma-miR166j-3p	- -		+		- -		zma-miR528b-5p	+ +		+ -		+ -
zma-miR166k-3p	- -		+		- -		zma-miR827-3p	+ -		- --		- -
zma-miR166l-3p	- -		+ -		+ +

Table 2

Table 3

Ear development heterosis associated miRNA target genes detected via genome wide degradome"

miRNA	靶基因 Target gene	分值 Score	校准范围 Alignment range	切割位点 Cleavage site	P值 P-value	GO注释 Annotation for GO
zma-miR156	GRMZM2G414805_T02	1	1546-1565	1556	0.056054	SPL protein 11
zma-miR156	GRMZM2G414805_T03	1	1875-1894	1885	0.056054	SPL protein 11
zma-miR156	GRMZM2G414805_T04	1	1353-1372	1363	0.056054	SPL protein 11
zma-miR156	GRMZM2G414805_T05	1	2100-2119	2110	0.056054	SPL protein 11
zma-miR159	AC209015.3_FGT004	2.5	328-348	339	0.019582	non
zma-miR159	GRMZM2G028054_T02	3	1419-1439	1430	0.034972	transcription factor GAMYB
zma-miR159	GRMZM2G028054_T03	3	1360-1380	1371	0.034972	transcription factor GAMYB
zma-miR159	GRMZM2G075064_T01	2.5	851-871	862	0.019582	DNA binding
zma-miR159	GRMZM2G423833_T01	2	905-925	916	0.005424	DNA binding
zma-miR159	GRMZM2G139688_T01	3.5	1399-1419	1410	0.031147	DNA binding
zma-miR160	AC207656.3_FGT002	1	1350-1370	1361	0.037830	regulation of transcription
zma-miR160	GRMZM2G081406_T01	2	1499-1519	1510	0.005424	regulation of transcription
zma-miR160	GRMZM2G153233_T01	1	1652-1672	1663	0.037830	auxin response factor 2
zma-miR160	GRMZM2G159399_T01	1	1746-1766	1757	0.037830	regulation of transcription
zma-miR160	GRMZM2G390641_T01	1	1790-1810	1801	0.037830	regulation of transcription
zma-miR160	GRMZM2G390641_T02	1	1690-1710	1701	0.037830	regulation of transcription
zma-miR160	GRMZM5G808366_T01	1.5	1295-1315	1306	0.005915	auxin response factor 5
zma-miR160	GRMZM2G063522_T01	2	895-915	906	0.007152	regulation of transcription
zma-miR164	GRMZM2G139700_T01	2	737-757	748	0.026826	Nam2 protein
miRNA	靶基因 Target gene	分值 Score	校准范围 Alignment range	切割位点 Cleavage site	P值 P-value	GO注释 Annotation for GO
zma-miR164	GRMZM2G393433_T01	2	854-874	865	0.026826	CUC2
zma-miR164	GRMZM2G393433_T02	2	814-834	825	0.026826	CUC2
zma-miR166	GRMZM2G003509_T01	3	736-756	747	0.068720	regulation of transcription
zma-miR166	GRMZM2G003509_T02	3	805-825	816	0.068720	regulation of transcription
zma-miR166	GRMZM2G042250_T01	3	628-648	639	0.068720	rolled leaf 2
zma-miR166	GRMZM2G042250_T02	3	714-734	725	0.068720	rolled leaf 2
zma-miR166	GRMZM2G042250_T03	3	628-648	639	0.068720	rolled leaf 2
zma-miR166	GRMZM2G042250_T04	3	628-648	639	0.068720	rolled leaf 2
zma-miR166	GRMZM2G109987_T01	3	1039-1059	1050	0.068720	transcription factor activity
zma-miR166	GRMZM2G109987_T02	3	1039-1059	1050	0.068720	transcription factor activity
zma-miR166	GRMZM2G109987_T03	3	1039-1059	1050	0.068720	transcription factor activity
zma-miR166	GRMZM2G109987_T04	3	1039-1059	1050	0.068720	transcription factor activity
zma-miR166	GRMZM2G109987_T05	3	774-794	785	0.068720	transcription factor activity
zma-miR166	GRMZM2G123644_T01	4	545-565	556	0.020551	DNA binding
zma-miR166	GRMZM2G178102_T01	3	1035-1055	1046	0.068720	transcription factor activity
zma-miR166	GRMZM2G336718_T01	3	105-124	115	0.013260	DNA binding
zma-miR167	GRMZM2G078274_T03	4	2531-2552	2542	0.034017	regulation of transcription
