Mendelian and Non-Mendelian Regulation of Gene Expression in Maize
[['The maize species exhibits high levels of phenotypic variation , which is likely the result of both genetic and epigenetic variation [1] .', 'Dissection of genetic and epigenetic variation may shed light on the understanding of phenotypic variation and provide tools to accelerate maize breeding .', 'The maize genome has a complex organization with interspersed repetitive elements and genes [2] .', 'The genomes of different maize inbreds can vary substantially due to single nucleotide polymorphisms [3] , small insertions/deletions [4]–[5] , gene copy number variation ( CNV ) and genomic presence-absence variation ( PAV ) [2] , [6]–[7] .', 'Transposable elements , discovered in maize by Barbara McClintock [8]–[9] , comprise a significant portion of the maize genome [2] , [10]–[13] and can contribute substantially to genomic variation among lines [14]–[17] .', 'There are many examples illustrating the potential for transposons to capture and mobilize genes or gene fragments [14] , [18]–[24] .', 'In addition to genetic changes , there is also evidence for epigenetic variation among maize inbred lines .', 'The epigenetic differences vary within maize populations and show relatively stable trans-generational inheritance [25] .', 'These diverse forms of genetic and epigenetic variation likely interact to affect relative transcript abundance , which contributes to phenotypic variation among maize individuals .', 'Exploring transcriptome variation and elucidating the underlying mechanisms of transcriptional regulation may further our understanding of the molecular bases of phenotypic variation [26]–[27] .', 'Several groups have used microarray profiling to compare the transcriptomes of maize inbreds [28]–[33] .', 'A comparison of the F1 hybrids and the parents revealed that much of the parental variation resulted in additive expression with some rare examples of unexpected expression in the F1 [28] , [33] .', 'A recent RNA-seq based analysis of transcriptomic variation in 21 maize elite inbred lines found that a substantial number of genes showed presence/absence expression patterns [34] .', 'Genetical genomics or expression quantitative trait loci ( eQTL ) mapping is an efficient method for understanding the genetic basis of transcriptome variation [26]–[27] , [35]–[36] .', 'eQTL mapping uses transcript abundance as a phenotypic trait and maps the genomic loci controlling the transcript abundance [35] .', 'eQTL are generally classified as cis- or trans- depending on whether they are physically linked to the gene that is regulated or unlinked , respectively .', 'Both cis- and trans-eQTLs have been identified in plants and while trans-eQTLs are more abundant , they generally explain less expression variation than cis-eQTLs [37]–[42] .', 'Several eQTL mapping experiments have utilized microarrays to reveal the complexity of transcriptome variation and their underlying genetic regulators such as trans-eQTL hotspots in human , animals and plants [37] , [39] , [42]–[44] .', 'eQTL mapping of transcriptome variation has also been employed directly to help dissect phenotypic variation [42] , [45]–[46] .', 'The analyses of transcriptome variation in segregating populations have generally focused on exploring how a single locus contributes variation to transcript abundance in a Mendelian fashion .', 'However , there is also the potential for non-Mendelian segregation of gene expression levels [47] .', 'RNA-based sequencing ( RNA-Seq ) provides several key advantages for transcriptome research including robust expression detection especially for lowly expressed genes , unprecedented access to the fine structure of the transcriptome , and powerful detection of all the transcripts not depending on the reference genome annotation [48]–[49] .', 'Here , we employed RNA-Seq on shoot apices of a well-studied maize intermated RIL population derived from B73 and Mo17 ( IBM ) [50] .', 'We characterized the relationship of transcriptional variation between the progeny population and the parents in detail to understand how the parental variation combines to affect transcript abundance .', 'This analysis identified a number of genes that exhibit unexpected patterns of expression variation including paramutation-like segregation patterns and presence/absence expression patterns between progeny and parents .', 'Meanwhile , global eQTL mapping , a pair-wise epistasis scan and co-expression analysis were conducted to dissect the possible factors underlying this variation .'], ['A population of RILs is expected to segregate 1∶1 for the parental alleles and provides an opportunity to examine variation in transcript abundance within the RILs and the relationship between the population and the parents .', 'We first focused on the expression levels of 22 , 242 genes that were detected in both parents and at least 90% of the IBM RILs .', 'The mean expression levels in the RILs were similar to the mid-parent values for most genes ( Figure 1B ) .', 'Transgressive segregation , defined here as at least 10% of RILs exhibiting expression levels outside the parental range , was observed for 598 genes ( 2 . 