Genetic diversity inChaenomeles (Rosaceae) revealed by RAPD analysis

Genetic relatedness inChaenomeles was studied by RAPD analysis in 42 plants representing accessions of three wild species and one hybrid taxon. Amplification with 17 primers yielded a total of 156 polymorphic RAPD bands. Estimates of genetic relatedness suggest thatC. cathayensis andC. japonica are the most distantly related species, and that the former is comparatively homogeneous.Chaenomeles speciosa, which may have arisen through hybridization betweenC. cathayensis andC. japonica, takes an intermediate position between these two species. Analysis of diagnostic bands demonstrate that neitherC. speciosa norC. ×superba has any bands that do not occur in at least one ofC. cathayensis orC. japonica. Moreover,C. speciosa and the partly overlapping taxonC. ×superba are comparatively heterogeneous, which is also in accordance with a hybrid origin. Intraspecific variation was studied mainly inC. japonica; plants obtained from different sources of material formed well separated groups in the cluster analysis.     

Intraspecific evolution ofMicroseris pygmaea (Asteraceae,Lactuceae) analyzed by cosegregation of phenotypic characters (QTLs) and molecular markers (RAPDs)

The Chilean annual,Microseris pygmaea, has differentiated in distinct coastal and inland series of populations after long-distance dispersal from western North America. Two plants from the most diverse biotypes were crossed, a large F₂ was raised and analysed for segregation of 30 phenotypic characters. Segregation of molecular markers (47 RAPDs, 1 RFLP, 2 isozymes) was determined in a subpopulation of 45 plants which include all extremes for the phenotypic characters. 32 marker/character cosegregations were significant at the 1% level in t-tests between dominant and homozygous recessive marker genotypes. Considering linkage among markers and pleiotropy of certain marker loci, the number of independent quantitative trait loci (QTLs) is reduced to about 18. Interactions among 2 or 3 QTLs affecting one character have been characterized. The phenotypic differentiation ofM. pygmaea during its evolution from a single founder individual begins to be understood at the level of single-gene mutants.     

Specific genetic markers for wheat, spelt, and four wild relatives: comparison of isozymes, RAPDs, and wheat microsatellites.

Three types of markers-isozymes, RAPDs (random amplified polymorphic DNAs), and wheat microsatellites- were tested on wheat, spelt, and four wild wheat relatives (Aegilops cylindrica, Elymus caninus, Hordeum marinum, and Agropyron junceum). The aim was to evaluate their capability to provide specific markers for differentiation of the cultivated and wild species. The markers were set up for subsequent detection of hybrids and introgression of wheat DNA into wild relatives. All markers allowed differentiation of the cultivated from the wild species. Wheat microsatellites were not amplified in all the wild relatives, whereas RAPDs and isozymes exhibited polymorphism for all species. The dendrograms obtained with RAPD and isozyme data separated Swiss wheat cultivars from those collected in Austria and England, while no difference was found between Swiss spelt and wheat. RAPD data provided a weak discrimination between English and Austrian E. caninus. The microsatellite-based dendrogram discriminated populations of Ae. cylindrica, but no clear separation of H. marinum from E. caninus was revealed. The similarity matrices based on the three different sets of data were strongly correlated. The highest value was recorded between the matrices based on RAPDs and isozymes (Mantel's test, r = 0.93). Correlations between the similarity matrix based on microsatellites and matrices based on RAPDs and isozymes were lower: 0.74 and 0.68, respectively. While microsatellites are very useful for comparisons of closely related accessions, they are less suitable for studies involving less-related taxa. Isozymes provide interesting markers for species differentiation, but their use seems less appropriate for studies of within-species genetic variation. RAPDs can produce a large set of markers, which can be used for the evaluation of both between- and within-species genetic variation, more rapidly and easily than isozymes and microsatellites.     

Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged sites

 We have investigated the genetic diversity of 11 natural populations of C. japonica using 13 polymorphic STS markers. The average unbiased heterozygosities (H _e ), the average number of alleles per locus (N _a ) and the proportion of polymorphic loci (Pl) were 0.281, 1.93 and 76.92%, respectively. Coefficients of linkage disequilibrium were calculated, and no significant deviation was found except in four combinations – which might have occurred by chance alone. The fixation index (F _IS ) for 3 loci showed statistically significant values at the 1% level. The genetic differentiation between populations was only 0.047, and there were no clear geographical tendencies in the allele frequencies or the heterozygosities among populations. Consequently, the results from STS-based co-dominant DNA marker analysis were very similar to those from a previous allozyme study. However, the resolution of the technique is greater than allozyme analysis because many loci with high heterozygosities can be evaluated, and it is very simple. Therefore, the STS-based marker approach is very useful and convenient for population genetics and genome mapping of C. japonica. Received: 18 July 1998 / Accepted: 13 August 1998     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

Evaluation of cleaved amplified polymorphic sequence markers for <Emphasis Type="Italic">Chamaecyparis obtusa</Emphasis> based on expressed sequence tag information from <Emphasis Type="Italic">Cryptomeria japonica</Emphasis>

We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (~30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (P<0.01) deviation from the expected segregation ratio. In total, 136 polymorphic markers were developed using C. japonica-based STS primers without any sequence modification. In addition, the applicability of STS-based markers developed in one species to other species was found to closely reflect the evolutionary distance between the species, which is roughly concordant with the difference between their rbcL sequences. We plan to use these markers for genetic studies in C. obtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.     

Development and polymorphism of microsatellite markers for Fagus crenata and the closely related species, F. japonica

 We have developed microsatellite markers (SSRs) applicable to Fagus crenata using the RAHM method and investigated their polymorphisms. We also applied the SSRs in an analysis of a closely related species, F. japonica. Here we describe the isolation and characterization of nine polymorphic microsatellite markers, of which eight are applicable to both species. Among 30 individuals of each of F. crenata and F. japonica we detected a total of 79 and 77 alleles, respectively, with an average of 9.9 and 8.6 alleles per locus. The mean expected heterozygosity (He) was 0.615 (range: 0.216–0.925) in F. crenata and 0.660 in F. japonica (range: 0.259–0.827). The He values were considerably higher than those previously found for isozymes. Paternity exclusion probabilities for multiple loci, calculated over all loci, were extremely high (0.999 and 0.998 in F. crenata and F. japonica, respectively): sufficiently high to study pollen flow in both species. Received: 5 December 1998 / Accepted: 28 December 1998     

Genetics and polymorphism of a duplicated malate dehydrogenase (MDH) locus in the grasshopperOxya japonica japonica (Orthoptera:Acrididae:Oxyinae)

A biochemical genetic study of the enzyme malate dehydrogenase (MDH) was conducted in the grasshopperOxya j. japonica. Analysis of MDH electrophoretic variation in this species of grasshopper shows that one of the two autosomal loci for MDH in grasshoppers, the Mdh-2 locus, controlling the anodal set of MDH isozymes, is duplicated. Results of breeding studies confirm this and the observed polymorphism at theMdh-2 locus in the two populations ofOxya j. japonica studied can be attributed to three forms of linked alleles at the duplicated locus in equilibrium in both populations. In this respect, all individuals of this species possess heterozygous allelic combinations at the duplicatedMdh-2 locus, which may account for the spread of the duplicated locus in the populations of this species of grasshopper.This research was supported by a grant (Vote F) from the University of Malaya, Kuala Lumpur.     

Genetic structure of island populations of <Emphasis Type="Italic">Prunus lannesiana</Emphasis> var. <Emphasis Type="Italic">speciosa</Emphasis> revealed by chloroplast DNA,AFLP and nuclear SSR loci analyses