zma-miR169	GRMZM2G000686_T01	3.5	2120-2140	2131	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T02	3.5	1010-1030	1021	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T03	3.5	1006-1026	1017	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T04	3.5	962-982	973	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T05	3.5	934-954	945	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T06	3.5	890-910	901	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T08	3.5	1106-1126	1117	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T09	3.5	991-1011	1002	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G000686_T10	3.5	1300-1320	1311	0.057604	CCAAT-binding factor
zma-miR169	GRMZM2G091964_T01	4	1317-1338	1329	0.010329	nuclear transcription factor Y subunit A-1
zma-miR169	GRMZM2G091964_T02	4	1314-1335	1326	0.010329	nuclear transcription factor Y subunit A-1
zma-miR169	GRMZM2G091964_T03	4	1429-1450	1441	0.010329	nuclear transcription factor Y subunit A-1
zma-miR169	GRMZM2G165488_T01	3	1586-1606	1597	0.068720	transcription factor activity
zma-miR169	GRMZM2G165488_T02	3	2140-2160	2151	0.068720	transcription factor activity
zma-miR169	GRMZM2G165488_T03	3	1357-1377	1368	0.068720	transcription factor activity
zma-miR169	GRMZM5G829103_T02	3	1815-1835	1826	0.068720	NTF-Y subunit A-10
zma-miR169	GRMZM5G829103_T03	3	1321-1341	1332	0.068720	NTF-Y subunit A-10
zma-miR169	GRMZM5G829103_T04	3	1965-1985	1976	0.068720	NTF-Y subunit A-10
zma-miR169	GRMZM5G829103_T06	3	1288-1308	1299	0.068720	NTF-Y subunit A-10
zma-miR169	GRMZM5G829103_T07	3	1360-1380	1371	0.068720	NTF-Y subunit A-10
zma-miR171	GRMZM2G037792_T01	1	1322-1342	1333	0.056205	hypothetical protein
zma-miR171	GRMZM2G098800_T01	1	920-940	931	0.056205	hypothetical protein
zma-miR171	GRMZM2G098800_T02	1	1391-1411	1402	0.056205	hypothetical protein
zma-miR171	GRMZM2G110579_T01	1	1078-1098	1089	0.056205	putative uncharacterized protein
zma-miR171	GRMZM2G418899_T02	1	45-65	56	0.056205	non
zma-miR171	GRMZM5G825321_T01	1	507-527	518	0.056205	putative uncharacterized protein
zma-miR171	GRMZM2G418899_T01	1	45-65	56	0.056205	non
miRNA	靶基因 Target gene	分值 Score	校准范围 Alignment range	切割位点 Cleavage site	P值 P-value	GO注释 Annotation for GO
zma-miR171	GRMZM5G825321_T02	1	1460-1480	1471	0.056205	putative uncharacterized protein
zma-miR172	GRMZM2G076602_T01	3	898-917	908	0.039256	putative uncharacterized protein
zma-miR172	GRMZM2G174784_T01	3	2242-2261	2252	0.039256	regulation of transcription
zma-miR172	GRMZM2G174784_T03	3	2367-2386	2377	0.039256	regulation of transcription
zma-miR172	GRMZM5G862109_T01	1	1559-1578	1569	0.050120	indeterminate spikelet1
zma-miR172	GRMZM5G862109_T02	1	1685-1704	1695	0.050120	indeterminate spikelet1
zma-miR172	GRMZM5G862109_T03	1	1671-1690	1681	0.050120	indeterminate spikelet1
zma-miR172	GRMZM2G174784_T02	3	2370-2389	2380	0.039256	regulation of transcription
zma-miR172	GRMZM2G700665_T02	1	1773-1792	1783	0.050120	AP2 transcription factor
zma-miR319	AC205574.3_FGT006	4	1456-1475	1466	0.023935	mutant cincinnata
zma-miR319	GRMZM2G015037_T01	4	1735-1754	1745	0.023935	glutamate 5-kinase activity
zma-miR319	GRMZM2G020805_T01	3	1429-1448	1439	0.008860	hypothetical protein
zma-miR319	GRMZM2G180568_T01	3.5	852-871	862	0.023453	transcribed locus
zma-miR319	GRMZM2G412073_T01	3.5	232-251	242	0.023453	hypothetical protein
zma-miR390	GRMZM2G084821_T02	4	1210-1230	1221	0.047298	hypothetical protein
zma-miR390	GRMZM2G084821_T04	4	611-631	622	0.047298	hypothetical protein
zma-miR390	GRMZM2G084821_T05	4	634-654	645	0.047298	hypothetical protein
zma-miR528	GRMZM2G107562_T01	2.5	570-589	580	0.004932	copper ion binding
zma-miR827	GRMZM2G044788_T01	2.5	245-265	256	0.001304	hypothetical protein

