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John H Willis - One of the best experts on this subject based on the ideXlab platform.
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Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes
Frontiers in Plant Science, 2020Co-Authors: Miguel A. Flores-vergara, John H Willis, Elen Oneal, Mario Costa, Gonzalo H. Villarino, Caitlyn Roberts, Maria Angels De Luis Balaguer, Sílvia Coimbra, Robert G. FranksAbstract:The double fertilization of the female gametophyte initiates embryogenesis and endosperm development in seeds via the activation of genes involved in cell differentiation, organ patterning, and growth. A subset of genes expressed in endosperm exhibit imprinted expression, and the correct balance of gene expression between parental alleles is critical for proper endosperm and seed development. We use a transcriptional time series analysis to identify genes that are associated with key shifts in seed development, including genes associated with secondary cell wall synthesis, mitotic cell cycle, chromatin organization, auxin synthesis, fatty acid metabolism, and seed maturation. We relate these genes to morphological changes in Mimulus seeds. We also identify four endosperm-expressed transcripts that display imprinted (paternal) expression bias. The imprinted status of these four genes is conserved in other flowering plants, suggesting that they are functionally important in endosperm development. Our study explores gene regulatory dynamics in a species with ab initio cellular endosperm development, broadening the taxonomic focus of the literature on gene expression in seeds. Moreover, it is the first to validate genes with imprinted endosperm expression in Mimulus guttatus, and will inform future studies on the genetic causes of seed failure in this model system.
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differential adaptation to a harsh granite outcrop habitat between sympatric Mimulus species
Evolution, 2018Co-Authors: Kathleen G Ferris, John H WillisAbstract:Understanding which environmental variables and traits underlie adaptation to harsh environments is difficult because many traits evolve simultaneously as populations or species diverge. Here, we investigate the ecological variables and traits that underlie Mimulus laciniatus' adaptation to granite outcrops compared to its sympatric, mesic-adapted progenitor, Mimulus guttatus. We use fine-scale measurements of soil moisture and herbivory to examine differences in selective forces between the species' habitats, and measure selection on flowering time, flower size, plant height, and leaf shape in a reciprocal transplant using M. laciniatus × M. guttatus F4 hybrids. We find that differences in drought and herbivory drive survival differences between habitats, that M. laciniatus and M. guttatus are each better adapted to their native habitat, and differential habitat selection on flowering time, plant stature, and leaf shape. Although early flowering time, small stature, and lobed leaf shape underlie plant fitness in M. laciniatus' seasonally dry environment, increased plant size is advantageous in a competitive mesic environment replete with herbivores like M. guttatus'. Given that we observed divergent selection between habitats in the direction of species differences, we conclude that adaptation to different microhabitats is an important component of reproductive isolation in this sympatric species pair.
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plastic breeding system response to day length in the california wildflower Mimulus douglasii
American Journal of Botany, 2018Co-Authors: Laryssa L Barnett, Ashley Troth, John H WillisAbstract:PREMISE OF THE STUDY: Angiosperms have evolved multiple breeding systems that allow reproductive success under varied conditions. Striking among these are cleistogamous breeding systems, where individuals can produce alternative flower types specialized for distinct mating strategies. Cleistogamy is thought to be environmentally-dependent, but little is known about environmental triggers. If production of alternate flowers is environmentally induced, populations may evolve locally adapted responses. Mimulus douglasii, exhibits a cleistogamous breeding system, and ranges across temperature and day-length gradients, providing an ideal system to investigate environmental parameters that control cleistogamy. METHODS: We compared flowering responses across Mimulus douglasii population accessions that produce distinct outcrossing and self-pollinating flower morphs. Under controlled conditions, we determined time to flower, and number and type of flowers produced under different temperatures and day lengths. KEY RESULTS: Temperature and day length both affect onset of flowering. Long days shift flower type from predominantly chasmogamous to cleistogamous. The strength of the response to day length varies across accessions whether temperature varies or is held constant. CONCLUSIONS: Cleistogamy is an environmentally sensitive polyphenism in Mimulus douglasii, allowing transition from one mating strategy to another. Longer days induce flowering and production of cleistogamous flowers. Shorter days induce chasmogamous flowers. Population origin has a small effect on response to environmental cues.