6% ) .', 'The other 21 , 644 ( 97 . 4% ) genes have expression levels in the RILs that are within the parental range .', "The level of variation for gene expression levels in the RILs was significantly correlated with the difference between the two parents ( Pearson's product-moment correlation: r\u200a=\u200a0 . 728 , P<2 . 2E-16; Figure 1C ) .", 'The type of distribution for expression levels within the RIL population relative to the parents was assessed using a τ score [52] .', 'We found that 4 , 822 ( 22% ) genes fit bimodal distributions , 14 , 564 exhibited normality ( 65% ) and the remaining 2 , 856 ( 13% ) showed other unclassified distributions .', 'Genes with little or no expression difference among the parents typically exhibited a normal distribution in the RILs ( Figure 1D ) .', 'However , many genes with large expression differences among the parents exhibited a bimodal distribution among the RILs ( Figure 1D ) .', 'These trends indicated that much of the variation in gene expression levels in the RILs is reflective of differences present between the parents .', 'While the majority of genes exhibit expression patterns in the RILs that are quite predictable from the parental levels , there were a subset of genes ( 0 . 7% ) that have average expression levels in the RILs that are greater than 2-fold different than the mid-parent , indicative of other potential patterns of expression variation .', 'It is possible that some of these genes may have expression patterns similar to those observed for genes that are subject to paramutation such that the expression levels in all RILs would be similar to the expression level of one of the parents [53] .', 'The distribution of expression patterns in the RILs was compared to the parental expression patterns for 8 , 269 out of 28 , 603 detected genes that have at least two-fold expression level difference between B73 and Mo17 .', 'There were 145 genes ( 86 of these genes are from the 22 , 242 genes expressed in both parents and 90% of the RILs ) with paramutation-like expression patterns for the RILs in which one parent was within the expression distribution ( two standard deviations from the population mean ) of the RILs but the other parent had an expression level at least three standard deviations from the population mean ( Figure 2A; Figure S2; Table S2 ) .', 'It is important to note that , while these genes exhibit patterns that are similar to those expected due to paramutation these genes may either be directly regulated by paramutation or be secondary targets that are influenced by another factor that is subject to paramutation .', 'For many ( 80/145 ) of these genes one of the two parents had an expression level that was outside the range of all RIL genotypes .', 'The expression levels of B73 and Mo17 relative to the population mean and standard deviation helps illustrate several trends observed for these genes ( Figure 2A ) .', 'The majority of these genes ( 124/145 ) had patterns in which the RILs were all expressed at levels similar to the lower parent as might be expected given that most examples of paramutation involve a paramutagenic allele that is expressed at lower levels than the paramutable allele ( Figure 2B ) .', 'The expression level for these genes was assessed in the F1 hybrid relative to the two parents ( Figure S3 ) .', 'Well characterized examples of paramutation in maize include some examples of dominant expression in the F1 as well as other examples that do not exert effects until the F2 generation [54]–[57] .', 'The genes that had high levels of expression in all RILs were expressed at additive levels in the F1 .', 'The genes that had expression levels similar to the lower parent included many examples of additive expression but also had a number of cases with partial to complete dominance in expression such that the F1 had levels more similar to the lower parent ( Figure S3 ) .', 'Ten of the genes with paramutation-like patterns were selected for analysis in F2 individuals ( Figure S4 ) .', 'Seven of the ten genes exhibited paramutation-like patterns in the F2 individuals and these include examples of both high and low expression .', 'The basis for the regulatory variation in transcript levels was examined using a high-resolution SNP genetic map of the IBM population based upon 7 , 856 high quality SNP markers derived from the RNA-seq data to perform eQTL analysis for the 22 , 242 genes that are expressed in both parents and at least 90% of the RILs .', 'This approach is likely to capture much of the variation for gene expression that segregates in a Mendelian fashion but is less likely to capture the basis of variation for examples of gene expression such as those described above .', 'A total of 30 , 774 eQTLs ( α\u200a=\u200a0 . 05 ) with a threshold logarithm of odds ( LOD ) >\u200a=\u200a4 . 17 were identified for 19 , 304 genes , of which 5 , 303 ( 27 . 