Table 3

Fig. 2

Fig. 3

Table 4

Table 5

Fig. 4

Fig. 5

Table 6

Sequencing row data"

NA	H16-RPM	H17-RPM	H18-RPM	H19-RPM	H20-RPM	H21-RPM	H22-RPM	H23-RPM	H24-RPM
zma-miR1432-5p	0.199941767	0.177102302	0.2273795	0.6338742	0	5.0137835	0.11827416	0.1136377	0.61734739
zma-miR156a-5p	0.649810743	0.590341006	1.7053465	1.8439978	1.7981694	1.3624412	0.17741123	0.3409131	1.23469477
zma-miR156b-5p	3.548966364	1.889091218	2.1032607	29.56159	4.7201947	43.434625	2.48375726	1.4772903	1.32967129
zma-miR156c	0.649810743	0.590341006	1.7053465	1.8439978	1.7981694	1.3624412	0.11827416	0.3409131	1.23469477
zma-miR156d-5p	4.398718873	2.538466325	2.7853993	29.964964	5.4844167	43.707113	3.78477297	2.386392	1.42464781
zma-miR156e-5p	0.29991265	0.413238704	0.8526732	0.2304997	0.6293593	1.1444506	0.11827416	0.1704566	0.94976521
zma-miR156f-5p	0.599825301	0.472272805	1.6485016	1.8439978	1.7082609	1.3079435	0.11827416	0.3409131	1.09222999
zma-miR156g-5p	0.599825301	0.472272805	1.6485016	1.8439978	1.7082609	1.3079435	0.11827416	0.3409131	1.09222999
zma-miR156h-5p	0.29991265	0.413238704	0.8526732	0.2304997	0.6293593	1.1444506	0.11827416	0.1704566	0.94976521
zma-miR156i-5p	0.29991265	0.413238704	0.7958284	0.2304997	0.6293593	1.1444506	0.11827416	0.1704566	0.94976521
zma-miR156j-5p	7.947685237	5.549205454	19.384105	8.7589895	35.918434	17.60274	19.8700581	39.148192	7.36068037
zma-miR156k-5p	33.59021685	20.1306283	6.1392473	52.784437	8.8559844	13.133933	23.6548311	6.4773496	3.65659605
zma-miR156l-5p	0.29991265	0.413238704	0.7958284	0.2304997	0.6293593	1.1444506	0.11827416	0.1704566	0.90227695
zma-miR159a-3p	110.8177243	61.6906351	164.3954	69.207542	37.851466	166.05433	56.8898687	60.512082	759.384772
zma-miR159b-3p	110.7677389	61.6906351	164.3954	69.207542	37.851466	166.05433	56.8898687	60.512082	759.289796
zma-miR159c-3p	0.099970883	0.118068201	0.3410693	0	0.0449542	0.2724882	0	0.0568189	0.75981217
zma-miR159d-3p	0.099970883	0.118068201	0.3410693	0	0.0449542	0.2724882	0	0.0568189	0.75981217
zma-miR159f-3p	110.5677971	61.631601	164.3954	69.207542	37.851466	165.61835	56.8898687	60.512082	758.957378
zma-miR159j-3p	110.5178117	61.631601	164.3954	69.207542	37.851466	165.61835	56.8898687	60.512082	758.862402
zma-miR159k-3p	110.5178117	61.631601	164.3954	69.207542	37.851466	165.61835	56.8898687	60.512082	758.862402
zma-miR160a-5p	8.347568771	0.767443307	0.2842244	0.4609994	1.1688101	1.1989482	2.83857973	6.6478062	1.94701868
zma-miR160b-5p	8.347568771	0.767443307	0.2842244	0.4609994	1.1688101	1.1989482	2.83857973	6.6478062	1.94701868
zma-miR160c-5p	8.347568771	0.767443307	0.2842244	0.4609994	1.1688101	1.1989482	2.83857973	6.6478062	1.94701868
zma-miR160d-5p	8.597495979	0.826477408	0.2842244	0.6338742	1.1688101	1.3624412	3.07512804	6.6478062	1.94701868
NA	H16-RPM	H17-RPM	H18-RPM	H19-RPM	H20-RPM	H21-RPM	H22-RPM	H23-RPM	H24-RPM
zma-miR160e	8.597495979	0.826477408	0.2842244	0.6338742	1.1688101	1.3624412	3.07512804	6.6478062	1.94701868
zma-miR160f-5p	8.597495979	0.826477408	0.2842244	0.6338742	1.1688101	1.3624412	3.07512804	6.6478062	1.94701868
zma-miR160g-5p	8.597495979	0.826477408	0.2842244	0.6338742	1.1688101	1.3624412	3.01599096	6.6478062	1.94701868
zma-miR162-3p	5.548384033	0.826477408	1.8190362	1.7863729	3.9559727	7.575173	2.1289348	1.5341091	4.3214317
zma-miR164a-5p	138.4596736	121.6692813	472.32413	101.36225	53.405632	262.07919	150.385589	62.61438	583.773185
