Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize.
We employed allele-specific expression (ASE) analyses to document biased allelic expression in maize (Zea mays). A set of 316 quantitative ASE assays were used to profile the relative allelic expression in seedling tissue derived from five maize hybrids. The different hybrids included in this study exhibit a range of heterosis levels; however, we did not observe differences in the frequencies of allelic bias. Allelic biases in gene expression were consistently observed for approximately 50% of the genes assayed in hybrid seedlings. The relative proportion of genes that exhibit cis- or trans-acting regulatory variation was very similar among the different genotypes. The cis-acting regulatory variation was more prevalent and resulted in greater expression differences than trans-acting regulatory variation for these genes. The ASE assays were further used to compare the relative expression of the B73 and Mo17 alleles in three tissue types (seedling, immature ear, and embryo) derived from reciprocal hybrids. These comparisons provided evidence for tissue-specific cis-acting variation and for a slight maternal expression bias in approximately 20% of genes in embryo tissue. Collectively, these data provide evidence for prevalent cis-acting regulatory variation that contributes to biased allelic expression between genotypes and between tissues.
Springer
Nathan M
NM
Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minesota, St. Paul, Minnesota 55108, USA. springer@umn.edu
Stupar
Robert M
RM
D000483:Alleles; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D014644:Genetic Variation; D005838:Genotype; D006824:Hybridization, Genetic; D009928:Organ Specificity; D011058:Pollen / Q000502:physiology; D012639:Seeds / Q000235:genetics*; D003313:Zea mays / Q000196:embryology / Q000235:genetics*
Nature. 2004 Jul 1;430(6995):85-8
15229602
Plant Cell. 2003 Oct;15(10):2236-9
14523245
Annu Rev Genet. 1991;25:173-99
1839877
Plant Cell. 1998 Jul;10(7):1075-82
9668128
Genetics. 2004 Nov;168(3):1413-20
15579694
Plant Cell. 2004 Dec;16(12):3174-80
15579806
Genetics. 2004 Dec;168(4):2217-26
15371349
Plant Cell. 2005 Feb;17(2):343-60
15659640
Plant Cell. 2005 Apr;17(4):1061-72
15749756
Mutat Res. 2005 Jun 3;573(1-2):83-95
15829239
Genetics. 2005 Apr;169(4):2295-303
15687266
Plant J. 2005 Dec;44(6):1054-64
16359397
Plant Cell. 2004;16 Suppl:S203-13
15010515
Genetics. 2005 Dec;171(4):2139-42
16143609
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7
16381974
Curr Opin Plant Biol. 2006 Apr;9(2):157-63
16459130
Genetics. 2006 Feb;172(2):1155-64
15956669
Genome Biol. 2006;7(3):R22
16542496
Mol Ecol. 2006 Apr;15(5):1351-65
16626458
Nat Genet. 2006 May;38(5):594-7
16642024
Proc Natl Acad Sci U S A. 2006 May 2;103(18):6805-10
16641103
Science. 2006 Jun 2;312(5778):1392-6
16614172
Genetics. 2006 Jul;173(3):1347-55
16624921
Genetics. 2006 Jul;173(3):1823-7
16702424
Theor Appl Genet. 2006 Sep;113(5):831-45
16868764
Genetics. 2006 Aug;173(4):2199-210
16702414
Theor Appl Genet. 2006 Nov;113(7):1283-94
16932881
Plant Mol Biol. 2006 Nov;62(4-5):579-91
16941221
Genetics. 2006 Oct;174(2):1017-28
16888343
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17644-9
17101975
Plant Mol Biol. 2007 Jan;63(1):21-34
17006594
Cell. 2006 Dec 29;127(7):1309-21
17190597
Genome Res. 2007 Jan;17(1):69-73
17095711
Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1708-13
17237218
Plant Mol Biol. 2007 Feb;63(3):381-91
17082872
Nat Rev Genet. 2007 Mar;8(3):206-16
17304246
Genome Res. 2007 Mar;17(3):264-75
17255553
Genetics. 2007 Mar;175(3):1441-50
17179097
J Hered. 2007 Mar-Apr;98(2):136-41
17208934
Annu Rev Plant Biol. 2007;58:377-406
17280525
Nature. 2000 Mar 2;404(6773):91-4
10716449
Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161-6
11470895
Nature. 2001 Dec 13;414(6865):709-10
11742384
Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9573-8
12060715
Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13606-11
12370431
Plant Cell. 2003 Feb;15(2):425-38
12566582
Nature. 2003 Mar 20;422(6929):297-302
12646919
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4649-54
12665616
Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):9055-60
12853580
Plant Cell. 2004 Jul;16(7):1707-16
15194819