5% ) were controlled only by a single cis-eQTL , 6 , 201 ( 32 . 1% ) controlled by both cis- and trans-eQTLs and 7 , 800 ( 40 . 4% ) only by trans-eQTLs .', 'The 30 , 774 eQTLs include 11 , 504 ( ∼37% ) cis-eQTLs and 19 , 270 ( ∼63% ) trans-eQTLs ( Figure 3A and Table S3 ) .', 'The number of eQTLs affecting the expression level of each gene ranged from zero to six .', 'In general , cis-eQTLs tend to have larger effects than trans-eQTLs ( Figure S5A ) .', 'For example , 83 . 7% of cis-eQTLs account for at least 20% of the expression variation in contrast to only 12 . 7% of the trans-eQTL meeting this criterion .', 'However , there are examples of trans-eQTLs that contribute substantially to expression variation .', 'There were 133 trans-eQTLs that contribute at least 60% of the variation for expression of a target gene .', 'The overall contribution of cis- and trans-eQTLs was heavily influenced by the level of expression variation in the parents ( Figure S5B ) .', 'The contribution of cis-eQTLs increased as the parental expression level became increasingly different .', 'In addition , the amount of variation explained by the cis-eQTL also increased as the parental expression levels become more different ( Figure S5C ) while the amounts of variation explained by trans-eQTL decreased as the parental differences increased ( Figure S5D ) .', 'The proportion of cis- and trans-eQTL for the 598 genes exhibiting transgressive segregation was similar to the proportion of cis- and trans-eQTL for the global eQTL analysis , however , the genes with transgressive segregation were more often ( 37% ) controlled by multiple eQTLs with opposite effects than all genes ( 27% ) .', '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 ( Figure 3B and Table S4 ) , including 10 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 B73 allele ( 49 ) at the trans-eQTL hotspot promoted higher expression of the target loci than the Mo17 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 ten trans-eQTL hotspots that had at least 200 targets ( Table 1 ) .', 'Nine of these ten trans-eQTL hotspots showed consistent haplotype bias ( six for B73 and three for Mo17 ) 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 ( Figure 3C , Table S6 ) .', 'These trans-eQTL hotspots may be due to functional differences in transcriptional regulators .', 'At least in some cases it might be expected that differential expression of a regulator present at the trans-eQTL hotspot is the cause of the differences in trans-regulation .', 'To examine the influence of structural rearrangements-gene copy number variation ( CNV ) and genomic presence/absence variation ( PAV ) on gene expression , we compared our transcriptomic data for the 28 , 603 expressed genes with previous Comparative Genomic Hybridization ( CGH ) data [59] .', 'We focused on the full set of 28 , 603 genes as the more limited set of 22 , 242 genes assessed for eQTL analysis required expression to be present in both parents while some of the PAV are expected to abolish expression in Mo17 .', 'There are 1 , 212 expressed genes with CNV/PAVs that affect the gene or flanking regions ( Table S7 ) .', 'The structural rearrangements include copy number gains in B73 or Mo17 as well as PAV that are present in B73 but absent in the Mo17 genome .', 'We might expect that copy number gains would lead to increased expression in the genotype with more copies while PAV would only be expressed in one genotype .', 'There was evidence that this was true in many cases ( Table S8 and Figure 4 ) .', 'eQTL mapping was conducted on these CNV/PAV-related genes and a total of 1 , 466 were identified for 1 , 009 genes , of which 704 ( 69 . 8% ) were controlled by cis-eQTLs .', 'The cis-eQTLs proportion of genes with CNV/PAVs nearby is significantly higher ( P\u200a=\u200a0 . 00 ) than those of all detected genes ( Figure 4A ) .', 'Noteworthy was the observation that 89 . 2% of these genes entirely within the PAV were controlled by cis-eQTLs , while ∼10% of these genes have trans-eQTLs , indicating that other regulators underlie the expression variation in addition to PAVs .', 'There was also evidence for an enrichment of cis-acting variation when the CNV/PAV occurred in regions surrounding the gene .', 'Nearly half ( 120/242 ) of the genes entirely within structural variants exhibit differential expression in B73 and Mo17 .', 'There were many examples in which the RIL genotype at the gene of interest was highly correlated with the expression difference ( Figure 4B , 4C ) .', "Typically , the copy number of genes entirely within CNV/PAV regions positively correlated with the genes' expression ( 99 out of the 120 differentially expressed genes between the two parents ) ( Figure 4B ) .", 'We also noted examples ( 21/120 ) in which a copy number gain was associated with lower expression in the parents ( Figure 4C ) .', 'We were struck that a large proportion of genes were only detected in a subset of the RILs or parents .', 'While there were 22 , 242 genes expressed in both parents and the RILs , there were an additional 6 , 361 genes that had detectable ( False Discovery Rate-FDR>0 . 