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population structure and local selection yield high genomic variation in Mimulus guttatus
Molecular Ecology, 2017Co-Authors: John H Willis, Joshua R Puzey, John KellyAbstract:Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.
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disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and Mimulus nudatus
New Phytologist, 2016Co-Authors: Elen Oneal, John H Willis, Robert G. FranksAbstract:Divergence of developmental mechanisms within populations could lead to hybrid developmental failure, and might be a factor driving speciation in angiosperms. We investigate patterns of endosperm and embryo development in Mimulus guttatus and the closely related, serpentine endemic Mimulus nudatus, and compare them to those of reciprocal hybrid seed. We address whether disruption in hybrid seed development is the primary source of reproductive isolation between these sympatric taxa. M. guttatus and M. nudatus differ in the pattern and timing of endosperm and embryo development. Some hybrid seeds exhibit early disruption of endosperm development and are completely inviable, while others develop relatively normally at first, but later exhibit impaired endosperm proliferation and low germination success. These developmental patterns are reflected in mature hybrid seeds, which are either small and flat (indicating little to no endosperm) or shriveled (indicating reduced endosperm volume). Hybrid seed inviability forms a potent reproductive barrier between M. guttatus and M. nudatus. We shed light on the extent of developmental variation between closely related species within the M. guttatus species complex, an important ecological model system, and provide a partial mechanism for the hybrid barrier between M. guttatus and M. nudatus.
Lila Fishman - One of the best experts on this subject based on the ideXlab platform.
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GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity
2019Co-Authors: Lex E. Flagel, Andrea L. Sweigart, Lila Fishman, Benjamin K. Blackman, Patrick J. Monnahan, John K. KellyAbstract:Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.
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Data from: Extreme copy number variation at a tRNA ligase gene affecting phenological and fitness traits in yellow monkeyflower
2018Co-Authors: Thom Nelson, John Kelly, Patrick Monnahan, Kayli Anderson, Mariah Mcintosh, Evan Macarthur-waltz, Findley R. Finseth, Lila FishmanAbstract:This xlsx file includes (after a brief readme sheet) 7 spreadsheets, each with genotype-phenotype-fitness or qpcr datasets presented in this paper. All plants in these datasets were derived from a single population of Mimulus guttatus (yellow monkeyflower) from Iron Mountain Oregon. Datasets are in the order they were presented in the paper
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genetic loci with parent of origin effects cause hybrid seed lethality in crosses between Mimulus species
New Phytologist, 2016Co-Authors: Austin G Garner, Amanda M. Kenney, Lila Fishman, Andrea L. SweigartAbstract:In flowering plants, F1 hybrid seed lethality is a common outcome of crosses between closely related diploid species, but the genetic basis of this early-acting and potentially widespread form of postzygotic reproductive isolation is largely unknown. We intercrossed two closely related species of monkeyflower, Mimulus guttatus and Mimulus tilingii, to characterize the mechanisms and strength of postzygotic reproductive isolation. Then, using a reciprocal backcross design, we performed high-resolution genetic mapping to determine the genetic architecture of hybrid seed lethality and directly test for loci with parent-of-origin effects. We found that F1 hybrid seed lethality is an exceptionally strong isolating barrier between Mimulus species, with reciprocal crosses producing < 1% viable seeds. This form of postzygotic reproductive isolation appears to be highly polygenic, indicating that multiple incompatibility loci have accumulated rapidly between these closely related Mimulus species. It is also primarily caused by genetic loci with parent-of-origin effects, suggesting a possible role for imprinted genes in the evolution of Mimulus hybrid seed lethality. Our findings suggest that divergence in loci with parent-of-origin effects, which is probably driven by genomic coevolution within lineages, might be an important source of hybrid incompatibilities between flowering plant species.
