Genomes Of Species Research Articles

Poisson Approximation for the Number of Repeats in a Stationary Markov Chain

Detection of repeated sequences within complete genomes is a powerful tool to help understanding genome dynamics and species evolutionary history. To distinguish significant repeats from those that can be obtained just by chance, statistical methods have to be developed. In this paper we show that the distribution of the number of long repeats in long sequences generated by stationary Markov chains can be approximated by a Poisson distribution with explicit parameter. Thanks to the Chen-Stein method we provide a bound for the approximation error; this bound converges to 0 as soon as the length n of the sequence tends to ∞ and the length t of the repeats satisfies n2ρt = O(1) for some 0 < ρ < 1. Using this Poisson approximation, p-values can then be easily calculated to determine if a given genome is significantly enriched in repeats of length t.

Poisson Approximation for the Number of Repeats in a Stationary Markov Chain

Detection of repeated sequences within complete genomes is a powerful tool to help understanding genome dynamics and species evolutionary history. To distinguish significant repeats from those that can be obtained just by chance, statistical methods have to be developed. In this paper we show that the distribution of the number of long repeats in long sequences generated by stationary Markov chains can be approximated by a Poisson distribution with explicit parameter. Thanks to the Chen-Stein method we provide a bound for the approximation error; this bound converges to 0 as soon as the length n of the sequence tends to ∞ and the length t of the repeats satisfies n 2ρ t = O(1) for some 0 < ρ < 1. Using this Poisson approximation, p-values can then be easily calculated to determine if a given genome is significantly enriched in repeats of length t.

Nuclear architecture and chromosome dynamics in the search of the pairing partner in meiosis in plants

The formation of haploid gametes in organisms with sexual reproduction requires regular bivalent chromosome pairing in meiosis. In many species, homologous chromosomes occupy separate territories at the onset of meiosis. To be paired at metaphase I, they need to be brought into a close proximity for interactions that include homology recognition and the establishment of some form of bonds. How homologues find each other is one of the least understood meiotic events. Plant species with large or medium sized genomes, such as wheat or maize, are excellent materials for the cytological analysis of chromosome dynamics at early meiosis, but genes that control meiosis have been identified mainly in small genome species such as Arabidopsis thaliana. This review is focused on the contribution studies on plants are providing to the knowledge of the initial steps of the meiotic process.

AFLP-based molecular characterization of Brassica rapa and diversity in Canadian spring turnip rape cultivars

Information on genetic diversity and genetic relationships among taxa of Brassica rapa (n = 10, AA genome) is currently limited. Grown for oil, vegetable and fodder use in Europe and Asia, previous studies have indicated western and eastern groups corresponding to independent centres of origin. This study evaluated patterns and levels of genetic diversity in 93 accessions [includes 25 Agriculture and Agri-Food Canada (AAFC) breeding lines (BL)] of B. rapa based on 307 amplified fragment length polymorphisms (AFLP), testing subspecific separateness and the affiliation of four previously unassigned AA genome species (B. perviridis, B. purpuraria, B. ruvo and B. septiceps). AFLP data revealed three main clusters (I, II, III) corresponding to European (I), Indian (III), and a mixed Asian/European/Indian (II) purported origins of the taxa, with several subclusters observed in I and II. Mean AFLP polymorphism levels for Asian, European, Indian and AAFC-BL accessions were 79, 74, 66 and 62%, respectively. Few of the subspecies formed unique clusters and some, particularly subspecies chinensis and pekinensis, were assigned to several clusters. AFLP-based genetic distance information can be used by breeders to select diverse genotypes for cultivar development and fingerprinting of genotypes/cultivars. For example, a single AFLP primer pair was sufficient to uniquely identify all breeding lines in the AAFC B. rapa breeding programme.