05 ) levels in at least 10% of the RILs or at least one of their parents .', 'These 6 , 361 genes may include', '( a ) some genes with very low expression levels that manage to cross the threshold of detectability in some samples but not others ,', '( b ) genes that are only expressed in one parent and that based on Mendelian segregation would therefore be expected to be expressed in only 50% of the RILs , and', '( c ) genes with unusual regulatory mechanisms .', 'We elected to impose a more restrictive set of filtering criteria for expression to limit the number of low-expressed genes near the detection threshold .', 'Based on the alignment of RNA-seq reads to non-genic genomic regions , an RPKM of 1 . 03 corresponds to a FDR of 0 . 01 and 499 of the 6 , 361 genes have a RPKM value of ≧1 . 03 in at least 10% of the RILs or at least one of their parents .', 'A substantial proportion of these genes ( 289/499 ) were expressed in only one of the parents and were observed in approximately 50% of the RILs ( with the Chi-square test at the P value<0 . 01 ) .', 'The lack of expression in one parent and half of the RILs may reflect differences in genome content or regulatory variation .', 'eQTL analysis of these genes revealed that 186 ( 64% ) of these genes had cis-eQTL that explained >20% of the expression variation and 54 of these genes intersect with CNV/PAVs .', 'However , there were also 92 ( 32% ) of these genes that had evidence for at least one strong trans-eQTL with R2>20% .', 'In total , eQTLs could explain more than 20% of the expression variation of 273 of these 289 genes ( 96 . 1% ) .', 'The other 210 of these genes exhibited unexpected patterns of expression that could be classified into four groups ( Table S9 ) .', 'The type I pattern included 40 genes that were expressed in both parents but were not detected ( RPKM\u200a=\u200a0 ) in over 10% of the RILs .', 'The type II pattern included 19 genes that were not detected ( RPKM\u200a=\u200a0 ) in the parents but were detected in at least 10% of the RILs .', 'The type III patterns include genes that were expressed in one parent but not the other and had expression in very few RILs ( type IIIA – 66 genes ) or the majority of the RILs ( type IIIB – 85 genes ) ( Figure 5A ) .', 'A subset of genes ( 2 type I genes and 19 type III genes ) with unexpected expression patterns also exhibited paramutation-like expression patterns .', 'These unexpected patterns of expression detected by RNA-seq were validated for the majority of genes tested ( 43/55 ) using RT-PCR on a subset of the RIL genotypes ( Figure S6 ) .', 'In addition , the same type of expression patterns could be observed in an independent set of B73×Mo17 F2 individuals for all the six tested genes ( Figure 5B ) .', 'These RT-PCR assays confirmed that the unexpected segregation patterns for presence or absence of gene expression observed in the RILs are reproducible .', 'Further , genomic PCR was employed to assess if the expression presence/absence transcript variation might be attributable to differences in genome content .', 'We found that genes exhibiting presence/absence transcript variation could be amplified from genomic DNA of each of the IBM RILs that were tested ( Figure S7 ) , indicating that the difference in expression was not due to segregation for genomic presence of the sequence .', 'For each of the four patterns , the proportion of RILs expressing a gene was compared to the mean expression level in genotypes that express the gene ( Figure 5C ) .', 'Some of these genes are quite highly expressed and there is a substantial range in the number of genotypes with expression .', 'To further distinguish the genes with unexpected expression patterns from the genes with very low expression levels that manage to cross the threshold of detectability , we examined the maximum expression levels , population mean RPKM and the standard deviations in the population of the genes with unexpected expression patterns in comparison to all detected genes expressed in more than 90% of the RILs .', 'Although the maximum expression levels , population mean RPKMs of genes with unexpected expression patterns are slightly lower than those of all expressed genes , the differences are not significant ( Figure S8 ) .', 'Importantly , the standard deviation of expression levels of genes with unexpected expression patterns is similar to that of all other genes ( Figure S8 ) .', 'The observation that there were many examples in which the proportions of RILs with detected expression was close to 25% or 75% ( Figure 5C ) may suggest that multiple genetic factors play interaction roles underlying the unexpected expression patterns for some of these genes .', 'To test this hypothesis , a genome-wide epistasis scan with all possible pair-wise marker interactions was employed to search for evidence of two-locus interactions that control expression for genes that were detected in approximately one-quarter or three-quarters of the RILs .', 'If two different loci are both required to achieve expression of a gene , these loci could both be present in one parent ( type III ) or could have one functional locus in either parent ( type II ) .', 'In these examples we would expect 25% of the RILs to exhibit expression of the gene .', 'There are 28 type IIIA and 10 type II genes with expression in only ∼25% of the RILs using Chi-square test with the p-value<0 . 