CACTA-like transposable element in
            <i>ZmCCT</i>
            attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize

Yang, Qin; Li, Zhi; Li, Wenqiang; Ku, Lixia; Chao, Wang; Ye, Jianrong; Li, Kun; Yang, Ning; Li, Yipu; Zhong, Tao; Li, Jiansheng; Chen, Yanhui; Yan, Jianbing; Yang, Xiaohong; Xu, Ming

doi:10.1073/pnas.1310949110

Cited by 298 publications

(345 citation statements)

References 45 publications

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“…In maize, insertion of a CACTA-like TE within the ZmCCT promoter epigenetically regulates photoperiod sensitivity and may have helped accelerate the spread of maize to long-day regions (Yang et al, 2013). In maize, the early-flowering inbred lines have high DNA methylation levels of a 5,122-bp CACTA-like TE inserted in the upstream region of ZmCCT; this represses ZmCCT transcription, attenuating photoperiod sensitivity for adaptation to longer days, similar to its rice homolog Ghd7 (Xue et al, 2008;Yang et al, 2013). However, the maize ancestor teosinte, which only flowers in short-day conditions, lacks the CACTA-like TE insertion.…”

Section: Tes Affect Phenotypic Variation By Epigenetic Mechanisms Te-mentioning

confidence: 99%

“…However, the maize ancestor teosinte, which only flowers in short-day conditions, lacks the CACTA-like TE insertion. Thus, this TE insertion may have enabled maize to spread from tropical to temperate zones (Yang et al, 2013). Such TE-induced epigenetic changes largely depend on genetic alterations, which may have significance for plant environmental adaptation and evolution.…”

Section: Tes Affect Phenotypic Variation By Epigenetic Mechanisms Te-mentioning

confidence: 99%

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The effect of transposable elements on phenotypic variation: insights from plants to humans

Wei

Cao

2016

Sci. China Life Sci.

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Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection. transposable elements, gene expression, phenotypic variation Citation:Wei, L., and Cao, X. (2016). The effect of transposable elements on phenotypic variation: insights from plants to humans. Sci China Life Sci 59, 24 -37.

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Section: Tes Affect Phenotypic Variation By Epigenetic Mechanisms Te-mentioning

confidence: 99%

Section: Tes Affect Phenotypic Variation By Epigenetic Mechanisms Te-mentioning

confidence: 99%

The effect of transposable elements on phenotypic variation: insights from plants to humans

Wei

Cao

2016

Sci. China Life Sci.

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“…The best studied of these is Vgt1, a natural variant linked to the insertion of a miniature inverted-repeat transposable element (MITE) in an enhancer ~70 kb upstream of the gene ZmRap2.7 (Vlăduţu et al 1999, Salvi et al 2007. Another is ZmCCT, caused by a CACTA-like transposon insertion in the promoter region that affects both flowering time and photoperiod sensitivity, especially in tropical maize (Yang et al 2013).…”

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confidence: 99%

Genome‐wide Association for Plant Height and Flowering Time across 15 Tropical Maize Populations under Managed Drought Stress and Well‐Watered Conditions in Sub‐Saharan Africa