Molecular phylogeny of RPB2 gene reveals multiple origin, geographic differentiation of H genome, and the relationship of the Y genome to other genomes in Elymus species

It has been hypothesized from isozymic and cytological studies of Elymus species that the Old and New World taxa may be of separate origin of the H genome in the StH genome species. To test this hypothesis, and estimate the phylogenetic relationships of polyploid Elymus species within the Triticeae, the second largest subunit of RNA polymerase II ( RPB2) sequence of 36 Elymus accessions containing StH or StY genomes was analyzed with those of Pseudoroegneria (St), Hordeum (H), Agropyron (P), Australopyrum (W), Lophopyrum ( E e ), Thinopyrum ( E b ) and Dasypyrum (V). Our data indicated that the H genome in Elymus species is differentiated in accordance with geographical origin, and that the Eurasian and American StH genome species have independent alloploid origins with different H-genome donors. Phylogenetic analysis of Y genome sequences with other genome donors (St, H, P, W) of Elymus revealed that W and P genomes are sister to Y genome with a 87% bootstrap support, and that StY and StH species group might have acquired their RPB2 St sequences from distinct Pseudoroegneria gene pools. Our data did not support the suggestion that the St and Y genomes have the same origin as put forward in a previous study using ITS data. Our result provides some insight on the origin of Y genome and its relationship to other genomes in Elymus.

Evolutionary analysis of two plastid DNA sequences in cultivated and wild species of Oryza

Oryza diploid species comprise AA, BB, CC, EE, FF, and GG genome groups. Cultivated rice, O. sativa L. of the AA genome, has two subspecies, indica and japonica. These two subspecies are differentiated in many characteristics, such as the number of nucleolar sites, annual-perennial habitat and polymorphism of plastid DNA. Although many researchers accept that japonica must originate from O. rufipogon, the evolutionary route of indica remains unclear. A 69-bp deletion in ORF100 is useful to discriminate between indica and japonica cultivars and between O. nivara and O. rufipogon; furthermore, PSID sequences of O. sativa–O. rufipogon complex contain hyper-variable sites consisting of C and A mononucleotide repeats, which are useful to classify wild accessions and cultivars into the six subtypes of 6C7A and 7C6A (japonica and O. rufipogon), 6C8A and 7C7A (O. nivara), 8C8A and 9C7A (indica). The 69-bp deletion is shared with O. nivara (6C8A, 7C7A) and indica (8C8A, 9C7A) but the 8C8A subtype is found only in indica. To elucidate variations of plastid DNA in the genus Oryza and cytoplasmic origin of indica, we compared two plastid sequences, ORF100 (676 bp) and PSBZ (629 bp), in 40 accessions of 14 Oryza diploid species. Sequence comparison showed that FF and GG genome species were distantly related to AA genome species. Both BB and CC genome species were related with AA genome species but were mutually differentiated. An evolutionary trace of ORF100 and PSBZ sequences indicated that O. barthii might have a consensus sequence among all AA genome species. Both O. longistaminata and O. glumaepatula were highly related with O. barthii; the O. sativa–O. rufipogon complex showed more various polymorphisms than other AA genome species. The results of this study show that 8C8A and 9C7A subtypes of plastids in indica cultivars are differentiated from 6C8A and 7C7A subtypes in O. nivara, despite sharing the same deletion in ORF100. In addition, 6C7A and 7C6A subtypes in japonica cultivars and O. rufipogon share identical sequences in PSBZ but differentiate at two SNP sites in ORF100.