zma-miR164b-5p	138.2597319	121.6692813	472.21044	101.247	53.315723	262.07919	150.326451	62.500742	583.725697
zma-miR164c-5p	138.2597319	121.6692813	472.21044	101.247	53.315723	262.07919	150.326451	62.500742	583.725697
zma-miR164d-5p	138.4596736	121.6692813	472.32413	101.36225	53.405632	262.07919	150.385589	62.61438	583.773185
zma-miR164e-5p	1.349606927	2.833636828	0.5116039	6.5116172	1.4834898	4.9592859	5.91370777	4.1477765	0.61734739
zma-miR164f-5p	138.4596736	121.6692813	472.32413	101.36225	53.360677	262.02469	150.385589	62.61438	583.725697
zma-miR164g-5p	138.2597319	121.6692813	472.21044	101.247	53.315723	262.07919	150.326451	62.500742	583.725697
zma-miR164h-5p	138.159761	121.3741108	471.86937	100.95888	53.135906	261.8067	150.267314	62.330286	583.013373
zma-miR166a-3p	8373.411244	2051.316927	5638.3302	6288.3206	2007.836	7944.231	3770.52094	2120.082	14058.0447
zma-miR166b-3p	8373.211302	2051.316927	5638.3302	6288.3206	2007.836	7944.3945	3770.4618	2120.082	14058.0447
zma-miR166c-3p	8373.161317	2051.316927	5638.3302	6288.3206	2007.836	7944.231	3770.40266	2120.082	14057.9972
zma-miR166d-3p	8373.211302	2051.316927	5638.3302	6288.3206	2007.836	7944.3945	3770.4618	2120.082	14058.0447
zma-miR166e	8373.261288	2051.316927	5638.3302	6288.3206	2007.8809	7944.7215	3770.4618	2120.082	14058.3296
zma-miR166f	8344.269731	2030.77306	5603.4843	6260.6606	1996.6424	7897.3631	3746.39301	2103.0932	13980.4489
zma-miR166g-3p	8344.219746	2030.832094	5603.5412	6260.6606	1996.5075	7897.3631	3746.39301	2102.9795	13980.4014
zma-miR166h-3p	8344.319717	2030.77306	5603.4843	6260.6606	1996.6424	7897.3631	3746.39301	2103.0932	13980.4489
zma-miR166i-3p	8372.011652	2051.021756	5636.2838	6287.1105	2007.7461	7940.4707	3769.33819	2119.8547	14050.874
zma-miR166j-3p	753.730476	307.8628345	265.18138	621.25438	424.81753	464.53794	401.185935	436.36882	312.187824
zma-miR166k-3p	754.4802576	307.7447663	264.954	621.94588	425.08725	465.19192	401.008524	436.59609	310.905641
zma-miR166l-3p	8375.410662	2055.626416	5639.1261	6288.8392	2008.7351	7947.1194	3772.82728	2121.6729	14058.0922
zma-miR166m-3p	8341.220619	2033.901867	5603.9959	6260.142	1995.5185	7898.889	3747.63489	2101.9568	13977.4571
zma-miR166n-3p	753.9304178	307.9218686	265.18138	621.312	425.0423	464.59244	401.245072	436.36882	312.235312
zma-miR167a-5p	6383.290867	3235.540984	1168.3329	4172.2755	864.29013	1672.2603	5075.91279	1339.9591	989.085488
zma-miR167b-5p	6383.390837	3235.304848	1168.3897	4172.3331	864.20022	1672.2603	5075.79451	1339.9591	989.085488
zma-miR167c-5p	6383.290867	3235.540984	1168.3329	4172.2755	864.29013	1672.2603	5075.91279	1339.9591	989.085488
zma-miR167d-5p	6383.290867	3235.540984	1168.3329	4172.2755	864.29013	1672.2603	5075.91279	1339.9591	989.085488
zma-miR167e-5p	6383.090925	3235.422916	1168.1055	4172.4484	864.29013	1672.1513	5074.84832	1340.1864	988.943023
zma-miR167f-5p	6383.14091	3235.422916	1168.1055	4172.4484	864.29013	1672.1513	5074.84832	1340.1864	988.943023
zma-miR167g-5p	6382.391129	3234.950643	1167.935	4171.8145	864.15527	1672.1513	5074.43436	1339.9591	988.943023
zma-miR167h-5p	6383.340852	3235.540984	1167.9918	4172.6789	864.20022	1672.5328	5075.02573	1340.5841	988.943023
zma-miR167i-5p	6383.390837	3235.600018	1167.9918	4172.6789	864.20022	1672.5328	5075.02573	1340.5841	988.943023
