Comparison of Maize (<i>Zea mays</i> L.) F1-Hybrid and Parental Inbred Line Primary Root Transcriptomes Suggests Organ-Specific Patterns of Nonadditive Gene Expression and Conserved Expression Trends

Hoecker, Nadine; Keller, Barbara; Muthreich, Nils; Chollet, Didier; Descombes, Patrick; Piepho, Hans‐Peter; Hochholdinger, Frank

doi:10.1534/genetics.108.088278

Cited by 108 publications

(82 citation statements)

References 42 publications

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“…For example, heterosis was observed in young primary roots 3.5 days after germination by comparing morphological traits of reciprocal hybrids and parental genotypes (Hoecker et al, 2006(Hoecker et al, , 2008. In the present study, we showed that F 1 hybrids exhibited heterosis during the five-leaf stage after confirming that these dates of measurement were sufficiently stable to allow the accurate determination of values for all three biological replicates.…”

Section: Discussionsupporting

confidence: 73%

Analysis of gene expression patterns and levels in maize hybrids and their parents

Hs¹,

Li²,

Xh³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Heterosis has greatly contributed to conventional plant breeding and is widely used to increase crop plant productivity. However, although some studies have explored the mechanisms of heterosis at the genomic and transcriptome level, these mechanisms still remain unclear. The growth and development of maize seedlings and immature embryos have an important impact on subsequent production. This study investigated differentially expressed genes (DEGs) between parents and reciprocal hybrids in the seedling leaves, roots, and immature embryo 15 days after pollination using amplified fragment length polymorphism (AFLP)-based transcript profiling (cDNA-AFLP). We isolated 180, 170, and 108 genes from the leaves, roots, and immature embryos, respectively, that were differentially expressed between hybrids and parents. Sequencing and functional analysis revealed that 107 transcriptderived fragments in the roots and leaves and 90 in the immature embryos were involved in known functions, whereas many DEGs had roles in plant growth and development, photosynthesis, signal transduction, and seed germination. Quantitative reverse-transcription polymerase chain reaction analysis of relative expression levels between reciprocal hybrids and both parental genotypes of selected genes produced results that 15400 H.S. Nie et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 15399-15411 (2015) were consistent with cDNA-AFLP. We validated the expression patterns of 15 selected genes related to heterosis formation and revealed that most showed non-additive expression in one or both hybrids, including dominant, underdominant, and overdominant expression. This indicates that gene-regulatory interactions among parental alleles play an important role in heterosis during the early developmental stages of maize.

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Section: Discussionsupporting

confidence: 73%

Analysis of gene expression patterns and levels in maize hybrids and their parents

Hs¹,

Li²,

Xh³

et al. 2015

Genet. Mol. Res.

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“…Such genes have been suggested to be associated with heterosis (Swanson-Wagner et al, 2006;Hoecker et al, 2008). In this study, thousands of genes displayed nonadditive expression under control (9,230) and water deficit (7,185) treatment.…”

Section: Discussionmentioning

confidence: 74%

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress

et al. 2016

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Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes only expressed in Mo17 displayed SPE complementation under control and water deficit conditions. As a consequence, the number of active genes in hybrids exceeded the number of active genes in the parental inbred lines significantly independent of treatment. SPE patterns were substantially more stable to expression changes by water deficit treatment than other genotype-specific expression profiles. While, on average, 75% of all SPE patterns were not altered in response to polyethylene glycol treatment, only 17% of the remaining genotype-specific expression patterns were not changed by water deficit. Nonsyntenic genes that lack syntenic orthologs in other grass species, and thus evolved late in the grass lineage, were significantly overrepresented among SPE genes. Hence, the significant overrepresentation of nonsyntenic genes among SPE patterns and their stability under water limitation might suggest a function of these genes during the early developmental manifestation of heterosis under fluctuating environmental conditions in hybrid progeny of the inbred lines B73 and Mo17.

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“…] with the early stages of lateral root initiation prior to the first cell divisions (Woll et al, 2005). Similarly, significant differences in global gene expression levels have also been observed in primary roots of different maize inbred lines and hybrids prior to the manifestation of morphological differences between the roots of these genotypes (Hoecker et al, 2008;Paschold et al, 2012). The increasing numbers of differentially expressed genes after the initial cell divisions in the crown root primordia (t2) and shortly before the appearance of the crown roots (t4) correspond to the increasing histological differences in the coleoptilar nodes of the wild type and rtcs that are a result of the cell divisions leading to crown roots in wild-type coleoptilar nodes (Hoppe et al, 1986).…”

Section: Rtcs-dependent Regulation Of Gene Expression During Crown Romentioning

confidence: 96%

Comparative Transcriptome Profiling of Maize Coleoptilar Nodes during Shoot-Borne Root Initiation

et al. 2013

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Maize (Zea mays) develops an extensive shoot-borne root system to secure water and nutrient uptake and to provide anchorage in the soil. In this study, early coleoptilar node (first shoot node) development was subjected to a detailed morphological and histological analysis. Subsequently, microarray profiling via hybridization of oligonucleotide microarrays representing transcripts of 31,355 unique maize genes at three early stages of coleoptilar node development was performed. These pairwise comparisons of wild-type versus mutant rootless concerning crown and seminal roots (rtcs) coleoptilar nodes that do not initiate shoot-borne roots revealed 828 unique transcripts that displayed RTCS-dependent expression. A stage-specific functional analysis revealed overrepresentation of "cell wall," "stress," and "development"-related transcripts among the differentially expressed genes. Differential expression of a subset of 15 of 828 genes identified by these microarray experiments was independently confirmed by quantitative real-time-polymerase chain reaction. In silico promoter analyses revealed that 100 differentially expressed genes contained at least one LATERAL ORGAN BOUNDARIES domain (LBD) motif within 1 kb upstream of the ATG start codon. Electrophoretic mobility shift assay experiments demonstrated RTCS binding for four of these promoter sequences, supporting the notion that differentially accumulated genes containing LBD motifs are likely direct downstream targets of RTCS.

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Comparison of Maize (Zea mays L.) F1-Hybrid and Parental Inbred Line Primary Root Transcriptomes Suggests Organ-Specific Patterns of Nonadditive Gene Expression and Conserved Expression Trends

Abstract: The

Cited by 108 publications

References 42 publications

Analysis of gene expression patterns and levels in maize hybrids and their parents

Analysis of gene expression patterns and levels in maize hybrids and their parents

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress

Comparative Transcriptome Profiling of Maize Coleoptilar Nodes during Shoot-Borne Root Initiation

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