01 as the cut-off .', 'A genome-wide scan for two-locus interactions that control the variation of expression for these 38 genes found that 92% of these could be explained by a two locus interaction ( Figure S9A , S9B ) .', 'In half of the cases in which a two-locus interaction explained a significant proportion of the expression variation we found that one of the two loci mapped in cis to the gene itself .', 'We could also envision a scenario in which two different loci are required for loss of expression of a gene and this would be expected to result in expression in 75% of the RILs .', 'There are 71 type IIIB and 28 type I genes that are expressed in ∼75% of the RILs and for 91% of these genes the pattern of presence/absence can be explained by a two-locus interaction , including 12 examples in which one of the two loci maps in cis to the gene itself ( Figure S9C , S9D ) .', 'This suggests that a significant subset of the genes with unexpected patterns of presence-absence for expression can be explained by two-locus interactions .', 'The genes that exhibit presence/absence expression patterns in progeny relative to their parents were further characterized .', 'As a group , these genes with unexpected expression patterns were enriched for single copy genes , and for low copy number gene families relative to all maize genes ( Table 2 ) .', 'The FGS ( Filtered Gene Set ) genes of maize represent an attempt to identify higher confidence gene models and remove gene fragments and transposon-derived sequences [2] .', 'However , there are likely a number of gene fragments and transposon-derived sequences still present within the FGS .', 'Comparative genomic localization can provide more confidence in syntenic genes as “real” genes [60] .', 'Only 36/210 genes with presence/absence expression patterns are in syntenic locations relative to other grass species ( Figure 5D ) .', 'This is a smaller proportion than expected based on the finding that 67 . 5% of all FGS genes are located in syntenic positions .', 'It is worth noting that while the genes with unexpected patterns are enriched for non-synteny there is a subset of these genes that do have synteny and likely represent functional genes ( Table S9 ) .', 'Annotation of the syntenic genes with unexpected presence/absence expression patterns reveal a variety of putative functions such as serine threonine protein kinase , electron transport sco1 family protein and basic leucine-zipper 44 protein , but there is no evidence for GO enrichments within this set of genes .', 'The 174 genes with unexpected segregation patterns that are non-syntenic with other grass species may represent insertions of these genes or gene fragments in the maize genome .', 'To test the hypothesis , the genomic regions surrounding these genes were examined for enrichment of specific classes of repetitive sequences ( Figure S10 ) .', 'Over one-third ( 65 ) of the 174 genes had a CACTA-like element within 20 kb and these include examples of all types of unexpected expression patterns .', 'This is significant ( P\u200a=\u200a0 . 00 ) enrichment of CACTA-like transposable elements surrounding these genes relative to the expected genomic frequency ( Figure 6A ) .', 'The 65 genes with CACTA-like sequences nearby ( 3 . 20 exons ) and the other 145 genes with unexpected segregation patterns ( 3 . 10 exons ) tended to have fewer exons ( P\u200a=\u200a0 . 00 ) than the average exon number ( 4 . 88 exons ) of all maize genes ( Figure 6B ) .', 'These features , less exons , non-syntenic genomic localization and CACTA-like element enrichment , suggest that many of these genes may be gene fragments that were captured and transposed by CACTA-like transposons .', 'We proceeded to assess whether the non-syntenic gene fragments with presence/absence expression might affect the regulation of homologous full-length syntenic genes ( ancestral syntenic genes ) elsewhere in the maize genome .', 'All 174 of the non-syntenic genes were homologous to at least a portion of another maize gene ( E value<1 . 