zma-miR167j-5p	6382.741027	3235.009677	1167.935	4171.8145	864.20022	1672.1513	5074.61177	1339.9591	988.990512
zma-miR168a-5p	5945.968237	5786.1093	7505.1162	13021.563	6575.9505	6315.2964	9509.95174	8001.7996	14166.9828
zma-miR168b-5p	5945.968237	5786.1093	7505.1162	13021.563	6575.9505	6315.2964	9509.95174	8001.7996	14166.9828
zma-miR169a-5p	0.699796184	0.944545609	3.9791418	2.2473723	1.3486271	1.9619153	0.35482247	1.6477468	3.37166649
zma-miR169b-5p	0.699796184	0.944545609	3.9791418	2.2473723	1.3486271	1.9619153	0.35482247	1.6477468	3.37166649
zma-miR169c-5p	0.699796184	0.590341006	2.5580197	2.1897474	0.9889932	0.9809577	0.35482247	1.4772903	2.32692476
NA	H16-RPM	H17-RPM	H18-RPM	H19-RPM	H20-RPM	H21-RPM	H22-RPM	H23-RPM	H24-RPM
zma-miR169f-5p	4.248762548	2.06619352	0.2842244	10.141988	4.6302863	0.1089953	1.30101571	2.7273051	0.2374413
zma-miR169g	4.248762548	2.06619352	0.2842244	10.141988	4.6302863	0.1089953	1.30101571	2.7273051	0.2374413
zma-miR169h	4.248762548	2.06619352	0.2842244	10.141988	4.6302863	0.1089953	1.30101571	2.7273051	0.2374413
zma-miR169i-5p	4.248762548	2.06619352	0.2842244	10.141988	4.6302863	0.1089953	1.30101571	2.7273051	0.2374413
zma-miR169j-5p	4.248762548	2.06619352	0.2842244	10.141988	4.6302863	0.1089953	1.30101571	2.7273051	0.2374413
zma-miR169k-5p	4.248762548	2.06619352	0.2842244	10.141988	4.6302863	0.1089953	1.30101571	2.7273051	0.2374413
zma-miR169p-5p	4.29874799	2.00715942	0.2842244	10.199613	4.6302863	0.1089953	1.36015279	2.7273051	0.2374413
zma-miR169r-5p	0.699796184	0.590341006	2.5580197	2.1897474	0.9889932	0.9809577	0.35482247	1.4772903	2.32692476
zma-miR171b-3p	0.099970883	0.118068201	0.2842244	0.1152499	0.1348627	0.5994741	0.11827416	0	0.56985913
zma-miR171b-5p	0.099970883	0	0.6821386	0.2881247	0	1.2534459	0.17741123	0.1704566	0.56985913
zma-miR171d-3p	11.09676807	4.191421141	52.126757	11.582611	3.0119338	44.797066	8.51573919	2.8977617	30.4399749
zma-miR171d-5p	8.447539654	1.121647911	43.031576	6.8573668	1.0339474	51.990755	6.15025608	1.2500148	102.194736
zma-miR171e-3p	11.09676807	4.191421141	52.126757	11.582611	3.0119338	44.797066	8.51573919	2.8977617	30.4399749
zma-miR171e-5p	8.647481421	1.239716112	44.111629	6.9726166	0.9889932	52.099751	5.97284485	1.2500148	103.049525
zma-miR171f-3p	0.099970883	0.118068201	0.2842244	0.1152499	0.1348627	0.5994741	0.11827416	0	0.56985913
zma-miR171h-3p	0.699796184	0.059034101	0.3979142	0.5186244	0.0899085	0.3269859	0.47309662	0.2272754	0.09497652
zma-miR171h-5p	1.14966516	0.767443307	0.2842244	0.1152499	0.0449542	0.1089953	0.59137078	0.4545509	0.09497652
zma-miR171i-3p	11.09676807	4.13238704	52.013068	11.582611	3.056888	44.524578	8.51573919	2.8977617	30.2500219
zma-miR171j-3p	11.09676807	4.13238704	52.126757	11.582611	3.056888	44.797066	8.51573919	2.8977617	30.4399749
zma-miR171k-3p	0.699796184	0.059034101	0.3979142	0.5186244	0.0899085	0.3269859	0.47309662	0.2272754	0.09497652
zma-miR171k-5p	1.14966516	0.767443307	0.2842244	0.1152499	0.0449542	0.1089953	0.59137078	0.4545509	0.09497652
zma-miR171l-3p	1.549548694	1.121647911	5.4571087	2.1321224	0.6743135	9.7550789	1.83324941	0.2840943	12.7743421
zma-miR171m-3p	1.549548694	1.121647911	5.4571087	2.1321224	0.6743135	9.7550789	1.83324941	0.2840943	12.7743421
zma-miR172a	30.49111946	12.86943393	4.2633662	155.64494	15.913799	6.2672294	24.0096535	24.148014	0.14246478
zma-miR172b-3p	30.5411049	12.86943393	4.2633662	155.64494	15.913799	6.2672294	24.0096535	24.148014	0.14246478
