A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

Hou, Jilun; Long, Yan; Raman, Harsh; Zou, Xuefeng; Wang, Jing; Dai, Shutao; Xiao, Qinqin; Liu, Cong; Fan, Longjiang; Liu, Bin; Meng, Jianghong

doi:10.1186/1471-2229-12-238

Cited by 94 publications

(105 citation statements)

References 54 publications

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“…It is perhaps unsurprising, then, that Table 2 reveals a wide diversity in the nature of the mutations that underlie domestication-related phenotypes. These include cis -regulatory mutations that increase gene expression (e.g., rapeseed BnFLC.A10 , controlling vernalization; Hou et al, 2012), and mutations in coding regions that result in modified proteins that remain functional but have altered activity (e.g., sunflower HaFT1 , controlling flowering time; Blackman et al, 2010). The largest proportion of these domestication-related genetic changes, however, are those that result in a loss of gene function.…”

Section: Genetic Basis Of Domestication Phenotypesmentioning

confidence: 99%

“…In this case, exposure of ripening fruits to cold induces retrotransposon-mediated transcriptional activation of Ruby , a Myb regulatory gene in the anthocyanin synthesis pathway (Butelli et al, 2012). Other domestication-related traits that have evolved through TE activity include determinate growth in common bean ( PvTFL1y ; Repinski et al, 2012); vernalization requirement in rapeseed ( BnFLC.A10 ; Hou et al, 2012) and wheat ( Vrn1 ; Golovnina et al, 2010); and photoperiod sensitivity in rice ( Ehd1 ; Saito et al, 2009). …”

Section: Genetic Basis Of Domestication Phenotypesmentioning

confidence: 99%

“…This growth habit is adaptive in climates with mild winters and hot, dry summers that are inhospitable for growth. Selection for the acquisition of a vernalization requirement has occurred in winter wheat varieties (Yan et al, 2003) and some varieties of rapeseed (Hou et al, 2012). In contrast, selection for a loss of vernalization requirement has occurred in spring barley (e.g., Turner et al, 2005; Comadran et al, 2012) and spring wheat (Yan et al, 2004), where the spring growth habit allows planting and harvesting in northern latitudes with short growing seasons.…”

Section: Parallel Evolution In Domesticated Cropsmentioning

confidence: 99%

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Crop plants as models for understanding plant adaptation and diversification

Olsen¹,

Wendel²

2013

Front. Plant Sci.

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Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of “domestication syndrome” traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various “omics” involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution.

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Section: Genetic Basis Of Domestication Phenotypesmentioning

confidence: 99%

Section: Genetic Basis Of Domestication Phenotypesmentioning

confidence: 99%

Section: Parallel Evolution In Domesticated Cropsmentioning

confidence: 99%

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Crop plants as models for understanding plant adaptation and diversification

Olsen¹,

Wendel²

2013

Front. Plant Sci.

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“…In B. napus , a Tourist -like MITE, Monkey King , was identified in the promoter region of BnFLC.A10 , a homologue of Arabidopsis FLOWERING LOCUS C ( FLC ) [31]. In this study, we found that Monkey King elements are not restricted to Brassica species, but are specific to the Brassicaceae family.…”

Section: Introductionmentioning

confidence: 78%

Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae

et al. 2015

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BackgroundMiniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae.ResultsThe characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened.ConclusionMonkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0490-9) contains supplementary material, which is available to authorized users.

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“…Association and QTL mapping studies have also associated variation in flowering time or vernalization response with polymorphisms in the FLC homologs of Brassica oleracea, Brassica rapa, and Brassica napus (Zhao et al, 2010;Hou et al, 2012;Wu et al, 2012;Irwin et al, 2016). For instance, one of two major FLC haplotypes in B. oleracea is transcriptionally repressed by cold exposure more slowly than the other (Irwin et al, 2016).…”

Section: Diversity In How Long Winter Needs To Be Experiencedmentioning

confidence: 99%

Changing Responses to Changing Seasons: Natural Variation in the Plasticity of Flowering Time

Blackman

2016

Plant Physiol.

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For plants that live in seasonally changing environments, timing is everything. Matching developmental transitions with the best times of year for growth and reproduction is necessary to maintain high fitness. Consequently, plants employ many mechanisms to sense and integrate multiple predictive seasonal cues to regulate their major developmental shifts. As the annual timing with which the growing season starts and ends changes across the landscape, natural selection has led to the evolution of the mechanisms that regulate the developmental plasticity of flowering among populations or varieties of species and crop plants that inhabit broad geographic ranges. There has been significant recent progress in describing the diversity of this variation in flowering time plasticity and in identifying the specific genetic changes responsible. Such work is an essential step toward understanding the processes that have shaped current and past adaptation, managing genetic diversity and improving crops in the face of climate change, and forecasting how populations may respond plastically and evolutionarily to future environmental challenges. In this Update, I review the findings of recent studies of natural variation in the plasticity of flowering to photoperiod, vernalization, and ambient temperature, and the implications and open questions raised by this work are considered.A fundamental adaptation of plants inhabiting seasonal environments is their ability to match the annual timing of major life history transitions to the local growing season. Most species achieve this synchrony through developmental plasticity. In other words, individuals sense how environmental cues like daylength and temperature change from winter to spring to summer to fall. The information gleaned from these cycles is then integrated molecularly so that germination, flowering, and other key transitions occur during periods favorable for growth, reproduction, and seed set. However, as the climate changes over the 21st century and the relative timing of annual cycles in temperature and precipitation shifts, once adaptive responses will no longer effectively predict the best calendar dates to initiate these essential developmental events (Nicotra et al., 2010;Wilczek et al., 2010). Because natural populations and cultivated landraces of many taxa have evolved to thrive in geographically diverse habitats and climates as their ranges have expanded, they harbor natural variants that may prove instructive in breeding crops and conserving native plant diversity in the face of future environmental challenges. Thus, a critical objective in plant biology is

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A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

Cited by 94 publications

References 54 publications

Crop plants as models for understanding plant adaptation and diversification

Crop plants as models for understanding plant adaptation and diversification

Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae

Changing Responses to Changing Seasons: Natural Variation in the Plasticity of Flowering Time

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