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chromosomal rearrangements and the genetics of reproductive barriers in Mimulus monkey flowers
Evolution, 2013Co-Authors: Lila Fishman, Paul M Beardsley, Angela Stathos, Charles F Williams, Jeffrey P HillAbstract:Chromosomal rearrangements may directly cause hybrid sterility and can facilitate speciation by preserving local adaptation in the face of gene flow. We used comparative linkage mapping with shared gene-based markers to identify potential chromosomal rearrangements between the sister monkeyflowers Mimulus lewisii and Mimulus cardinalis, which are textbook examples of ecological speciation. We then remapped quantitative trait loci (QTLs) for floral traits and flowering time (premating isolation) and hybrid sterility (postzygotic isolation). We identified three major regions of recombination suppression in the M. lewisii × M. cardinalis hybrid map compared to a relatively collinear Mimulus parishii × M. lewisii map, consistent with a reciprocal translocation and two inversions specific to M. cardinalis. These inferences were supported by targeted intraspecific mapping, which also implied a M. lewisii-specific reciprocal translocation causing chromosomal pseudo-linkage in both hybrid mapping populations. Floral QTLs mapped in this study, along with previously mapped adaptive QTLs, were clustered in putatively rearranged regions. All QTLs for male sterility, including two underdominant loci, mapped to regions of recombination suppression. We argue that chromosomal rearrangements may have played an important role in generating and consolidating barriers to gene flow as natural selection drove the dramatic ecological and morphological divergence of these species.
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the nuclear component of a cytonuclear hybrid incompatibility in Mimulus maps to a cluster of pentatricopeptide repeat genes
Genetics, 2010Co-Authors: Camille M Barr, Lila FishmanAbstract:Characterizing the genetic and molecular basis of hybrid incompatibilities is a first step toward understanding their evolutionary origins. We fine mapped the nuclear restorer (Rf) of cytoplasm-dependent anther sterility in Mimulus hybrids by identifying and targeting regions of the Mimulus guttatus genome containing large numbers of candidate pentatricopeptide repeat genes (PPRs). The single Mendelian locus Rf was first isolated to a 1.3-cM region on linkage group 7 that spans the genome's largest cluster of PPRs, then split into two tightly linked loci (Rf1 and Rf2) by <10 recombination events in a large (N = 6153) fine-mapping population. Progeny testing of fertile recombinants demonstrated that a dominant M. guttatus allele at each Rf locus was sufficient to restore fertility. Each Rf locus spans a physical region containing numerous PPRs with high homology to each other, suggesting recent tandem duplication or transposition. Furthermore, these PPRs have higher homology to restorers in distantly related taxa (petunia and rice) than to PPRs elsewhere in the Mimulus genome. These results suggest that the cytoplasmic male sterility (CMS)–PPR interaction is highly conserved across flowering plants. In addition, given our theoretical understanding of cytonuclear coevolution, the finding that hybrid CMS results from interactions between a chimeric mitochondrial transcript that is modified by Rf loci identified as PPRs is consistent with a history of selfish mitochondrial evolution and compensatory nuclear coevolution within M. guttatus.
H D Bradshaw - One of the best experts on this subject based on the ideXlab platform.
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rational design of a novel hawkmoth pollinator interaction in Mimulus section erythranthe
Frontiers in Ecology and Evolution, 2021Co-Authors: Kelsey J R P Byers, H D BradshawAbstract:Diversification of the ca. 275,000 extant flowering plant species has been driven in large part by coevolution with animal pollinators. A recurring pattern of pollinator shifts from hummingbird to hawkmoth pollination has characterized plant speciation in many western North American plant taxa, but in the genus Mimulus (monkeyflowers) section Erythranthe the evolution of hawkmoth pollination from hummingbird-pollinated ancestors has not occurred. We manipulated two flower color loci and tested the attractiveness of the resulting four color phenotypes (red, yellow, pink, and white) to naive hawkmoths (Manduca sexta). Hawkmoths strongly prefer derived colors (yellow, pink, white) over the ancestral red when choosing an initial flower to visit, and generally preferred derived colors when total visits and total visit time were considered, with no hawkmoth preferring ancestral red over derived colors. The simple flower color genetics underlying this innate pollinator preference suggests a potential path for speciation into an unfilled hawkmoth-pollinated niche in Mimulus section Erythranthe, and the deliberate design of a hawkmoth-pollinated flower demonstrates a new, predictive method for studying pollination syndrome evolution.
