CORRECTION
Correction: Mendelian and Non-Mendelian
Regulation of Gene Expression in Maize
Lin Li, Katherine Petsch, Rena Shimizu, Sanzhen Liu, Wayne Wenzhong Xu, Kai Ying,
Jianming Yu, Michael J. Scanlon, Patrick S. Schnable, Marja C. P. Timmermans, Nathan
M. Springer, Gary J. Muehlbauer
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OPEN ACCESS
Citation: Li L, Petsch K, Shimizu R, Liu S, Xu WW,
Ying K, et al. (2018) Correction: Mendelian and
Non-Mendelian Regulation of Gene Expression in
Maize. PLoS Genet 14(2): e1007234. https://doi.
org/10.1371/journal.pgen.1007234
Published: February 14, 2018
Copyright: © 2018 Li et al. This is an open access
article distributed under the terms of the Creative
Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in
any medium, provided the original author and
source are credited.
There are errors with the eQTL effects reported in this article. The effects should be reversed;
specifically, the base allele in the contrast to derive the additive effects should be B73, rather
than Mo17. The authors apologize for the errors and provide further details and corrections to
the text, the Fig 3 legend, and Tables 1, S3 and S4 below. The reversal of the eQTL effect does
not affect the main conclusions of the manuscript, as subsequent results were gained by using
the RPKM values from individual RILs and not the eQTL mapping results.
In Table 1, the values of the 8th and 9th columns (B73c and Mo17d) should be switched.
Additionally, instead of ten eQTL hotspots that contain at least 200 eQTL there are only nine
eQTL hotspots that contain at least 200 eQTLs. The corrected version of Table 1 is below, and
includes only nine hotspots with at least 200 eQTLs.
In the legend for Fig 3, the phrase “the additive effects of the trans-eQTLs of Mo17 alleles”
should be “the additive effects of the trans-eQTLs of B73 alleles” and the phrase “10 transeQTLs hotspots” should be “nine trans-eQTLs hotspots”. The corrected legend and a copy of
the figure are included below.
In the Results section, the second paragraph under the sub-heading ‘Mapping the basis of
expression level variation’ should be corrected to reflect the changes made to Table 1 and the
Fig 3 legend:
“The genomic distribution of trans-eQTL was assessed in an attempt to identify potential
trans-eQTL hotspots that might reflect substantial regulatory differences between B73 and
Mo17. The analysis of trans-eQTL density in a 1 Mb (which is slightly larger than the average
physical distance between adjacent markers with a recombination event) sliding window
revealed 96 significant (P<0.01) trans-eQTL hotspots (Fig 3B and S4 Table), including nine
major hotspots that contain at least 200 trans-eQTLs (Table 1). These hotspots have many
more trans-eQTL than other genomic regions and in the majority (78%) of examples the target
genes regulated at the trans-eQTL hotspots show a consistent pattern with significantly more
target genes altered in expression in the same direction by the haplotype at the trans-eQTL
hotspot (haplotype bias). More examples in which the Mo17 allele (49) at the trans-eQTL hotspot promoted higher expression of the target loci than the B73 allele (26) were identified. The
lists of target genes regulated by each of the trans-eQTL hotspots were used to search for GO
enrichments; 43% of the trans-eQTL hotspots target lists exhibited enrichments for at least one
GO term (Table S5). We performed further analyses for the nine trans-eQTL hotspots that had
at least 200 targets (Table 1). Eight of these nine trans-eQTL hotspots showed consistent haplotype bias (five for Mo17 and three for B73) and the targets for each of these hotspots had GO
enrichments for at least one term. Multiple genes in the same MaizeCyc pathway [58] are
observed to be co-regulated by the same trans-eQTL hotspot (Fig 3C, Table S6). These transeQTL hotspots may be due to functional differences in transcriptional regulators. At least in
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Table 1. Trans-eQTL hotspots with at least 200 trans-eQTLs.
Hotspot_name
Chr StartPos
(Mb)
EndPos
(Mb)
#_cisa #_transb #_eQTL/
(Mb×#_gene)
B73C Mo17d Sig.Biase GO Term
enrichment
MaizeCyc
enrichment
Zm_eQTL_HS14 2
3
5
56
353
3.18
64
289
4.77E-33 Yes
No
Zm_eQTL_HS20 2
202
206
70
263
2.10
102
161
2.75E-04 Yes
No
Zm_eQTL_HS25 3
4
6
28
228
3.51
118
110
5.96E-01 Yes
No
Zm_eQTL_HS29 3
214
218
63
336
2.95
249
87
9.76E-19 No
No
Zm_eQTL_HS35 4
157
160
30
379
5.92
58
321
1.38E-41 Yes
Yes
Zm_eQTL_HS37 4
176
182
45
420
2.80
146
274
4.22E-10 Yes
Yes
Zm_eQTL_HS41 4
236
238
38
259
2.78
17
242
2.04E-44 Yes
Yes
Zm_eQTL_HS65 7
156
160
51
274
2.14
192
82
3.03E-11 Yes
Yes
Zm_eQTL_HS95 10
145
147
35
221
2.83
157
64
3.95E-10 Yes
Yes
a,b
: Indicates the number of cis- and trans-eQTLs in each eQTL hotspot, respectively.
c
: Indicates the number of eQTLs, where the B73 allele increased the expression level in the RIL population.
d
: Indicates the number of eQTLs, where the Mo17 allele increased the expression level in the RIL population.