et al. 2016

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2365RESEARCH M odern genotyping technologies have made genetic data for plant breeding relatively inexpensive; however, the generation of multilocation phenotypic data remains expensive and laborious. There is an increasing interest in reducing phenotyping costs, either by increasing the efficiency of phenotyping or by extracting maximum information from the available phenotypic data. This paper focuses on the latter by combining modern genotyping with phenotypic data from separate datasets to map important traits under well-watered and drought stress conditions in maize.The materials for this analysis were generated by CIMMYT under the Water-Efficient Maize for Africa (WEMA) project. This project is a public-private partnership that focuses on breeding drought-tolerant and water-efficient maize for Sub-Saharan Africa project to perform genome-wide association analysis. Each population was phenotyped in multilocation trials under water-stressed and well-watered environments and genotyped via genotyping-by-sequencing. We focused on flowering time and plant height and identified clear associations between known genomic regions and the traits of interest. Out of ~380,000 single-nucleotide polymorphisms (SNPs), we found 115 and 108 that were robustly associated with flowering time under well-watered and drought stress conditions, respectively, and 143 and 120 SNPs, respectively, associated with plant height. These SNPs explained 36 to 80% of the genetic variance, with higher accuracy under wellwatered conditions. The same set of SNPs had phenotypic prediction accuracies equivalent to genome-wide SNPs and were significantly better than an equivalent number of random SNPs, indicating that they captured most of the genetic variation for these phenotypes. These methods could potentially aid breeding efforts for maize in Sub-Saharan Africa and elsewhere. The methods will also help in mapping drought tolerance and related traits in this germplasm. We expect that analyses combining data across multiple populations will become more common and we call for the development of algorithms and software to enable routine analyses of this nature.

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“…It is unclear how pure epigenetic variation could occur, but failure to faithfully maintain methylation patterns by methyltransferase has been proposed as one possible mechanism (Schmitz et al 2011). Alternatively, DNA methylation variation could be dependent on genetic polymorphisms such as structural rearrangements (Melquist et al 1999) or polymorphic transposon insertions (Martin et al 2009;Eichten et al 2012;Yang et al 2013) that occur near the affected region. DNA methylation variation could also be triggered by signals from trans-acting loci (Cao and Jacobsen 2002;Riddle and Richards 2002;Bender 2004).…”

mentioning

confidence: 99%

Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines

Eichten

Hermanson

et al. 2014

Genetics

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DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-inherited DMRs provide an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at these DMRs during the generations of the NIL population development. DNA methylation level was associated with local genotypes in nearly all of the .30,000 potential cases of inheritance. The majority of the DMRs were not associated with small RNAs. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits locally (cis) inherited patterns, is highly stable, and does not require active programming by small RNAs for maintenance. DNA methylation may contribute to heritable epigenetic information in many eukaryotic genomes. In this study, we have documented the inheritance patterns and trans-generational stability for nearly 1000 DNA methylation variants in a segregating maize population. At most loci studied, the DNA methylation differences are locally inherited and are not influenced by the other allele or other genomic regions. The inheritance of DNA methylation levels across generations is quite robust with almost no examples of unstable inheritance, suggesting that DNA methylation differences can be quite stably inherited, even in segregating populations. MANY organisms exhibit abundant phenotypic diversity within a species. This observed diversity is often attributed to genetic variation, but there is a large part of this diversity that cannot be explained by genetic polymorphisms alone (Manolio et al. 2009). It has been proposed that epigenetic variation could be one component of this missing heritability (Petronis 2010). DNA methylation is a well-studied contributor to epigenetic information in many eukaryotes. In plants, DNA methylation occurs in three sequence contexts, CG, CHG, and CHH (where H = A, T, or C). It is widely accepted that de novo establishment of DNA methylation is often guided by small RNA (RNA-directed DNA methylation, RdDM), while maintenance of DNA methylation is performed by different methyltransferases, namely MET1 (METHYL-TRANSFERASE 1) for CG methylation, CMT3 (CHROMOME-THYLASE 3), and DRM1/2 (DOMAINS REARRANGED METHYLTRANSFERASE 1 and 2) for non-CG methylation (CHG and CHH) (Chan et al. 2005). Variation in DNA methylation profiles has been observed in many species (Vaughn et al. 2007;Eichten et al. 2011bEichten et al. , 2013Re...

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CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize

Cited by 298 publications

References 45 publications

The effect of transposable elements on phenotypic variation: insights from plants to humans

The effect of transposable elements on phenotypic variation: insights from plants to humans

Genome‐wide Association for Plant Height and Flowering Time across 15 Tropical Maize Populations under Managed Drought Stress and Well‐Watered Conditions in Sub‐Saharan Africa

Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines

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