Correction: Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

摘要

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 8~(th)and 9~(th)columns (B73~(c)and Mo17~(d)) 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. 10.1371/journal.pgen.1007234.t001 Table 1 Trans -eQTL hotspots with at least 200 trans -eQTLs. Hotspot_name Chr StartPos (Mb) EndPos (Mb) #_ cis ~(a) #_ trans ~(b) #_eQTL/ (Mb×#_gene) B73 ~(C) Mo17 ~(d) Sig.Bias ~(e) 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. ~(e): Shows the significance level deviating from the random distribution between B73 and Mo17. The GO enrichments and the pathway enrichments of the regulated 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. 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 trans -eQTLs hotspots” should be “ nine trans -eQTLs hotspots”. The corrected legend and a copy of the figure are included below. 10.1371/journal.pgen.1007234.g001 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 R ~(2)value. eQTLs with R ~(2)values greater than 20% were plotted in red, R ~(2)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 trans -eQTLs. (C) Genes regulated by three trans -eQTL hotspots are involved in specific metabolic pathways. The expression levels of these genes in 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. 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