zma-miR172c-3p	30.5411049	12.86943393	4.2633662	155.64494	15.913799	6.2672294	24.0096535	24.148014	0.14246478
zma-miR172d-3p	30.5411049	12.86943393	4.2633662	155.64494	15.913799	6.2672294	24.0096535	24.148014	0.14246478
zma-miR172e	4.348733431	6.375682862	1.8758811	6.684492	16.273433	0.5994741	3.37081343	16.079736	0.37990608
zma-miR319a-3p	29.89129416	9.327387891	1.3074323	28.178591	23.690882	1.1444506	9.69848074	23.523007	0.37990608
zma-miR319b-3p	30.14122137	9.386421992	1.5916567	28.87009	24.185379	1.4169388	9.81675489	23.977557	0.52237086
zma-miR319c-3p	29.84130872	9.327387891	1.3074323	28.178591	23.690882	1.1444506	9.69848074	23.523007	0.37990608
zma-miR319d-3p	30.14122137	9.386421992	1.5916567	28.87009	24.185379	1.4169388	9.81675489	23.977557	0.52237086
zma-miR390a-5p	21.64369627	11.21647911	38.142916	29.33109	14.789943	50.355826	30.455595	15.341091	136.908655
zma-miR390b-5p	21.64369627	11.21647911	38.142916	29.33109	14.789943	50.355826	30.455595	15.341091	136.908655
zma-miR395b-5p	2.049403111	3.483011934	0	0	0	0	2.83857973	1.3636526	0
zma-miR395e-5p	0.899737951	4.07335294	0	0.0576249	0	0	2.36548311	1.3636526	0
zma-miR395h-5p	0.899737951	4.07335294	0	0.0576249	0	0	2.36548311	1.3636526	0
zma-miR395i-5p	2.049403111	3.483011934	0	0	0	0	2.83857973	1.3636526	0
zma-miR395j-5p	0.899737951	4.07335294	0	0.0576249	0	0	2.36548311	1.3636526	0
zma-miR395p-5p	0.899737951	4.07335294	0	0.0576249	0	0	2.36548311	1.3636526	0
zma-miR396a-5p	0.249927209	0.472272805	0.2842244	0.9796238	0.2247712	0.1634929	0.17741123	0.4545509	0.04748826
NA	H16-RPM	H17-RPM	H18-RPM	H19-RPM	H20-RPM	H21-RPM	H22-RPM	H23-RPM	H24-RPM
zma-miR396b-5p	0.249927209	0.472272805	0.2842244	0.9796238	0.2247712	0.1634929	0.17741123	0.4545509	0.04748826
zma-miR396c	0.049985442	0	3.6949174	0.4609994	0	3.5968447	0.05913708	0.1136377	5.69859125
zma-miR396d	0.049985442	0	3.6949174	0.4609994	0	3.5968447	0.05913708	0.1136377	5.69859125
zma-miR396e-5p	0.199941767	0.472272805	0.2842244	0.864374	0.1798169	0.1634929	0.17741123	0.4545509	0.04748826
zma-miR396f-5p	0.199941767	0.472272805	0.2842244	0.864374	0.1798169	0.1634929	0.17741123	0.4545509	0.04748826
zma-miR397a-5p	0.099970883	0.236136402	0.4547591	0.0576249	0	0.4904788	0.29568539	0.1704566	0
zma-miR397b-5p	0.099970883	0.236136402	0.5684488	0.0576249	0	0.4904788	0.29568539	0.2840943	0.04748826
zma-miR398a-3p	0.149956325	0.059034101	4.831815	0.2304997	0.0449542	1.85292	0.05913708	0.0568189	0.52237086
zma-miR398b-3p	0.149956325	0.059034101	4.831815	0.2304997	0.0449542	1.9074177	0.05913708	0.0568189	0.52237086
zma-miR408b-5p	0.549839859	0.531306905	0.966363	1.0372488	0.2247712	1.5804318	1.30101571	0.795464	1.13971825
zma-miR444a	3.249053713	1.889091218	7.1056103	3.6879956	0.5844051	4.0873235	1.77411233	1.2500148	4.7963143
zma-miR444b	3.299039155	2.184261721	7.3329899	3.8608704	0.8990847	4.1418212	1.83324941	1.4772903	5.12873213
zma-miR528a-5p	512.3007924	282.6552736	25.693887	1062.7766	148.75357	220.71547	1562.28332	207.38883	113.876849
zma-miR528b-5p	512.4507487	282.89141	25.750732	1062.8918	148.75357	220.76997	1562.63814	207.55928	113.876849
zma-miR529-5p	45.18683933	5.07693265	0.3410693	27.371842	0.5844051	0.5449765	25.0149839	0.6818263	0.2374413
zma-miR827-3p	15.29554517	138.3759317	22.283194	14.809607	27.107404	31.990119	31.3426512	58.296147	13.9140603