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less is more independent loss of function ocimene synthase alleles parallel pollination syndrome diversification in monkeyflowers Mimulus
American Journal of Botany, 2017Co-Authors: Foen Peng, Kelsey J R P Byers, H D BradshawAbstract:PREMISE OF THE STUDY: Pollinator-mediated selection on flower phenotypes (e.g., shape, color, scent) is key to understanding the adaptive radiation of angiosperms, many of which have evolved specialized relationships with a particular guild of animal pollinators (e.g., birds, bats, moths, bees). E-β-Ocimene, a monoterpene produced by OCIMENE SYNTHASE (OS) in Mimulus lewisii, is a floral scent important in attracting the species' bumblebee pollinators. The taxa closely related to M. lewisii have evolved several different pollination syndromes, including hummingbird pollination and self pollination (autogamy). We are interested in how floral scent variation contributed to species diversification in this clade. METHODS: We analyzed variation in E-β-ocimene emission within this Mimulus clade and explored its molecular basis through a combination of DNA sequencing, reverse transcriptase PCR, and enzyme functional analysis in vitro. KEY RESULTS: We found that none of the taxa, other than M. lewisii, emitted E-β-ocimene from flowers. But the molecular basis underlying loss of E-β-ocimene emission is unique in each taxon, including deletion, missense, or frameshift mutations in the OS gene, and potential posttranscriptional downregulation. CONCLUSIONS: The molecular evidence suggests that parallel loss-of-function in OS is the best explanation for the observed pattern of E-β-ocimene emission, likely as the result of natural selection.
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floral volatile alleles can contribute to pollinator mediated reproductive isolation in monkeyflowers Mimulus
Plant Journal, 2014Co-Authors: Kelsey J R P Byers, Foen Peng, James P Vela, Jeffrey A Riffell, H D BradshawAbstract:SUMMARY Pollinator-mediated reproductive isolation is a major factor in driving the diversification of flowering plants. Studies of floral traits involved in reproductive isolation have focused nearly exclusively on visual signals, such as flower color. The role of less obvious signals, such as floral scent, has been studied only recently. In particular, the genetics of floral volatiles involved in mediating differential pollinator visitation remains unknown. The bumblebee-pollinated Mimulus lewisii and hummingbird-pollinated Mimulus cardinalis are a model system for studying reproductive isolation via pollinator preference. We have shown that these two species differ in three floral terpenoid volatiles - D-limonene, b-myrcene, and E-b-ocimene - that are attrac- tive to bumblebee pollinators. By genetic mapping and in vitro analysis of enzyme activity we demonstrate that these interspecific differences are consistent with allelic variation at two loci, LIMONENE-MYRCENE SYNTHASE (LMS) and OCIMENE SYNTHASE (OS). Mimulus lewisii LMS (MlLMS) and OS (MlOS) are expressed most strongly in floral tissue in the last stages of floral development. Mimulus cardinalis LMS (McLMS) is weakly expressed and has a nonsense mutation in exon 3. Mimulus cardinalis OS (McOS )i s expressed similarly to MlOS, but the encoded McOS enzyme produces no E-b-ocimene. Recapitulating the M. cardinalis phenotype by reducing the expression of MlLMS by RNA interference in transgenic M. lewisii produces no behavioral difference in pollinating bumblebees; however, reducing MlOS expression produces a 6% decrease in visitation. Allelic variation at the OCIMENE SYNTHASE locus is likely to contribute to dif- ferential pollinator visitation, and thus promote reproductive isolation between M. lewisii and M. cardinalis. OCIMENE SYNTHASE joins a growing list of 'speciation genes' ('barrier genes') in flowering plants.