The wild flowering cherry Prunus lannesiana var. speciosa is highly geographically restricted, being confined to the Izu Islands and neighboring peninsulas in Japan. In an attempt to elucidate how populations of this species have established we investigated the genetic diversity and differentiation in seven populations (sampling 408 individuals in total), using three kinds of genetic markers: chloroplast DNA (cpDNA), amplified fragment length polymorphisms (AFLPs), and 11 nuclear SSR polymorphic loci. Eight haplotypes were identified based on the cpDNA sequence variations, 64 polymorphic fragments were scored for the AFLP markers, and a total of 154 alleles were detected at the 11 nuclear SSR loci. Analysis of molecular variance showed that among-population variation accounted for 16.55, 15.04 and 7.45% of the total detected variation at the cpDNA, AFLPs, and SSR loci, respectively. Thus, variation within populations accounted for most of the genetic variance for all types of markers, although the genetic differentiation among populations was also highly significant. For cpDNA variation, no clear structure was found among the populations, except that of the most distant island, although an “isolation by distance” pattern was found for each marker. Both neighbor-joining trees and structure analysis indicate that the genetic relationships between populations reflect geological variations between the peninsula and the islands and among the islands. Furthermore, hybridization with related species may have affected the genetic structure, and some genetic introgression is likely to have occurred.     

NATURAL HYBRIDS BETWEEN ORYZOPSIS AND STIPA. I. ORYZOPSIS HYMENOIDES × STIPA SPECIOSA

Johnson , B. Lennart . (U. California, Los Angeles.) Natural hybrids between Oryzopsis and Stipa. I. Oryzopsis hymenoides × S. speciosa. Amer. Jour. Bot. 47(9): 736–742. Illus. 1960.—Spontaneous, sterile hybrids between Oryzopsis hymenoides and Stipa speciosa heretofore have been referred to O. bloomeri, which species in an earlier paper was shown to consist of a series of hybrids between O. hymenoides and various species of Stipa. On many morphological characters (O. hymenoides × speciosa) is intermediate between its parents and similar to the other hybrids formerly classed as O. bloomeri. It is distinct from the other hybrids on characters which reflect S. speciosa, except with respect to indument of the awn which is recessive. Somatic chromosome counts are: O. enoides, 48; S. speciosa, 64; hybrid, 56. Both parents exhibit regular bivalents at meiosis. The hybrid shows only occasional bivalents and mostly asynchronous splitting or random distribution of univalents at metaphase I. Pollen abortion is complete. No evidence of natural amphiploidy or introgression was found.     

Geographic variation in oviposition preference for male and female host plants in a geometrid moth: implications for evolution of host choice

Several dioecious plant species exhibit sexual dimorphisms in defensive traits. However, the effects of sexual dimorphism on defense against herbivores remain poorly understood. Eurya japonica (Thunb.) (Theaceae) is a dioecious shrub that shows sexual dimorphism in the chemical defense of flower buds. Female calyces contain higher concentrations of total phenolics and condensed tannins than do male calyces. Male flower buds are edible for a florivore moth, Chloroclystis excisa (Butler) (Lepidoptera: Geometridae), whereas the female flower buds are lethal to the moth larvae. The moths prefer to oviposit on male over female E. japonica flower buds. As the moths also occur in areas lacking E. japonica, we tested whether the oviposition preference for E. japonica flower sex differed between moths sympatric and allopatric with E. japonica. The moths sympatric with E. japonica showed a stronger preference for male E. japonica than the moths allopatric with E. japonica. Our phylogeographic study using mitochondrial cytochrome oxidase subunit I gene sequences revealed little genetic differentiation between moth populations sympatric and allopatric with E. japonica. These results suggest that the adaptive oviposition preference for flower sex of E. japonica has evolved rapidly in C. excisa.     