Analysis of 142 genes resolves the rapid diversification of the rice genus

The relationships among all diploid genome types of the rice genus were clarified using 142 single-copy genes

Genomic scale analysis of lateral gene transfer in Apicomplexan parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development

The protozoan phylum Apicomplexa is comprised of >5000 species, including Toxoplasma gondii (a prominent opportunistic infection in AIDS), and the Plasmodium parasites responsible for malaria. Complete genome sequences are now available for several apicomplexan species, including both T. gondii and Plasmodium falciparum, making it possible to exploit comparative phylogenomic tools for insight into adaptations associated with intracellular parasitism, and in order to identify targets for therapeutic development. These parasites harbor a novel organelle, the 'apicoplast', which was acquired by endosymbiotic capture of a eukaryotic alga, and thus provides a dramatic example of lateral gene transfer (LGT). In order to determine the overall impact of LGT, we have employed phylogeny reconstruction to detect transfers on a genomicscale. Trees have been constructed for all genes in the Toxoplasma and Plasmodium genomes, and compared with a whole genome species treederived from 55 taxa represented in the orthologous protein database OrthoMCL-DB [1]. Non-apicomplexan specific ortholog groups containing4 to 100 sequences were examined, pruning outlying species based on their degree of connectivity to the group as a whole, and robustness of the resulting tree. A pilot study based on intensive manual curation of T. gondii genes coding for metabolic enzymes estimates that ~15% of these genes were acquired by LGT. Turning to the entire parasite genome(s), Horizstory software identifies 1552 groups where T. gondii gene placement contrasts with the species tree, and 1520 instances of potential LGTinvolving P. falciparum. In order to identify the most probable LGT events, we developed a strategy that ranks the probability ofLGT based on the taxonomic consistency of results for sibling species within the tree, and bootstrap support for the relevant internalnode(s). This 'LGTsmart' strategy yields a ranked list of probable lateral gene transfer events (Figure ​(Figure1)1) including 226 high confidence events that occurred at different times during the course of apicomplexan evolution. Many of these transfers involve genes exhibiting phylogenetic affinity with plants, consistent with the algal origin of the apicoplast endosymbiont. Additional, more recent, transfers appear to have a bacterial origin, and both classes of genes include promising targets for drug development. Interestingly, we also detected LGT of metazoan-like genes, possibly acquired through interaction with the host during adaptation to the parasitic lifestyle. Figure 1 Probable source of transfer events identified by the LGT smart algorithm. Parentheses indicate possible LGT events for each source clade; bold indicates high confidence transfers.

Genome Size Variation and Species Relationships in Hieracium Sub-genus Pilosella (Asteraceae) as Inferred by Flow Cytometry

Hieracium sub-genus Pilosella (hawkweeds) is a taxonomically complicated group of vascular plants, the structure of which is substantially influenced by frequent interspecific hybridization and polyploidization. Two kinds of species, 'basic' and 'intermediate' (i.e. hybridogenous), are usually recognized. In this study, genome size variation was investigated in a representative set of Central European hawkweeds in order to assess the value of such a data set for species delineation and inference of evolutionary relationships. Holoploid and monoploid genome sizes (C- and Cx-values) were determined using propidium iodide flow cytometry for 376 homogeneously cultivated individuals of Hieracium sub-genus Pilosella, including 24 species (271 individuals), five recent natural hybrids (seven individuals) and experimental F(1) hybrids from four parental combinations (98 individuals). Chromosome counts were available for more than half of the plant accessions. Base composition (proportion of AT/GC bases) was cytometrically estimated in 73 individuals. Seven different ploidy levels (2x-8x) were detected, with intraspecific ploidy polymorphism (up to four different cytotypes) occurring in 11 wild species. Mean 2C-values varied approx. 4.3-fold from 3.53 pg in diploid H. hoppeanum to 15.30 pg in octoploid H. brachiatum. 1Cx-values ranged from 1.72 pg in H. pilosella to 2.16 pg in H. echioides (1.26-fold). The DNA content of (high) polyploids was usually proportional to the DNA values of their diploid/low polyploid counterparts, indicating lack of processes altering genome size (i.e. genome down-sizing). Most species showed constant nuclear DNA amounts, exceptions being three hybridogenous taxa, in which introgressive hybridization was suggested as a presumable trigger for genome size variation. Monoploid genome sizes of hybridogenous species were always between the corresponding values of their putative parents. In addition, there was a good congruency between actual DNA estimates and theoretical values inferred from putative parental combinations and between DNA values of experimental F(1) hybrids and corresponding established hybridogenous taxa. Significant differences in genome size between hawkweed species from hybridogenous lineages involving the small-genome H. pilosella document the usefulness of nuclear DNA content as a supportive marker for reliable delineation of several of the most problematic taxa in Hieracium sub-genus Pilosella (including classification of borderline morphotypes). In addition, genome size data were shown to have a good predictive value for inferring evolutionary relationships and genome constitution (i.e. putative parental combinations) in hybridogenous species.