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transcriptional control of floral anthocyanin pigmentation in monkeyflowers Mimulus
New Phytologist, 2014Co-Authors: Yao-wu Yuan, James P Vela, Janelle M. Sagawa, Laura A Frost, H D BradshawAbstract:Summary � A molecular description of the control of floral pigmentation in a multi-species group displaying various flower color patterns is of great interest for understanding the molecular bases of phenotypic diversification and pollinator-mediated speciation. � Through transcriptome profiling, mutant analyses and transgenic experiments, we aim to establish a ‘baseline’ floral anthocyanin regulation model in Mimulus lewisii and to examine the different ways of tinkering with this model in generating the diversity of floral anthocyanin patterns in other Mimulus species. � We find one WD40 and one bHLH gene controlling anthocyanin pigmentation in the entire corolla of M. lewisii and two R2R3-MYB genes, PELAN and NEGAN, controlling anthocyanin production in the petal lobe and nectar guide, respectively. The autoregulation of NEGAN might be a critical property to generate anthocyanin spots. Independent losses of PELAN expression (via different mechanisms) explain two natural yellow-flowered populations of M. cardinalis (typically red-flowered). The NEGAN ortholog is the only anthocyanin-activating MYB expressed in the M. guttatus flowers. � The mutant lines and transgenic tools available for M. lewisii will enable gene-by-gene replacement experiments to dissect the genetic and developmental bases of more complex floral color patterns, and to test hypotheses on phenotypic evolution in general.
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genetic dissection of a major anthocyanin qtl contributing to pollinator mediated reproductive isolation between sister species of Mimulus
Genetics, 2013Co-Authors: Yao-wu Yuan, Janelle M. Sagawa, Riane C Young, Brian J Christensen, H D BradshawAbstract:Prezygotic barriers play a major role in the evolution of reproductive isolation, which is a prerequisite for speciation. However, despite considerable progress in identifying genes and mutations responsible for postzygotic isolation, little is known about the genetic and molecular basis underlying prezygotic barriers. The bumblebee-pollinated Mimulus lewisii and the hummingbird-pollinated M. cardinalis represent a classic example of pollinator-mediated prezygotic isolation between two sister species in sympatry. Flower color differences resulting from both carotenoid and anthocyanin pigments contribute to pollinator discrimination between the two species in nature. Through fine-scale genetic mapping, site-directed mutagenesis, and transgenic experiments, we demonstrate that a single-repeat R3 MYB repressor, ROSE INTENSITY1 (ROI1), is the causal gene underlying a major quantitative trait locus (QTL) with the largest effect on anthocyanin concentration and that cis-regulatory change rather than coding DNA mutations cause the allelic difference between M. lewisii and M. cardinalis. Together with the genomic resources and stable transgenic tools developed here, these results suggest that Mimulus is an excellent platform for studying the genetics of pollinator-mediated reproductive isolation and the molecular basis of morphological evolution at the most fundamental level—gene by gene, mutation by mutation.
David B. Lowry - One of the best experts on this subject based on the ideXlab platform.
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genomic studies on the nature of species adaptation and speciation in Mimulus
Molecular Ecology, 2015Co-Authors: Alex D Twyford, David B. Lowry, Matthew A Streisfeld, Jannice FriedmanAbstract:Evolutionary biology is in an exciting era, in which powerful genomic tools make the answers accessible to long-standing questions about variation, adaptation and speciation. The availability of a suite of genomic resources, a shared knowledge base and a long history of study have made the phenotypically diverse plant genus Mimulus an important system for understanding ecological and evolutionary processes. An international Mimulus Research Meeting was held at Duke University in June 2014 to discuss developments in ecological and evolutionary genetic studies in Mimulus. Here, we report major recent discoveries presented at the meeting that use genomic approaches to advance our understanding of three major themes: the parallel genetic basis of adaptation; the ecological genomics of speciation; and the evolutionary significance of structural genetic variation. We also suggest future research directions for studies of Mimulus and highlight challenges faced when developing new ecological and evolutionary model systems.
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Five anthocyanin polymorphisms are associated with an R2R3-MYB cluster in Mimulus guttatus (Phrymaceae)
American journal of botany, 2011Co-Authors: David B. Lowry, Calvin C. Sheng, Jesse R. Lasky, John H WillisAbstract: Premise of study: Botanists have long been interested in the reasons for genetic variation among individuals, populations, and species of plants. The anthocyanin pathway is ideal for studying the evolution of such phenotypic variation. Methods: We used a combination of quantitative trait loci mapping and association studies to understand the genetic basis of variation in fi anthocyanin phenotypes including calyx, corolla, and leaf coloration patterns that vary within and among populations of Mimulus guttatus. We then examined what genes might be responsible for this phenotypic variation and whether one of the traits, calyx spotting, is randomly distributed across the geographic range of the species. Key results: All fi ve phenotypes in M. guttatus were primarily controlled by the same major locus ( PLA1 ), which contains a tandem array of three R2R3-MYB genes known to be involved in the evolution of flcolor in a related species of Mimulus . Calyx spotting was nonrandomly distributed across the range of M. guttatus and correlated with multiple climate variables. Conclusions: The results of this study suggest that variation in R2R3-MYB genes is the primary cause of potentially important anthocyanin phenotypic variation within and among populations of M. guttatus , a fi nding consistent with recent theoretical and empirical research on flcolor evolution.