Sika deer presence affects the host–parasite interface of a Japanese land leech

Since the 1990s, increasing populations of a blood feeding land leech (Haemadipsa japonica) have become a serious issue in several Japanese prefectures, and it may be caused by the increases in sika deer (Cervus nippon) populations seen over the last quarter of the century. Therefore, this study aimed to reveal the host animal species of H. japonica using iDNA (vertebrate DNA isolated from invertebrates) and to test the hypothesis that the increasingly widespread distribution of sika deer results in increased H. japonica populations through changes to the host–parasite interface. We amplified mitochondrial DNA 16S ribosome RNA fragments from iDNA isolated from the blood clots of H. japonica collected across Japan. We identified 17 host animal species, including four orders of Mammalia (Carnivora, Artiodactyla, Rodentia, and Lagomorpha) and two orders of Amphibia (Caudata and Anura). The sika deer was the dominant host species of H. japonica. Additionally, the host animal species composition of H. japonica differed according to the presence or absence of sika deer. In the sites where sika deer were not found, Anura (frog) species were the most commonly identified hosts of H. japonica. These results suggest that the increases in H. japonica populations might have occurred via a change in host preference to sika deer. This change might be driven by the increases in sika deer populations and subsequent increase in the frequency that H. japonica uses the sika deer as easy prey, as well as by sika deer providing more reproductive energy per blood meal than blood meal from frog species. The present study suggests that a more widespread distribution of sika deer resulted in an increase in H. japonica through a change in the host–parasite interface. Therefore, management that focuses on decreasing sika deer populations would likely be an effective method for the reduction of H. japonica populations.     

Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe)

We evaluated chloroplast DNA (cpDNA), isozymes, single to low-copy nuclear DNA (RFLPs), and random amplified polymorphic DNAs (RAPDs) in terms of concordance for genetic distance of 15 accessions each of Solanum etuberosum and S. palustre, and 4 accessions of S. fernandezianum. These self-compatible, diploid (2n=24), and morphologically very similar taxa constitute all species in Solanum sect. Etuberosum, a group of non-tuber-bearing species closely related to Solanum sect. Petota (the potato and its wild relatives). Genetic distance and multidimentional scaling results show general concordance of isozymes, RFLPs and RAPDs between all three taxa; cpDNA shows S. etuberosum and S. palustre to be more similar to each other than to S. fernandezianum. Interspecific sampling variance shows a gradation of resolution from allozyme (low) to RAPD to RFLP (high); while intraspecific comparisons graded from RFLPs (low) to RAPDs (high; lack of sufficient allozyme variability within species precluded comparisons for allozymes). Experimental error was low in RFLPs and RAPDs.Names are necessary to report factually and available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable     

基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构

薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。     

Collapse of species boundaries in the wild potatoSolanum brevicaule complex (Solanaceae, S. sect.Petota): Molecular data

TheSolanum brevicaule complex is a group of morphologically very similar wild and cultivated potato taxa (Solanum sect.Petota). This study uses single to low-copy nuclear RFLPs and RAPDs to investigate their species boundaries and relationships. Cladistic analyses of both data sets are largely concordant with each other and with a recently published phenetic analyses of the same accessions using morphology. All three data sets separate members of the complex into populations from Peru and immediately adjacent northwestern Bolivia, including most cultivated species accessions, and populations from northwestern Bolivia to Argentina. The molecular results suggest that the complex is paraphyletic as currently circumscribed. Many species of theS. brevicaule complex should be relegated to synonymy.     

An integrated SSR based linkage map for <Emphasis Type="Italic">Zoysia matrella</Emphasis> L. and <Emphasis Type="Italic">Z. japonica</Emphasis> Steud.

Japanese lawngrass (Zoysia japonica) and Manila grass (Z. matrella) are the two most important and commonly used Zoysia species. A consensus based SSR linkage map was developed for the genus by combining maps from each species. This used previously constructed maps for two Z. japonica populations and a new map from Z. matrella. The new SSR linkage map for Z. matrella was based on 86 F₂ individuals and contained 213 loci and covered a map distance of 1,351.2 cM in 32 linkage groups. Comparison of the three linkage maps constructed from populations with different genetic backgrounds indicated that most markers exhibited a consensus order, although some intervals or regions displayed discrepancy in marker orders or positions. The integrated map comprises 507 loci with a mean interval of 4.1 cM, covering a map distance of 2,066.6 cM in 22 linkage groups. The SSR-based map will allow marker-assisted selection and be useful for the mapping and cloning of economically important genes or quantitative trait loci.     