0E-10 ) .', 'The correlation between the expression level of each of these genes and the other homologous full-length sequences ( possible ancestral syntenic genes ) was assessed in the RIL population .', 'There were 25 examples in which the presence/absence expression patterns of the non-syntenic genes were correlated with transcript abundance for ancestral syntenic genes ( Table S10 ) .', 'For example , the presence/absence expression of a gene fragment located on chromosome 3 was highly correlated with the abundance of a transcript from its ancestral syntenic gene annotated as an Erwinia Induced Protein 1 located on chromosome 5 ( Figure 7A ) .', 'A comparison of the expression levels for the two sequences revealed an inverse correlation such that the presence/absence of transcripts from the gene fragment correlated with low or high expression of the ancestral syntenic gene ( Figure 7B ) .', 'However , the presence/absence of transcripts from the transposed fragment does not result from genomic differences among RILs because according to the genomic PCR amplifications this gene fragment exists in all tested RILs ( Figure 7C ) .', 'The expression pattern of gene GRMZM2G004617 was also identified to be controlled by two-locus interaction ( Figure 7D ) .', 'Many ( 20 ) of the other 25 examples involve similar negative correlations between presence/absence of a gene fragment and abundance of a full-length transcript ( Table S10 ) .', 'These examples provide evidence for the ability of transposed gene fragments to influence transcript abundance of their ancestral syntenic genes .'], ['The analysis of eQTLs allows for the dissection of the genomic regions that affect transcript abundance .', 'Cis-regulatory eQTL reflect regulatory variation that is tightly linked to a gene and affects the allelic expression levels .', 'In contrast , trans-eQTL reflects regulatory variation at unlinked genomic positions .', 'The analysis of all trans-eQTL can reveal trans-eQTL hotspots , also known as trans-eQTL clusters , which are genomic regions that affect the expression of many unlinked loci [39] , [61] .', 'These trans-eQTLs are thought to reflect differences in gene regulation that may be important for phenotypic variation [39] , [41]–[42] , [44] .', 'Due to the limitations of mapping resolution , the identified trans-eQTL hotspots could result from the presence of a single causal regulatory factor ( pleiotropic effects ) or several tightly linked loci that affect transcript levels of different genes ( genetic coupling ) [62] .', 'In addition , each trans-eQTL hotspot is relatively large ( ∼1 Mb ) and will likely include the targets of the hotspot itself as well as several other trans-eQTLs that only regulate a small number of genes .', 'Most of the trans-eQTL hotspots identified in our study showed significant haplotype effect bias , which means the haplotype of one parent could increase expression levels of significantly more target genes than expected .', 'The hotspots with haplotype effect bias are more likely to reflect “master regulators” , while some of the others may be a result of genetic linkage , even though we had already taken gene density into account .', 'It might be expected that variation in an important regulatory locus may result in variation for transcript levels for a number of genes that share related GO annotation or are present in the same biochemical pathway .', 'Here , the expression level of genes involved in these pathways were found to be consistently altered in the same direction by trans-eQTL hostpots , which implies that pathway variation may exhibit genetic variation underlying the phenotypic variation among different elite inbred lines .', 'The regulatory variation provided by the trans-eQTL could be the result of differences in the expression level for a regulator located within the trans-eQTL ( a cis-eQTL ) or it could be the result of a qualitative variant for a gene located within the genomic region .', 'If the cause of the trans-eQTL hotspot is a cis-regulatory variant then we would expect to find a cis-eQTL located within the trans-eQTL that is highly correlated with the expression level of the target genes .', 'The analysis of these cis-eQTLs located within the trans-eQTL hotspot did not find enrichment for transcription factors .', 'However , we did identify transcription factors or other putative regulatory genes .', 'These candidate genes provide a potential avenue for future research to understand the basis of regulatory variation in maize ( Table S11 ) .', 'The majority of genes behave in a manner that is predictable based on the expression levels of the parents .', 'In general , genes with relatively little expression variation in the parental genotypes exhibit a normal distribution of expression levels centered on the parental levels in the offspring and the genes with variation between the parents exhibit a bimodal distribution in the offspring .', 'Our results showed that for the majority of genes expression trait variation is mainly caused by additive effects , which differs from the results observed in Arabidopsis , and rice where non-additive gene action was the more common form of regulating transcript accumulation [39]–[42] .', 'However , a portion of genes exhibit transgressive segregation in the RILs such that at least 10% of the RILs exhibit expression levels outside the parental range .', 'The proportion of transgressive segregation for expression traits was small ( 2% ) compared with the levels reported in