Genetic relationships among Arachis hypogaea L. (AABB) and diploid Arachis species with AA and BB genomes

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid, with two types of genomes, classified as AA and BB, according to cytogenetic characters. Similar genomes to those of A. hypogaea are found in the wild diploid species of section Arachis, which is one of the nine Arachis sections. The wild species have resistances to pests and diseases that affect the cultivated peanut and are a potential source of genes to increase the resistance levels in peanut. The aim of this study was to analyze the genetic variability within AA and BB genome species and to evaluate how they are related to each other and to A. hypogaea, using RAPD markers. Eighty-seven polymorphic bands amplified by ten 10-mer primers were analyzed. The species were divided into two major groups, and the AA and the BB genome species were, in general, separated from each other. The results showed that high variation is available within species that have genomes similar to the AA and the BB genomes of A. hypogaea.

A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza

AbstractTo systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylo‐genetic branch. Ninety‐four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments.

An integrated molecular linkage map of diploid wheat based on a Triticum boeoticum × T. monococcum RIL population

Diploid A genome species of wheat harbour immense variability for biotic stresses and productivity traits, and these could be transferred efficiently to hexaploid wheat through marker assisted selection, provided the target genes are tagged at diploid level first. Here we report an integrated molecular linkage map of A genome diploid wheat based on 93 recombinant inbred lines (RILs) derived from Triticum boeoticum x Triticum monococcum inter sub-specific cross. The parental lines were analysed with 306 simple sequence repeat (SSR) and 194 RFLP markers, including 66 bin mapped ESTs. Out of 306 SSRs tested for polymorphism, 74 (24.2%) did not show amplification (null) in both the parents. Overall, 171 (73.7%) of the 232 remaining SSR and 98 (50.5%) of the 194 RFLP markers were polymorphic. Both A and D genome specific SSR markers showed similar transferability to A genome of diploid wheat species. The 176 polymorphic markers, that were assayed on a set of 93 RILs, yielded 188 polymorphic loci and 177 of these as well as two additional morphological traits mapped on seven linkage groups with a total map length of 1,262 cM, which is longer than most of the available A genome linkage maps in diploid and hexaploid wheat. About 58 loci showed distorted segregation with majority of these mapping on chromosome 2A(m). With a few exceptions, the position and order of the markers was similar to the ones in other maps of the wheat A genome. Chromosome 1A(m) of T. monococcum and T. boeoticum showed a small paracentric inversion relative to the A genome of hexaploid wheat. The described linkage map could be useful for gene tagging, marker assisted gene introgression from diploid into hexaploid wheat as well as for map based cloning of genes from diploid A genome species and orthologous genes from hexaploid wheat.

Molecular phylogeny of the genus Triticum L

The genus Triticum L. includes the major cereal crop, common or bread wheat (hexaploid Triticum aestivum L.), and other important cultivated species. Here, we conducted a phylogenetic analysis of all known wheat species and the closely related Aegilops species. This analysis was based on chloroplast matK gene comparison along with trnL intron sequences of some species. Polyploid wheat species are successfully divided only into two groups – Emmer (sections Dicoccoides and Triticum) and Timopheevii (section Timopheevii). Results reveal strictly maternal plastid inheritance of synthetic wheat amphiploids included in the study. A concordance of chloroplast origin with the definite nuclear genomes of polyploid species that were inherited at the last hybridization events was found. Our analysis suggests that there were two ancestral representatives of Aegilops speltoides Tausch that participated in the speciation of polyploid wheats with B and G genome in their genome composition. However, G genome species are younger in evolution than ones with B genome. B genome-specific PCR primers were developed for amplification of Acc-1 gene.