Development of chloroplast markers for Japanese and snow camellias

Eight chloroplast markers were developed from Japanese and snow camellia (Camellia japonica and C. rusticana). Six markers were based on mononucleotide repeats, while the other two resulted from indels of larger units. Polymorphisms were screened using 15 individuals from all over the Japanese archipelago, including C. japonica, C. japonica var. macrocarpa, C. japonica var. hozanensis, and C. rusticana. Polymorphisms within a single population were searched in 22 and 26 individuals of C. japonica and C. rusticana, respectively. The number of alleles per locus ranged from two to three, resulting in eight haplotypes, two of which were specific to C. rusticana. No polymorphisms were detected within a single population for both C. japonica and C. rusticana. The eight markers developed in the present study will be useful for analyzing the genetic diversity and tracing maternal origins of Japanese and snow camellias.     

Do molecular markers reflect patterns of differentiation in adaptive traits of conifers?

We have examined patterns of variation of several kinds of molecular markers (isozymes, RFLPs of ribosomal DNA and anonymous low-copy number DNA, RAPDs and microsatellites) and an adaptive trait [date of bud set in Scots pine (Pinus sylvestris L.)]. The study included Finnish Scots pine populations (from latitude 60°N to 70°N) which experience a steep climatic gradient. Common garden experiments show that these populations are adapted to the location of their origin and genetically differentiated in adaptive quantitative traits, e.g. the date of bud set in first-year seedlings. In the northernmost population, bud set took place about 21 days earlier than in the southernmost population. Of the total variation in bud set, 36.4% was found among the populations. All molecular markers showed high levels of within-population variation, while differentiation among populations was low. Among all the studied markers, microsatellites were the most variable (H_e=0.77). Differences between populations were small, G_ST was less than 0.02. Our study suggests that molecular markers may be poor predictors of the population differentiation of quantitative traits in Scots pine, as exemplified here by bud-set date.     

A SCAR MOLECULAR MARKER SPECIFICALLY RELATED TO THE FEMALE GAMETOPHYTES OF SACCHARINA (LAMINARIA) JAPONICA (PHAEOPHYTA)1

PCR amplification was employed to identify female or male gametophyte associated markers in Saccharina japonica (Aresch.) C. E. Lane, C. Mayes et G. W. Saunders (=Laminaria japonica Aresch.). One pair of the primers, P5, was screened from five pairs designed based on a specific sequence (GenBank accession no. AB069714 ) of Marchantia polymorpha Y chromosome, resulting in a differential band ～500 bp in size between female and male gametophytes of Rongfu strain of S. japonica. According to the SCAR (sequence‐characterized amplified regions) strategies, one pair of primers, P51, was designed on the basis of the sequence of this band that was only present in female gametophytes. A SCAR marker, designated FRML‐494 (494‐bp Female‐Related Marker of S. japonica, GenBank accession no. EU931619 ), was developed successfully by PCR amplification using the designed P51 primer pair. The SCAR marker was verified to be present only in female gametophytes of another variety 901 of this kelp that was a hybrid between S. japonica as paternal and S. longissima (Miyabe) C. E. Lane, C. Mayes, Druehl et G. W. Saunders (=Laminaria longissima Miyabe) as maternal, suggesting that the FRML‐494 marker was specifically related to female gametophytes of the genus. This marker is the first molecular tool reported for sex identification in kelps. This study was beneficial for identifying gametophyte gender during vegetative growth and for judging whether the monogenetic sporophytes came from exclusive male or female gametophytes, as well as for further research on sex determination at the molecular level in kelps.     

Extent and structure of genetic variation in two colonising Diplotaxis species (Brassicaceae) with contrasting breeding systems

Genetic variation within two closely related Diplotaxis species was studied as indicated by isozymes and RAPDs. These species differ in their mating systems, their life forms, and in their evolutionary history, but both are successful colonisers. The diploid perennial D. tenuifolia is an outbreeder, the allotetraploid annual to biennial D. muralis is predominantly selfing. D. muralis was nearly devoid of genetic variation due to a young phylogenetic age and/or population history. Estimations of genetic variation within D. tenuifolia and F-statistics indicated random mating at the species and population level and confirms obligate outbreeding. However, influence of genetic drift relative to gene flow was high and mirrors colonisation processes as indicated by considerable heterogeneity across populations and the lack of correlation between population divergence and geographic distance.