: Shows the significance level deviating from the random distribution between B73 and Mo17. The GO enrichments and the pathway enrichments of the regulated
e
genes by hotspots were conducted using BiNGO plugin in Cytoscape based on the annotation information from AgriGO and MaizeCyc database, respectively. The
results of GO enrichments and pathway enrichments are in Table S5 and Table S6, respectively.
https://doi.org/10.1371/journal.pgen.1007234.t001
some cases it might be expected that differential expression of a regulator present at the transeQTL hotspot is the cause of the differences in trans-regulation.”
In S3 Table, the footnote is incorrect. The phrase “the allele from Mo17 increases the phenotypic value” should read “the allele from B73 increases the phenotypic value”. In S4 Table,
the values in the 9th and 10th (B73c and Mo17d) should be switched. Corrected versions of S3
and S4 Tables are provided below.
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Fig 3. eQTL mapping, trans-eQTL hotspots, and pathways regulated by three trans-eQTL hotspots. (A) Genomic distribution of eQTLs
identified in maize shoot apices. The x-axis indicates the genomic positions of eQTLs, while the y-axis shows the genomic positions of expressed
genes (e-traits). The 10 maize chromosomes are separated by grey lines. The color of each point reflects the R2 value. eQTLs with R2 values greater
than 20% were plotted in red, R2 values less than 20% are indicated in blue. Totally, 30,774 eQTLs were divided into 11,504 (*37%) cis-eQTLs and
19,270 (*63%) trans-eQTLs. (B) The distribution of trans-eQTLs hotspots. The x-axis shows the genomic position of detected eQTLs (unit = 1 Mb),
while the y-axis represents the number of trans-eQTLs in each 1 Mb length genomic region. The horizontal blue line for eQTL hotspots indicates the
threshold, which is represented by the maximum number of trans-eQTLs expected to randomly fall into any interval with a genome-wide P = 0.01.
The 10 maize chromosomes were divided by vertical black lines. The black lines linking (A) and (B) show several examples of the corresponding
trans-eQTL hotspots in (A) and (B). A total of 96 trans-eQTLs hotspots were identified and nine trans-eQTLs hotspots regulated at least 200 transeQTLs. (C) Genes regulated by three trans-eQTL hotspots are involved in specific metabolic pathways. The expression levels of these genes in
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pathways were regulated by trans-eQTLs located in these hotspots. The numbers beside these genes are the proportional changes which were the
additive effects of the trans-eQTLs of B73 alleles divided by the population mean of expression levels of the target genes.
https://doi.org/10.1371/journal.pgen.1007234.g001
Supporting information
S3 Table. eQTL mapping of the maize shoot apex. a, b indicate the chromosome and genetic
position of e-traits, respectively; c shows the physical chromosomal location on the B73 reference genome (AGPv2) of e-traits; d shows the middle physical position (equals the sum of the
position of the transcription start site and the termination site divided by 2) of e-traits; e indicates the genetic position of the peak of the eQTL; f is the genetic position of the inferior support interval left bound of the eQTL; g is the genetic position of the inferior support interval
right bound of the eQTL; h represents the physical position of the peak of the eQTL on the
B73 reference genome (AGPv2); i is the Logarithm of Odds (LOD) score of the eQTL; j is the
additive effect, the positive value indicates that the allele from B73 increases the phenotypic
value; k indicates the amount of expression variation of the e-trait explained by the eQTL;
Type shows the relationship between e-traits and the eQTLs.
(XLS)
S4 Table. Summary of trans-eQTL hotspots. a, b show the number of cis- and trans-eQTLs
in each eQTL hotspot, respectively; c indicates the number of eQTLs, where the B73 allele
increased the expression level; d indicates the number of eQTLs, where the Mo17 allele
increased the transcript-level in the RIL population. e shows the significant level deviating
from the random distribution between B73 and Mo17.
(XLS)
Reference
1.
Li L, Petsch K, Shimizu R, Liu S, Xu WW, Ying K, et al. (2013) Mendelian and Non-Mendelian Regulation of Gene Expression in Maize. PLoS Genet 9(1): e1003202. https://doi.org/10.1371/journal.pgen.
1003202 PMID: 23341782
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