Simple sequence repeats reveal uneven distribution of genetic diversity in chloroplast genomes of Brassica oleracea L. and (n = 9) wild relatives

Diversity in the chloroplast genome of 171 accessions representing the Brassica 'C' (n = 9) genome, including domesticated and wild B. oleracea and nine inter-fertile related wild species, was investigated using six chloroplast SSR (microsatellite) markers. The lack of diversity detected among 105 cultivated and wild accessions of B. oleracea contrasted starkly with that found within its wild relatives. The vast majority of B. oleracea accessions shared a single haplotype, whereas as many as six haplotypes were detected in two wild species, B. villosa Biv. and B. cretica Lam.. The SSRs proved to be highly polymorphic across haplotypes, with calculated genetic diversity values (H) of 0.23-0.87. In total, 23 different haplotypes were detected in C genome species, with an additional five haplotypes detected in B. rapa L. (A genome n = 10) and another in B. nigra L. (B genome, n = 8). The low chloroplast diversity of B. oleracea is not suggestive of multiple domestication events. The predominant B. oleracea haplotype was also common in B. incana Ten. and present in low frequencies in B. villosa, B. macrocarpa Guss, B. rupestris Raf. and B. cretica. The chloroplast SSRs reveal a wealth of diversity within wild Brassica species that will facilitate further evolutionary and phylogeographic studies of this important crop genus.

Molecular Mapping of a Pollen Killer Gene S29(t) in Oryza Glaberrima and Co-Linear Analysis with S22 in O. Glumaepatula

Two species in genus Oryza, O. glaberrima and O. glumaepatula, are valuable and potential sources of useful genes of interest for rice improvement. However, the hybrid sterility between O. sativa and these two species is a main reproduction barrier when transferring the favorable traits/genes to mbox{O. sativa.} To overcome it, the nature of hybrid sterility should be understood further. The objective in the report is to map a new hybrid sterility gene as a Mendelian factor from O. glaberrima and analyze the co-linear of hybrid sterility S loci mbox{between} mbox{O. glaberrima} and mbox{O. glumaepatula} via comparative mapping approach. A BC2F2 population, derived from a single semi-sterility plant of BC2F1 of WAB56-104/ WAB450-11-1-2-P41-HB (WAB450-6) //WAB56-104///WAB56-104 was employed to map this pollen killer in O. glaberrima since WAB450-6 is a progeny of interspecific hybrid between O. sativa and O. glaberrima. A new pollen killer locus, S29(t) in O. glaberrima, was identified and mapped to interval between SSR marker RM7033 (1.1 cM) and RM7562 (1.3 cM) on rice chromosome 2. Comparative mapping indicated that S29(t) closely corresponded to S22 which is also a pollen killer gene in O. glumaepatula and is tightly linked with RFLP marker S910 on the short arm of rice chromosome 2. The good co-linear between S29(t) and S22 implied that there might exist common (orthologous) hybrid sterility loci controlled the reproduction barrier among AA genome species of genus Oryza, which will contribute significantly to our understanding of speciation and operation of hybrid sterility between O. sativa and its AA genome relatives.