Table 6

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新的miRNA Novel miRNA	序列 Sequence (5°-3°)	位置 Location	自由能指数 MFEI	IM to SPM	SPM to SM	FM
zma-miR-n1	AAAAAGAAACGGAGAGAGTAG	1:104607732:104607838: +	1.615137	D	+	-
zma-miR-n2	GTTTCTTTTTATTAGTCGTTG	4:21820530:21820628: -	1.300130	D	-	- -
zma-miR-n3	ATCCGACGCAAACGAACAAGG	10:1924407:1924548: -	1.027248	--	+	+
zma-miR-n4	ATCCGACGCAAACGAACAAGG	4:215015818:215015940: -	0.953020	--	+	+
zma-miR-n5	ACACAGTTGCTGTGCTCGCCG	9:149911503:149911831: +	0.947278	D	+ +	+ +
zma-miR-n6	AGGGCTTGTTCGTTTACGTCG	4:189032126:189032271: -	0.875367	++	--	+ +
zma-miR-n7a	GCCTGAGGTCGGACAGTCCGC	1:52926508:52926666: -	0.874422	-	D	-
zma-miR-n7b	GCCTGAGGTCGGACAGTCCGC	1:52934608:52934766: -	0.874422	-	D	-

Investigation of Maize miRNA Involved in Developing-ear Heterosis

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