Miki Okada

University of California, Davis, Davis, California, United States

Are you Miki Okada?

Claim your profile

Publications (11)29.84 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as hybrids. Amplified fragment length polymorphism (AFLP) marker analysis was performed on 378 specimens collected from northern California and Nevada. Population structure was inferred using a Bayesian/Markov chain Monte Carlo method, which probabilistically assigns individuals to genetic clusters. Three genetic clusters provided the best fit for the data. C. eurytheme individuals were primarily assigned to two closely related clusters, and C. eriphyle individuals were mostly assigned to a third, more distantly related cluster. There appeared to be significant hybridization between the two species. Individuals of intermediate phenotype (putative hybrids) were found to be genetically indistinguishable from C. eriphyle, indicating that previous work based on the assumption that these intermediate forms are hybrids may warrant reconsideration.
    Ecology and Evolution 06/2015; 5(14):n/a-n/a. DOI:10.1002/ece3.1574 · 2.32 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Conyza canadensis (horseweed), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n=2X=18) with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic basis of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000 and PacBio RS) using various libraries with different insertion sizes (~350 bp, ~600 bp, ~3 kb and ~10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (~350× coverage) of data, the genome was assembled into 13,966 scaffolds with N50 =33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (~153 kb) and a nearly-complete mitochondrial genome (~450 kb in 120 scaffolds). The nuclear genome is comprised of 44,592 protein-coding genes. Genome re-sequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness, the evolution of herbicide resistance, and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this paper represents the first published draft genome of an agricultural weed.
    Plant physiology 09/2014; 166(3):1241-1254. DOI:10.1104/pp.114.247668 · 6.84 Impact Factor
  • Miki Okada · Marie Jasieniuk
    [Show abstract] [Hide abstract]
    ABSTRACT: Inheritance of glyphosate resistance was investigated in hairy fleabane populations from California as part of providing the information needed to predict and manage resistance and to gain insight into resistance mechanism (or mechanisms) present in the populations. Three glyphosate-resistant individuals grown from seed collected from distinct sites near Fresno, CA, were crossed to individuals from the same susceptible population to create reciprocal F-1 populations. A single individual from each of the F-1 populations was used to create a backcross population with a susceptible maternal parent, and an F-2 population. Based on dose response analyses, reciprocal F-1 populations were not statistically different from each other, more similar to the resistant parent, and statistically different from the susceptible parent, consistent with nuclear control of the trait and dominance to incomplete dominance of resistance over susceptibility in all three crosses. Glyphosate resistance in two of the three crosses segregated in the backcross and the F-2 populations as a single-locus trait. In the remaining cross, the resistant parent had approximately half the resistance level as the other two resistant parents, and the segregation of glyphosate resistance in backcross and F-2 populations conformed to a two-locus model with resistance alleles acting additively and at least two copies of the allele required for expression of resistance. This two-locus model of the segregation of glyphosate resistance has not been reported previously. Variation in the pattern of inheritance and the level of resistance indicate that multiple resistance mechanisms may be present in hairy fleabane populations in California.
    Weed Science 04/2014; 62(2):258-266. DOI:10.1614/WS-D-13-00111.1 · 1.87 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent increases in glyphosate use in perennial crops of California, USA, are hypothesized to have led to an increase in selection and evolution of resistance to the herbicide in Conyza canadensis populations. To gain insight into the evolutionary origins and spread of resistance and to inform glyphosate resistance management strategies, we investigated the geographical distribution of glyphosate resistance in C. canadensis across and surrounding the Central Valley, its spatial relationship to groundwater protection areas (GWPA), and the genetic diversity and population structure and history using microsatellite markers. Frequencies of resistant individuals in 42 sampled populations were positively correlated with the size of GWPA within counties. Analyses of population genetic structure also supported spread of resistance in these areas. Bayesian clustering and approximate Bayesian computation (ABC) analyses revealed multiple independent origins of resistance within the Central Valley. Based on parameter estimation in the ABC analyses, resistant genotypes underwent expansion after glyphosate use began in agriculture, but many years before it was detected. Thus, diversity in weed control practices prior to herbicide regulation in GWPA probably kept resistance frequencies low. Regionally coordinated efforts to reduce seed dispersal and selection pressure are needed to manage glyphosate resistance in C. canadensis.
