The Genetic Architecture of Flowering Time and Photoperiod Sensitivity in Maize as Revealed by QTL Review and Meta Analysis

Xu, Jie; Liu, Yaxi; Liu, Jian; Cao, Mengji; Wang, Jing; Long, Hai; Xu, Yunbi; Lu, Yanli; Pan, Guangtang; Tang, Rong

doi:10.1111/j.1744-7909.2012.01128.x

Cited by 51 publications

(59 citation statements)

References 111 publications

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“…However, the high sensitivity of tropical maize germplasms to photoperiods limits its planting distribution and production [5, 7]. Photoperiod-sensitive maize lines/hybrids with tropical germplasm are characterized in part by delayed flowering and/or failure of seed setting under long photoperiods (LP) [8].…”

Section: Introductionmentioning

confidence: 99%

A photoperiod-responsive protein compendium and conceptual proteome roadmap outline in maize grown in growth chambers with controlled conditions

Fan

Chen

et al. 2017

PLoS ONE

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Maize (Zea mays L.) is one of the major staple food crops of the world. However, high photoperiod sensitivity, especially for tropical germplasms, impedes attempts to improve maize agronomical traits by integration of tropical and temperate maize germplasms. Physiological and phenotypic responses of maize to photoperiod have widely been investigated based on multi-site field observations; however, proteome-based responsive mechanisms under controlled photoperiod regimes, nutrient and moisture soils are not yet well understood. In the present study, we sequenced and analyzed six proteomes of tropically-adapted and photoperiod-sensitive M9 inbred line at the vegetative 3 stage and proteomes from tropically-adapted and photoperiod-sensitive Shuang M9 (SM9) inbred line at the vegetative-tasseling stage. All plants were grown in growth chambers with controlled soil and temperature and three photoperiod regimes, a short photoperiod (SP) of 10 h light/14 h dark, a control neutral photoperiod (NP) of 12 h light/12 h dark, and a long photoperiod (LP) of 16 h light/8 h dark for a daily cycle. We identified 4,395 proteins of which 401 and 425 differentially-expressed proteins (DPs) were found in abundance in M9 leaves and in SM9 leaves as per SP/LP vs. NP, respectively. Some DPs showed responses to both SP and LP while some only responded to either SP or LP, depending on M9 or SM9. Our study showed that the photoperiodic response pathway, circadian clock rhythm, and high light density/intensity crosstalk with each other, but apparently differ from dark signaling routes. Photoperiod response involves light-responsive or dark-responsive proteins or both. The DPs positioned on the signaling routes from photoperiod changes to RNA/DNA responses involve the mago nashi homolog and glycine-rich RNA-binding proteins. Moreover, the cell-to-cell movement of ZCN14 through plasmodesmata is likely blocked under a 16-h-light LP. Here, we propose a photoperiodic model based on our findings and those from previous studies.

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Section: Introductionmentioning

confidence: 99%

A photoperiod-responsive protein compendium and conceptual proteome roadmap outline in maize grown in growth chambers with controlled conditions

Fan

Chen

et al. 2017

PLoS ONE

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“…Maize genes and noncoding regions involved in the timing of the vegetative-to-floral transition include Vegetative to generative transition1, Zea CENTRORAPIALIS8, and indeterminate1 (Salvi et al, 2007;Lazakis et al, 2011). Substantial natural phenotypic variation has been reported for these traits in maize (Chardon et al, 2004;Salvi et al, 2007;Buckler et al, 2009;Chen et al, 2012;Xu et al, 2012). However, to date, the genetic architecture of these important developmental transitions has not been explored in the context of a species pan-genome.…”

Section: Introductionmentioning

confidence: 99%

Insights into the Maize Pan-Genome and Pan-Transcriptome

et al. 2014

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Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.

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“…The expression of the maize ZmDof1 gene in rice promoted N assimilation under low-N conditions (Kurai et al 2011) and NUE is apparently improved because of the overexpression of the GS gene (a member of the GS1 gene family) in maize transgenic lines (Fu et al 2013;Martin et al 2006). Currently many data on low-N tolerance QTLs and large-scale gene expression at the genomic-wide level have already been released (Xu et al 2012b;Eveland et al 2010), along with the functionally identified low-N-related genes, which comes a great opportunity to further dissect this complex trait by integrating these information. In this study, we employed meta-analysis to obtain specific low-N-induced cQTLs in the first place, excluding the cQTL detected under both low-N and other environmental conditions in maize.…”

Section: Discussionmentioning

confidence: 97%

Mining for low-nitrogen tolerance genes by integrating meta-analysis and large-scale gene expression data from maize

et al. 2015

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Nitrogen (N) is the most important macronutrient for plant growth and development. Hence, understanding genetic architectures and functional genes involved in the response to N deficiency can greatly facilitate the development of low-Ntolerant cultivars. In this study, we collected 212 quantitative trait loci (QTL) of agronomically important traits under low-N stress conditions in maize. We then identified 21 consensus QTL (cQTL) strongly induced for low-N tolerance after excluding overlapping cQTL containing QTL simultaneously identified in meta-analyses of studies performed under other environmental conditions. Among the 21 cQTL, 30 candidate maize genes were identified from maize large-scale differential expression data derived from analyses of low-N stress, and the 12 most important maize orthologs were identified using homologous BLAST analyses of genes with known functions in N use efficiency in model plants. Furthermore, maize orthologs associated with low-N tolerance and metabolism were also predicted using large-scale expression data from other model plants. The present genetic loci and candidate genes indicate the molecular mechanisms of low-N tolerance in maize and may provide information for QTL fine mapping and molecular marker-assisted selection.

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The Genetic Architecture of Flowering Time and Photoperiod Sensitivity in Maize as Revealed by QTL Review and Meta Analysis

Cited by 51 publications

References 111 publications

A photoperiod-responsive protein compendium and conceptual proteome roadmap outline in maize grown in growth chambers with controlled conditions

A photoperiod-responsive protein compendium and conceptual proteome roadmap outline in maize grown in growth chambers with controlled conditions

Insights into the Maize Pan-Genome and Pan-Transcriptome

Mining for low-nitrogen tolerance genes by integrating meta-analysis and large-scale gene expression data from maize

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