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Natural variation for drought-response traits in the Mimulus guttatus species complex.
Oecologia, 2009Co-Authors: David B. Lowry, Laura I. Nutter, John H WillisAbstract:Soil moisture is a key factor affecting plant abundance and distribution, both across and within species. In response to water limitation, plants have evolved numerous morphological, physiological, and phenological adaptations. In both well-watered and water-limited conditions, we identified considerable natural variation in drought-related whole-plant and leaf-level traits among closely related members of the Mimulus guttatus species complex that occupy a diversity of habitats in the field. The self-fertilizing Mimulus nasutus and serpentine-endemic Mimulus nudatus demonstrated the overall greatest tolerance to soil water limitation, exhibiting the smallest reduction in seed set relative to well-watered conditions. This may be due in part to early flowering, faster fruit development, and low stomatal density. In contrast, flowering of coastal M. guttatus was so delayed that it precluded any seed production in water-limited conditions. This range of phenotypic responses to soil water deficit in Mimulus, coupled with developing genomic resources, holds considerable promise for identifying genomic variation responsible for adaptive responses to soil water availability.
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Mimulus is an emerging model system for the integration of ecological and genomic studies
Heredity, 2008Co-Authors: David B. Lowry, Arielle M Cooley, Kevin M Wright, Young Lee, John H WillisAbstract:The plant genus Mimulus is rapidly emerging as a model system for studies of evolutionary and ecological functional genomics. Mimulus contains a wide array of phenotypic, ecological and genomic diversity. Numerous studies have proven the experimental tractability of Mimulus in laboratory and field studies. Genomic resources currently under development are making Mimulus an excellent system for determining the genetic and genomic basis of adaptation and speciation. Here, we introduce some of the phenotypic and genetic diversity in the genus Mimulus and highlight how direct genetic studies with Mimulus can address a wide spectrum of ecological and evolutionary questions. In addition, we present the genomic resources currently available for Mimulus and discuss future directions for research. The integration of ecology and genetics with bioinformatics and genome technology offers great promise for exploring the mechanistic basis of adaptive evolution and the genetics of speciation.
Yao-wu Yuan - One of the best experts on this subject based on the ideXlab platform.
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a tetratricopeptide repeat protein regulates carotenoid biosynthesis and chromoplast development in monkeyflowers Mimulus
The Plant Cell, 2020Co-Authors: Lauren E Stanley, Baoqing Ding, Connor Hill, Shilin Chen, Yao-wu YuanAbstract:Little is known about the factors regulating carotenoid biosynthesis in flowers. Here, we characterized the REDUCED CAROTENOID PIGMENTATION2 (RCP2) locus from two monkeyflower (Mimulus) species, the bumblebee-pollinated species Mimulus lewisii and the hummingbird-pollinated species Mimulus verbenaceus. We show that loss-of-function mutations of RCP2 cause drastic down-regulation of the entire carotenoid biosynthetic pathway. The causal gene underlying RCP2 encodes a tetratricopeptide repeat protein that is closely related to the Arabidopsis (Arabidopsis thaliana) REDUCED CHLOROPLAST COVERAGE proteins. RCP2 appears to regulate carotenoid biosynthesis independently of RCP1, a previously identified R2R3-MYB master regulator of carotenoid biosynthesis. We show that RCP2 is necessary and sufficient for chromoplast development and carotenoid accumulation in floral tissues. Simultaneous down-regulation of RCP2 and two closely related paralogs, RCP2-L1 and RCP2-L2, yielded plants with pale leaves deficient in chlorophyll and carotenoids and with reduced chloroplast compartment size. Finally, we demonstrate that M. verbenaceus is just as amenable to chemical mutagenesis and in planta transformation as the more extensively studied M. lewisii, making these two species an excellent platform for comparative developmental genetics studies of closely related species with dramatic phenotypic divergence.