    Evolutionary Applications 03/2013; 6(5). DOI:10.1111/eva.12061 · 3.90 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Resistance to the thiocarbamates has been selected in early watergrass populations within the rice-growing region of California. To elucidate the processes contributing to the spread of resistance among rice fields, we characterized the genetic diversity and differentiation of thiobencarb-resistant (R) and thiobencarb-susceptible (S) populations across the Central Valley using microsatellite markers. A total of 406 individuals from 22 populations were genotyped using seven nuclear microsatellite primer pairs. Three analytical approaches (unshared allele, Shannon–Weaver, and allelic-phenotype statistics) were used to assess genetic diversity and differentiation in the allohexaploid species. Low levels of genetic variation were detected within populations, consistent with other highly selfing species, with S populations tending to be more diverse than R populations. FST values indicated that populations were genetically differentiated and that genetic differentiation was greater among S populations than R populations. Principal coordinate analysis generated two orthogonal axes that explained 88% of the genetic variance among early watergrass populations and differentiated populations by geographical region, which was associated with resistance phenotype. A Mantel test revealed that genetic distances between R populations were positively correlated with the geographical distances separating populations. Taken together, our results suggest that both short- and long-distance seed dispersal, and multiple local and independent evolutionary events, are involved in the spread of thiobencarb-resistant early watergrass across rice fields in the Sacramento Valley. In contrast, resistance was not detected in early watergrass populations in the San Joaquin Valley.
    Weed Science 04/2011; 59(April-June 2011):195-201. DOI:10.1614/WS-D-10-00124.1 · 1.87 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Ludwigia hexapetala and L. grandiflora are recent, aggressive invaders of freshwater wetlands in California. To assess the relative role of sexual versus clonal reproduction in invasive spread, we used AFLPmarkers to genotype 794 ramets of L. hexapetala sampled from 27 populations in three watersheds of California, and 150 ramets of L. grandiflora from five populations in a fourth watershed. We then used two analytical methods, similarity thresholds and character incompatibilities, to distinguish genotypic variation within genets (clones) from variation between genets. Our analyses revealed extremely limited genotypic and genet variation in invasive L. hexapetala and L. grandiflora within California. Within L. hexapetala, 95% of the ramets analyzed represented a single genet. The genet was the only one detected in 20 populations. The remaining seven populations contained two to nine genets. Within L. grandiflora, all ramets were of only one genotype. Thus, invasive spread within and between populations, and across watersheds, appears to be almost exclusively clonal and brought about by the dispersal of vegetative propagules. The extremely low seedling recruitment indicates that management should target vegetative dispersal and growth.
    Aquatic Botany 03/2009; 91((2009)):123-129. DOI:10.1016/j.aquabot.2009.03.006 · 1.61 Impact Factor
  • Miki Okada · Mark Lyle · Marie Jasieniuk
    [Show abstract] [Hide abstract]
    ABSTRACT: Aim  Reconstructing the introduction history of exotic species is critical to understanding ecological and evolutionary processes that underlie invasive spread and to designing strategies that prevent or manage invasions. The aims of this study were to infer the introduction history of the invasive apomictic bunchgrass Cortaderia jubata and to determine if molecular data support the postulated horticultural origin of invasive populations.Location  Invaded areas in the USA (California, Maui) and New Zealand; native areas in Bolivia, Ecuador and Peru.Methods  We used nuclear microsatellite markers to genotype 281 plants from invaded areas in California, Maui and New Zealand, and 77 herbarium specimens from native South America, and compared the genotypic and clonal variation of C. jubata from the invaded and native ranges. Clonal diversity was determined from genotypic diversity using two analytical methods.Results  Invasive