Dynamic patterns of gene expression and regulatory variation in the maize seed coat

BMC Plant Biology

Table 1 Classification of expression patterns of DEGs in hybrids and their parental lines at 3 DAP and 8 DAP

Categories	Expression patterns of genes														Total DEGs
	Addtivity			Nonaddtivity
	M vs. P Non-DEGs	M vs. P DEGs		Dominance				Overdominance
				M vs. P DEGs				M vs. P Non-DEGs		M vs. P DEGs		M vs. P Non-DEGs	M vs. P DEGs
				ELD_M		ELD_P		Transgressive upregulation				Transgressive downregulation
Cl	2	6	11	10	5	7	12	1	8		9	3	4	13
asses	2	6	11	10	5	7	12	1	8		9	3	4	13
Relative expression	M-H-P	M-H-P	M-H-P	M-H-P	M-H-P	M-H-P	M-H-P	M-H-P	M-H-P		M-H-P	M-H-P	M-H-P	M-H-P
3 DAP	17,045	1075	1594	622	790	1385	529	15	3		4	70	12	0	23,145
Sum	19,714			1412		1914		22				82
Proportion of total DEGs(%)	85.18			6.10		8.27		0.10				0.35
8 DAP	16,899	1129	1432	1360	403	998	239	12	3		2	29	3	0	22,509
Sum	19,460			1763		1237		17				32
Proportion of total DEGs(%)	86.45			7.83		5.50		0.08				0.14

DEG expression patterns were classified according to the expression levels of the parents and hybrid. Additive expression of genes: classes 2, 6 and 11 (blue); dominant expression of genes: classes 10, 5, 7 and 12 (green); and overdominant expression of genes: classes 1, 8, 9, 3, 4 and 13 (red). Classes 1, 8 and 9 represent transgressive upregulation and classes 3, 4 and 13 represent transgressive downregulation [28]. Diagrams of each class represent the relative expression levels observed in the maternal line (left), hybrids (middle), and paternal line (right). DEGs, differentially expressed genes, M, maternal line, H, hybrid, P, paternal line, ELD, expression–level dominance, additivity: H≈ 1/2 (M + P), nonadditivity: H > 1/2 (M + P) or H < 1/2 (M + P), ELD_M: H ≈ M > P or H ≈ M < P, ELD_P: H≈ P > M or H ≈ P < M, transgressive upregulation: H > M and H > P, transgressive downregulation: H < M and H < P

ISSN: 1471-2229