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transcriptional control of floral anthocyanin pigmentation in monkeyflowers Mimulus
New Phytologist, 2014Co-Authors: Yao-wu Yuan, James P Vela, Janelle M. Sagawa, Laura A Frost, H D BradshawAbstract:Summary � A molecular description of the control of floral pigmentation in a multi-species group displaying various flower color patterns is of great interest for understanding the molecular bases of phenotypic diversification and pollinator-mediated speciation. � Through transcriptome profiling, mutant analyses and transgenic experiments, we aim to establish a ‘baseline’ floral anthocyanin regulation model in Mimulus lewisii and to examine the different ways of tinkering with this model in generating the diversity of floral anthocyanin patterns in other Mimulus species. � We find one WD40 and one bHLH gene controlling anthocyanin pigmentation in the entire corolla of M. lewisii and two R2R3-MYB genes, PELAN and NEGAN, controlling anthocyanin production in the petal lobe and nectar guide, respectively. The autoregulation of NEGAN might be a critical property to generate anthocyanin spots. Independent losses of PELAN expression (via different mechanisms) explain two natural yellow-flowered populations of M. cardinalis (typically red-flowered). The NEGAN ortholog is the only anthocyanin-activating MYB expressed in the M. guttatus flowers. � The mutant lines and transgenic tools available for M. lewisii will enable gene-by-gene replacement experiments to dissect the genetic and developmental bases of more complex floral color patterns, and to test hypotheses on phenotypic evolution in general.
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fine scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing
Proceedings of the National Academy of Sciences of the United States of America, 2013Co-Authors: Uffe Hellsten, John H Willis, Yao-wu Yuan, Kevin M Wright, Jerry Jenkins, Shengqiang Shu, Susan R Wessler, Jeremy Schmutz, Daniel S RokhsarAbstract:Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9–knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.
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genetic dissection of a major anthocyanin qtl contributing to pollinator mediated reproductive isolation between sister species of Mimulus
Genetics, 2013Co-Authors: Yao-wu Yuan, Janelle M. Sagawa, Riane C Young, Brian J Christensen, H D BradshawAbstract:Prezygotic barriers play a major role in the evolution of reproductive isolation, which is a prerequisite for speciation. However, despite considerable progress in identifying genes and mutations responsible for postzygotic isolation, little is known about the genetic and molecular basis underlying prezygotic barriers. The bumblebee-pollinated Mimulus lewisii and the hummingbird-pollinated M. cardinalis represent a classic example of pollinator-mediated prezygotic isolation between two sister species in sympatry. Flower color differences resulting from both carotenoid and anthocyanin pigments contribute to pollinator discrimination between the two species in nature. Through fine-scale genetic mapping, site-directed mutagenesis, and transgenic experiments, we demonstrate that a single-repeat R3 MYB repressor, ROSE INTENSITY1 (ROI1), is the causal gene underlying a major quantitative trait locus (QTL) with the largest effect on anthocyanin concentration and that cis-regulatory change rather than coding DNA mutations cause the allelic difference between M. lewisii and M. cardinalis. Together with the genomic resources and stable transgenic tools developed here, these results suggest that Mimulus is an excellent platform for studying the genetics of pollinator-mediated reproductive isolation and the molecular basis of morphological evolution at the most fundamental level—gene by gene, mutation by mutation.
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Bulk Segregant Analysis of an Induced Floral Mutant Identifies a MIXTA-like R2R3 MYB Controlling Nectar Guide Formation in Mimulus lewisii
Genetics, 2013Co-Authors: Yao-wu Yuan, Janelle M. Sagawa, Verónica S. Di Stilio, Harvey D. BradshawAbstract:The genetic and developmental basis of many ecologically important floral traits (e.g., carotenoid pigmentation, corolla tube structure, nectar volume, pistil and stamen length) remains poorly understood. Here we analyze a chemically induced floral mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments and identify a MIXTA-like R2R3 MYB gene that controls nectar guide formation in M. lewisii flowers, which involves epidermal cell development and carotenoid pigmentation.