C. jubata from invaded regions in California, Maui and New Zealand consisted of the same single clone that probably originated from a single introduced genotype. In contrast, 14 clones were detected in herbarium specimens from the native areas of Bolivia, Ecuador and Peru. The invasive clone matched the most common clone identified in herbarium specimens from southern Ecuador where horticultural stock is presumed to have originated.Main conclusions  The lack of clonal and genotypic diversity in invasive plants, but moderately high diversity detected in native plants, indicates a significant reduction in genetic variation associated with the introduction of C. jubata outside of its native range. Based on historical accounts of the horticultural introduction of C. jubata and the results of this study, a severe founder effect probably occurred during deliberate introduction of C. jubata into cultivation. Our results are consistent with the postulated horticultural origin of invasive C. jubata and point to southern Ecuador as the geographical source of invasive populations.
    Diversity and Distributions 10/2008; 15(1):148 - 157. DOI:10.1111/j.1472-4642.2008.00530.x · 3.67 Impact Factor
  • Miki Okada · Riaz Ahmad · Marie Jasieniuk
    [Show abstract] [Hide abstract]
    ABSTRACT: International trade in horticultural plants is a major pathway of introduction of invasive species. Pampas grass (Cortaderia selloana) is an invasive species of horticultural origin that is native to South America but cultivated as an ornamental in regions with Mediterranean climates worldwide. To gain insight into the introduction history of invasive populations in California, we analysed microsatellite marker variation in cultivated and invasive C. selloana. We sampled 275 cultivated plants from diverse sources and 698 invasive plants from 33 populations in four geographical regions of California. A model-based Bayesian clustering analysis identified seven distinct gene pools in cultivated C. selloana. Probabilities of assignment of invasive individuals to cultivated gene pools indicated that two gene pools accounted for the genomic origin of 78% of the invasive C. selloana sampled. Extensive admixture between cultivated source gene pools was detected within invasive individuals. Sources of admixed invasive individuals are probably landscape plantings. Consistent with the Bayesian assignment results indicating that multiple cultivated gene pools and landscape plantings are probable sources of invasive populations, F(ST) and neighbour-joining clustering analyses indicated multiple escapes from shared sources in each geographical region. No isolation by distance or geographical trend in reduction of genetic diversity was evident. Furthermore, a generally random and discontinuous distribution of proportional assignments of invasive populations to cultivated gene pools suggests that introductions occurred recurrently within each geographical region. Our results strongly suggest that dispersal through local landscape plantings has contributed to the range expansion of invasive C. selloana in California.
    Molecular Ecology 01/2008; 16(23):4956-71. DOI:10.1111/j.1365-294X.2007.03568.x · 6.49 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We isolated and characterized microsatellite loci in the ornamental pampas grass Lonaaena selloana (Scnuit. & Schult, f.) Asch. & Graebn. for purposes of identifying cultivars and assessing genetic relationships among cultivars. Small insert genomic libraries were enriched for dinucleotide (CT)n and (CA)n repeats. Ninety clones were sequenced of which 76% contained at least one microsatellite with a basic motif greater than six repeat units. Nine primer pairs amplified 10 polymorphic and putatively disomic loci, and were used to genotype 88 individuals representing 17 named cultivars and four selections. In total, 93 alleles were detected with a maximum of two to 19 per locus. Effective number of alleles varied from 1.3 to 9.5. Observed heterozygosity ranged from 0.07 to 0.81. The 10 microsatellite loci distinguished the majority of pampas grass cultivars. An unweighted pair group method with arithmetic mean (UPGMA) cluster analysis, based on proportion of shared alleles among individuals, revealed groups of cultivars corresponding to origin and morphological characteristics. With few exceptions, individuals of a single cultivar clustered together with moderate to strong bootstrap support (greater than 50%). Interestingly, 'Pumila' from Europe and the United States formed separate clusters indicating independent origins. A large, diverse cluster with low bootstrap support consisted of selections and cultivars sold as seed, rather than potted or bare-root clonal plants. Primers designed for C. selloana amplified microsatellite loci in other Cortaderia Stapf species concordant with phylogenetic relationships among the species. Cross-amplification was 100% in C. jubata (Lemoine ex Carrière) Stapf; 77% in C. pilosa (d'Urv.) Hack, and C. rudiuscula Stapf; 66% in C. fulvida (Buch.) Zotov; and 55% in C. richardii (Endl.) Zotov and C. toetoe Zotov.