High-frequency Ds remobilization over multiple generations in barley facilitates gene tagging in large genome cereals

Transposable elements have certain advantages over other approaches for identifying and determining gene function in large genome cereals. Different strategies have been used to exploit the maize Activator/dissociation (Ac/Ds) transposon system for functional genomics in heterologous species. Either large numbers of independent Ds insertion lines or transposants (TNPs) are generated and screened phenotypically, or smaller numbers of TNPs are produced, Ds locations mapped and remobilized for localized gene targeting. It is imperative to characterize key features of the system in order to utilize the latter strategy, which is more feasible in large genome cereals like barley and wheat. In barley, we generated greater than 100 single-copy Ds TNPs and determined remobilization frequencies of primary, secondary, and tertiary TNPs with intact terminal inverted repeats (TIRs); frequencies ranged from 11.8 to 17.1%. In 16% of TNPs that had damaged TIRs no transposition was detected among progeny of crosses using those TNPs as parental lines. In half of the greater than 100 TNP lines, the nature of flanking sequences and status of the 11 bp TIRs and 8-bp direct repeats were determined. BLAST searches using a gene prediction program revealed that 86% of TNP flanking sequences matched either known or putative genes, indicating preferential Ds insertion into genic regions, critical in large genome species. Observed remobilization frequencies of primary, secondary, tertiary, and quaternary TNPs, coupled with the tendency for localized Ds transposition, validates a saturation mutagenesis approach using Ds to tag and characterize genes linked to Ds in large genome cereals like barley and wheat.

Aegilops kotschyi and Aegilops tauschii as sources for higher levels of grain Iron and Zinc

AbstractMicronutrient malnutrition affects a very large proportion of the world's population. For combating micronutrient malnutrition, biofortification through genetic manipulation has been proposed as an alternative to traditional fortification for increasing the bioavailable nutrient content of food crops. Wheat, being a staple food for a large section of the world's population, is targeted for increasing the Fe and Zn content in the grains. The cultivated germplasm of wheat does not have sufficient variability for grain Fe and Zn content but the wild species of wheat do show wider variation for grain micronutrient density. The analysis of Aegilops kotschyi and A. tauschii for Fe and Zn content in the grains using an atomic absorption spectrophotometer (AAS) indicated that the S and D genome species accumulate significantly higher iron and zinc in the grains than the cultivated wheats. One of the CIMMYT synthetics also had significantly higher Fe and Zn in the grains as compared with the cultivated wheats. Aegilops kotschyi as a promising source for Fe and Zn, is reported for the first time. A systematic programme to identify and utilize the additional sources for high Fe and Zn has been initiated.

Accumulation of genome‐specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton

Gene expression during the early stages of fiber cell development and in allopolyploid crops is poorly understood. Here we report computational and expression analyses of 32 789 high-quality ESTs derived from Gossypium hirsutum L. Texas Marker-1 (TM-1) immature ovules (GH_TMO). The ESTs were assembled into 8540 unique sequences including 4036 tentative consensus sequences (TCs) and 4504 singletons, representing approximately 15% of the unique sequences in the cotton EST collection. Compared with approximately 178 000 existing ESTs derived from elongating fibers and non-fiber tissues, GH_TMO ESTs showed a significant increase in the percentage of genes encoding putative transcription factors such as MYB and WRKY and genes encoding predicted proteins involved in auxin, brassinosteroid (BR), gibberellic acid (GA), abscisic acid (ABA) and ethylene signaling pathways. Cotton homologs related to MIXTA, MYB5, GL2 and eight genes in the auxin, BR, GA and ethylene pathways were induced during fiber cell initiation but repressed in the naked seed mutant (N1N1) that is impaired in fiber formation. The data agree with the known roles of MYB and WRKY transcription factors in Arabidopsis leaf trichome development and the well-documented phytohormonal effects on fiber cell development in immature cotton ovules cultured in vitro. Moreover, the phytohormonal pathway-related genes were induced prior to the activation of MYB-like genes, suggesting an important role of phytohormones in cell fate determination. Significantly, AA sub-genome ESTs of all functional classifications including cell-cycle control and transcription factor activity were selectively enriched in G. hirsutum L., an allotetraploid derived from polyploidization between AA and DD genome species, a result consistent with the production of long lint fibers in AA genome species. These results suggest general roles for genome-specific, phytohormonal and transcriptional gene regulation during the early stages of fiber cell development in cotton allopolyploids.