other species [39]–[42] .', 'The measurement of eQTL for many genes at once provides an opportunity to assess the potential causes of transgressive segregation .', 'One likely cause of transgressive segregation would be the presence of multiple trans-eQTL including examples in which both parental haplotypes promote expression .', 'For example , if a single gene has two trans-eQTLs for which the B73 allele promotes higher expression and two other trans-eQTLs in which the Mo17 allele promotes higher expression then one might expect to observe a number of RILs with expression levels that are higher or lower than the parental values due to segregation of these trans-eQTLs .', 'Indeed , we found that the 598 genes with transgressive segregation tended to have higher numbers of trans-eQTL than the other genes and that these frequently included a mixture of B73/Mo17 favorable alleles for the underlying gene expression trait .', 'While the majority of genes behaved in predictable fashions in the RILs relative to parents and had variation that could be attributed to eQTL there were some genes with unexpected expression patterns .', 'We focused our analysis on a couple of subsets of these genes including genes with paramutation-like pattern of expression and genes with unexpected patterns of presence/a
['Introduction', 'Results', 'Discussion', 'Materials and Methods']
['Transcriptome variation plays an important role in affecting the phenotype of an organism .', 'However , an understanding of the underlying mechanisms regulating transcriptome variation in segregating populations is still largely unknown .', 'We sought to assess and map variation in transcript abundance in maize shoot apices in the intermated B73×Mo17 recombinant inbred line population .', 'RNA–based sequencing ( RNA–seq ) allowed for the detection and quantification of the transcript abundance derived from 28 , 603 genes .', 'For a majority of these genes , the population mean , coefficient of variation , and segregation patterns could be predicted by the parental expression levels .', 'Expression quantitative trait loci ( eQTL ) mapping identified 30 , 774 eQTL including 96 trans-eQTL “hotspots , ” each of which regulates the expression of a large number of genes .', 'Interestingly , genes regulated by a trans-eQTL hotspot tend to be enriched for a specific function or act in the same genetic pathway .', 'Also , genomic structural variation appeared to contribute to cis-regulation of gene expression .', 'Besides genes showing Mendelian inheritance in the RIL population , we also found genes whose expression level and variation in the progeny could not be predicted based on parental difference , indicating that non-Mendelian factors also contribute to expression variation .', 'Specifically , we found 145 genes that show patterns of expression reminiscent of paramutation such that all the progeny had expression levels similar to one of the two parents .', 'Furthermore , we identified another 210 genes that exhibited unexpected patterns of transcript presence/absence .', 'Many of these genes are likely to be gene fragments resulting from transposition , and the presence/absence of their transcripts could influence expression levels of their ancestral syntenic genes .', 'Overall , our results contribute to the identification of novel expression patterns and broaden the understanding of transcriptional variation in plants .']
['Phenotypes are determined by the expression of genes , the environment , and the interaction of gene expression and the environment .', 'However , a complete understanding of the inheritance of and genome-wide regulation of gene expression is lacking .', 'One approach , called expression quantitative trait locus ( eQTL ) mapping provides the opportunity to examine the genome-wide inheritance and regulation of gene expression .', 'In this paper , we conducted high-throughput sequencing of gene transcripts to examine gene expression in the shoot apex of a maize biparental mapping population .', 'We quantified expression levels from 28 , 603 genes in the population and showed that the vast majority of genes exhibited the expected pattern of Mendelian inheritance .', 'We genetically mapped the expression patterns and identified genomic regions associated with gene expression .', 'Notably , we detected gene expression patterns that exhibited non-Mendelian inheritance .', 'These included 145 genes that exhibited expression patterns in the progeny that were similar to only one of the parents and 210 genes with unexpected presence/absence expression patterns .', 'The findings of non-Mendelian inheritance underscore the complexity of gene expression and provide a framework for understanding these complexities .']
['plant biology', 'population genetics', 'crop genetics', 'plant science', 'cereals', 'crops', 'plant genomics', 'population biology', 'genetic polymorphism', 'maize', 'gene expression', 'plant genetics', 'biology', 'agriculture', 'plant breeding', 'agronomy', 'genetics', 'genetics and genomics']