    Journal of the American Society for Horticultural Science. American Society for Horticultural Science 07/2006; 131(4). · 1.28 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Conyza canadensis, which is in the Compositae (Asteraceae) family, was the first broadleaf weed to evolve glyphosate resistance and is now a problematic weed worldwide. It is a true diploid (2n=2X=18) with the smallest genome of any agricultural weed (335 Mb) and thus among the best model weed candidates for genomic studies. C. canadensis populations are highly self-fertilizing and homozygous. Individual plants can produce over 200,000 wind-dispersed seeds and are easily grown under experimental conditions. In addition, we have developed a plant transformation and regeneration method that allows analyses of overexpression and silencing of potential genes. The reference genome would be not only useful to elucidate the herbicide resistance mechanism, but also beneficial for the study of other economically important plants in the family. We performed 454 and Illumina HiSeq transcriptome runs of resistant and susceptible horseweed samples, which generated ~45,000 unique gene sequences that are being mined for potential resistance genes. Known repeat elements were analyzed; the results show horseweed has a very compact genome structure and suggested the de novo assembly could be easier than initially expected. For the genome assembly, we combined data from multiplex platforms (454 GS-FLX, Illumina HiSeq 2000 and PacBio RS) and various libraries (shotgun, paired-end and mate-paired) of different sizes (~350 bp, ~600 bp, ~3 kb and ~10 kb) to generate comprehensive reads. Two plates of 454 runs of three shotgun libraries produced 2,238,807 raw reads with an average read length of ~390 bp, for a yield total of ~860 Mb data. Two lanes of HiSeq 2000 runs (2 x 100 bp) of two short paired-end libraries produced 786,389,990 raw reads, for a yield total of ~77 Gb data. One lane of HiSeq 2000 run (2x 100 bp) of one 3 Kb mate-paired library produced 381,844,926 raw reads, for a yield total of ~37 Gb data. Ten SMRT cell of PacBio runs produced 513,084 sequences with an average read length of 3.1 Kb, for a yield total of 1.44 Gb data. From de novo assembly of these data, we have obtained an accurate whole chloroplast genome (~153 Kb), most of the mitochondrial genome (~450 Kb), and 99% of the whole genome assembled into draft scaffolds. Taken together, these resources should enable gene discovery and basic research of weeds and their relatives in the Compositae.
    International Plant and Animal Genome Conference XXI 2013;
  • Marie Jasieniuk · Miki Okada
    [Show abstract] [Hide abstract]
    ABSTRACT: Strong selection by herbicides has resulted in the widespread evolution and spread of herbicide resistance in agricultural weed populations. During resistance evolution and spread, local mutation and selection, interpopulation gene flow, and founder events lead to the spatial structuring of genetic variation across the agricultural landscape. To elucidate the origins and invasion routes of glyphosate-resistant plants within orchards and vineyards across the Central Valley of California, we sampled and genotyped 1,262 Conyza canadensis individuals from 43 populations at 12 microsatellite loci and 1,077 C. bonariensis individuals from 40 populations at 15 loci. Seedling offspring from each population were phenotyped for resistance or susceptibility to glyphosate at one and/or two times the recommended field rate. The model-based Bayesian clustering analysis STRUCTURE identified two distinct genetic clusters at the highest hierarchical level within both species. However, the geographical distribution of proportional assignments of populations to the genetic clusters differed markedly between species. For C. canadensis, populations exhibited a strong north-south distribution of genetic clusters, which corresponded to the geographical distribution of resistant and susceptible phenotypes. For C. bonariensis, most populations assigned partially to both genetic clusters, with one cluster predominant at the center of the sampled range and the second cluster predominant at the extremes. The majority of populations contained resistant phenotypes, but populations in the center of the range revealed more consistent and less variable glyphosate responses. Our results strongly suggest that the processes underlying the evolution and spread of glyphosate resistance differ for the two species.
    International Plant and Animal Genome Conference XX 2012;

Publication Stats

72 Citations
29.84 Total Impact Points


  • 2008–2015
    • University of California, Davis
      • Department of Plant Sciences
      Davis, California, United States
  • 2014
    • University of Chicago
      Chicago, Illinois, United States