Usefulness of SSR Derived from Tetraploid Gossypium spp. for Analyses of Diploid Gossypium spp.

This investigation is the first attempt to utilize tetraploid species-derived primers to generate markers for mapping in diploid cotton species. About 113 individual F2 plants, developed from the cross between Gossypium nelsoni and G. australe, were used to construct a linkage map. One allotetraploid (ADj) G. hirsutum (TM-1) plant and its putative diploid ancestors, G. arboreum (A2) and G. raimondii (D5), were also included for comparative analysis. We developed a high-throughput multi-mix PCR assay for simple sequence repeat (SSR) marker separation using fluorescent-labeled capillary electrophoresis. Of a total of 205 tetraploid-derived SSR primers, 83% amplified in all four diploid species, indicating that flanking primer sequences are conserved in the diploid and tetraploid ADj genome of cotton. DNA sequence information of 18 randomly selected clones revealed that all of the clones contained SSR repeat motifs in the diploid species, suggesting that SSR markers including the flanking primer sequences have been conserved at the inter-specific level in genomic DNA across years of evolution. About 85% of the amplified primers showed polymorphism among the diploid genome species. Forty percent of SSRs in the diploid G. nelsoni and 35% in G. australe amplified the same size DNA fragment as in the tetraploid, (TM-1). This is further evidence that many of the tetraploid SSRs are conserved across diploid and tetraploid species. G. nelsoni compared with G. australe had more conserved genomic regions in common with G. hirsutum. From 73 markers scored in the F2 population, 50 exhibited codominance and 23 dominance. There were 47 markers linked across 10 linkage groups covering a total map distance of 754 cM with an average of 16 cM per marker. One linkage group (lg-3) with six loci has been assigned to chromosome 20. Comparative analysis of DNA sequences between G. hirsutum and its two putative parental diploid species indicated that changes within a few selected clones have occurred during evolution as follows: (1) by increasing or decreasing the number of the repeat motif, (2) by single nucleotide mutations occurring within or outside of the repeat motif, (3) by inter conversion of a simple to a compound SSR motif, and (4) by inversion of the repeat regions. Tetraploid-derived microsatellites should be useful in comparative genetic mapping of both tetraploid and diploid Gossypium species for evolutionary studies and introgression of agriculturally important traits from exotic diploid and tetraploid germplasm sources.

Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos

Microsatellite (SSR) markers can reveal a high level of polymorphic loci, and are increasingly being used in population genetic structure studies. On the Vientiane plain of Laos all components of the rice crop complex exist, wild annual (O. nivara), wild perennial (O. rufipogon) and weedy relatives of rice as well as rice itself. To understand gene flow in the rice complex, the genetic structures of O. rufipogon (10 populations), O. nivara (10 populations) and O. sativa (24 samples) from across the Vientiane Plain, Laos, were compared. Higher genetic differentiation was detected among O. nivara populations (G ST = 0.77, R ST = 0.71) than O. rufipogon populations (G ST = 0.29, R ST = 0.28), whereas genetic diversity for all populations of these two wild species showed similar values (H T = 0.77 and 0.64 in O. rufipogon and O. nivara, respectively). Based on neighbor-joining tree constructed on the basis of genetic distance (D A), three genetic clusters were detected, corresponding to (1) O. sativa samples, (2) O. nivara populations and (3) O. rufipogon populations. Pairwise tests confirmed the genetic differentiation of the three species. Although none of the wild rice individuals used in this study had any cultivated-specific phenotypic traits, genetic admixture analysis detected more than 10% O. sativa membership in three O. rufipogon and one O. nivara populations, indicating that O. sativa alleles may cryptically persist in natural populations of O. rufipogon and O. nivara on the Vientiane Plain.