Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

Iowa State University, Ames, IA 50011, USA.
Science (Impact Factor: 33.61). 11/2009; 326(5956):1118-20. DOI: 10.1126/science.1178294
Source: PubMed


Heterosis refers to the superior performance of hybrid progeny relative to their inbred parents, but the mechanisms responsible are unknown. Hybrids between the maize inbred lines B73 and Mo17 exhibit heterosis regardless of cross direction. These reciprocal hybrids differ from each other phenotypically, and 30 to 50% of their genes are differentially expressed. We identified approximately 4000 expression quantitative trait loci (eQTL) that allowed us to identify markers linked to variation in expression. We found that over three-quarters of these eQTL act in trans (78%) and that 86% of these differentially regulate transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. This result suggests that widespread imprinting contributes to the regulation of gene expression in maize hybrids.

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Available from: Tieming Ji, Mar 18, 2015
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    • "In the previous studies, a large number of genetic loci with dominance effect were detected in F1 hybrids [46-48]. eQTL analysis revealed that the gene expression regulation was an complicated regulation networks [49-51]. So, the phenomena of the phenotypes and the transcriptomes biased to high GCA parents in F1 hybrids might be consequence of the accumulation of the loci with dominance effect in the elite parents through artificial selection. "
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    ABSTRACT: Sprague and Tatum (1942) introduced the concepts of general combining ability (GCA) and specific combining ability (SCA) to evaluate the breeding parents and F1 hybrid performance, respectively. Since then, the GCA was widely used in cross breeding for elite parent selection. However, the molecular basis of GCA remains to unknown. We studied the transcriptomes of three varieties and three F1 hybrids using RNA-Sequencing. Transcriptome sequence analysis revealed that the transcriptome profiles of the F1s were similar to the positive GCA-effect parent. Moreover, the expression levels of most differentially expressed genes (DEGs) were equal to the parent with a positive GCA effect. Analysis of the gene expression patterns of gibberellic acid (GA) and flowering time pathways that determine plant height and flowering time in rice validated the preferential transcriptome expression of the parents with positive GCA effect. Furthermore, H3K36me3 modification bias in the Pseudo-Response Regulators (PRR) gene family was observed in the positive GCA effect parents and demonstrated that the phenotype and transcriptome bias in the positive GCA effect parents have been epigenetically regulated by either global modification or specific signaling pathways in rice. The results revealed that the transcriptome profiles and DEGs in the F1s were highly related to phenotype bias to the positive GCA-effect parent. The transcriptome bias toward high GCA parents in F1 hybrids attributed to H3K36me3 modification both on global modification level and specific signaling pathways. Our results indicated the transcriptome profile and epigenetic modification level bias to high GCA parents could be the molecular basis of GCA.
    Full-text · Article · Apr 2014 · BMC Genomics
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    • "eQTLs may act either in cis, when mapped within 5 cM of the gene used for the expression analysis, or in trans, when mapped to a chromosome different from the gene used to measure expression (Swanson-Wagner et al., 2009). Also, it is possible that the expression of a gene may be controlled by multiple QTLs (Potokina et al., 2008; Swanson-Wagner et al., 2009). According to these criteria, two cis-eQTLs and a third transeQTL were mapped in the LD00-2817P by LDX01-1- 65 population. "

    Full-text · Dataset · Dec 2012
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    • "Plant GWAS can be performed in large numbers of samples in replicated trials using inbreds, double haploid (DH) lines and recombinant inbred lines (RILs) [39]. The determination of large numbers of genome variants in combination with transcription profiling can be used to determine expression quantitative loci (eQTLs) [40], mapping regions with cis- and trans-effects [41,42,43,44]. Bulked segregant analysis can be used as a time- and cost-effective way to identify markers associated to specific phenotypes without the need of having a linkage map or sampling large numbers of samples in a population [45]. "
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    ABSTRACT: The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.
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