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PubMed2001

Allozyme analysis of the hybrid origin of Arisaema ehimense (Araceae).

Allozyme diversity was examined in the Japanese jack-in-the pulpit species, Arisaema serratum and A. tosaense, and their putative hybrid species, A. ehimense (all diploid). Arisaeme ehimense contains mostly alleles found in one or both of the putative parent species but few unique alleles, partially supporting the hypothesis that A. ehimense is of hybrid origin from the two species, although the possibility that A. ehimense arose via divergent speciation cannot be excluded. Because only limited information was gained from the survey of allozyme variation, additional taxon-specific markers from A. serratum and A. tosaense are required to test rigorously the hybrid origin of A. ehimense. A phenogram based on allele frequencies suggested that introgression occurs between A. serratum and A. tosaense where these species are sympatric.

Alleles↗
PubMed2006

A Markov chain Monte Carlo method for estimating population mixing using Y-chromosome markers: mixing of the Han people in China.

We present a new approach for estimating mixing between populations based on non-recombining markers, specifically Y-chromosome microsatellites. A Markov chain Monte Carlo (MCMC) Bayesian statistical approach is used to calculate the posterior probability distribution of population parameters of interest, including the effective population size and the time to most recent common ancestor (MRCA). To test whether two populations are homogeneously mixed we introduce a "mixing" statistic defined for each coalescent event that weights the contribution of that ancestor's descendants to the two subpopulations, and an associated population "purity" statistic. Using simulated data with low levels of migration between two populations, we demonstrate that our method is more sensitive than other commonly used distance-based methods such as R(ST) and D(SW). To illustrate our method, we analysed mixing between 11 pre-defined Chinese ethnic/regional populations, using 5 microsatellite markers from the non-recombining region of the Y-chromosome (NRY), demonstrating a significant clustering of a subset of subpopulations with a high mutual relative degree of mixing (homogeneous mixing with support >0.99). Our analysis suggests that there is a strong correlation between effective population size and mixing with other subpopulations. Thus, despite considerable mixing between these groups, the purity statistic still identifies significant heterogeneity, suggesting that periods of historical isolation continue to leave a recoverable signal despite modern introgression.

Asian People↗
PubMed2001

Chloroplast sharing in the Tasmanian eucalypts.

The biogeographic pattern of chloroplast DNA (cpDNA) haplotypes in Eucalyptus on the island of Tasmania is consistent with reticulate evolution, involving at least 12 Tasmanian species from the subgenus Symphyomyrtus. Intraspecific cpDNA polymorphism in 14 of 17 species is coupled with extensive sharing of identical haplotypes across populations of different species in the same geographic area. Haplotype diversity is lowest in central regions of Tasmania formerly occupied by alpine vegetation during glacial intervals and in northern regions that were periodically linked to continental Australia by land bridges. The observed distribution of several cpDNA haplotypes unique to Tasmania coincides with modeled locations of glacial refugia in coastal areas of Tasmania and shows the power of cpDNA in unraveling the complex history of past distributions of Eucalyptus. The results suggest that the model of evolution of the eucalypts should be reassessed to allow for the anastomosing effects of interspecific hybridization and introgression.

Base Sequence↗
PubMed2002

[About the possibility of hybridogenesis in the species origin of the midge Chironomus usenicus Loginova et Beljanina (Chironomidae, Diptera)].

Hybridogenesis as a possible way of speciation in Chironomidae was considered with special reference to the species Chironomus usenicus resulting from hybridization between C. plumosus and C. behningi. The three species had 2n = 8 and belonged to the thummi cytocomplex with chromosome arm combinations AB, CD, EF, and G. Arm G had a marker chromosome disk sequence (CDS) and was used to demonstrate the hybrid origin of C. usenicus. Most C. usenicus larvae were heterozygous in CDS of arm G. CDS use G2 proved to be identical to CDS beh G1 of C. behningi and CDS use G1, to CDS plu G1 of C. plumosus. It was assumed that C. usenicus results from hybridization between eurybiont C. plumosus and stenobiont C. behnigni at the boundary of their species areas, in freshwater or brackish water bodies of the southern Saratov oblast and northern Kazakhstan. Morphologically and karyotypically, the hybrid was probably similar to C. plumosus. Crosses with C. plumosus eliminated virtually all C. behningi chromosome sequences from the karyotype of the hybrid. Further chromosome divergence resulting in C. usenicus involved a number of chromosome rearrangements, including duplication of pericentric heterochromatin and other chromosome regions; inversion, which occurred in arm F (regions 13-16) and was fixed in the karyotype; and other paracentric inversions and deletions accumulated in heterozygote in the karyotype pool of the species. Since C. behningi was eliminated from the introgression zone and its species are reduced, the assimilation character was assumed for introgressive hybridization of C. behningi and C. plumosus.

Animals↗
PubMed2005

Identification of a rice gene (Bph 1) conferring resistance to brown planthopper (Nilaparvata lugens Stal) using STS markers.

This study was carried out to identify a high-resolution marker for a gene conferring resistance to brown planthopper (BPH) biotype 1, using japonica type resistant lines. Bulked segregant analyses were conducted using 520 RAPD primers to identify RAPD fragments linked to the BPH resistance gene. Eleven RAPDs were shown to be polymorphic amplicons between resistant and susceptible progeny. One of these primers, OPE 18, which amplified a 923 bp band tightly linked to resistance, was converted into a sequence-tagged-site (STS) marker. The STS marker, BpE18-3, was easily detectable as a dominant band with tight linkage (3.9cM) to Bph1. It promises to be useful as a marker for assisted selection of resistant progeny in backcross breeding programs to introgress the resistance gene into elite japonica cultivars.

Animals↗
PubMed2000

Dispersion of the Cf-4 disease resistance gene in Lycopersicon germplasm.

In the past, numerous Cf genes have been reported in tomato (Lycopersicon esculentum Mill.) that confer resistance against leaf mould (Cladosporium fulvum Cke.). We are interested in genetic variation at Cf loci. Therefore, previously uncharacterized Cf genes were further analysed. Recognition of the AVR4 elicitor, DNA gel blot analysis, PCR analysis and sequencing of part of the Cf-4 locus showed that a large proportion of the accessions tested harboured the Cf-4 resistance gene. We concluded that despite differences in nomenclature, all these accessions harbour the same Cf-4 locus, probably introgressed from the same donor. The origin of the Cf-4 locus and the reasons for discrepancies with earlier reports are discussed.

Blotting, Southern↗
PubMed2026

Cytonuclear conflict and reticulate evolution in the Morelloid clade (Solanum, Solanaceae): Insights from genome skimming and network Phylogenomics.

The Morelloid clade (black nightshades) is one of the most strongly supported clades within the megadiverse Solanum genus. It comprises 76 globally distributed, non-spiny herbaceous and suffrutescent species. While often erroneously considered poisonous weeds, several species are economically important as orphan crops. The clade is closely related to tomato and potato but, due to a lack of focused breeding efforts, remains a putative reservoir of genetic diversity for crop improvement. Despite this potential, we lack fundamental knowledge on the evolution of the Morelloid clade. The group includes polyploid species with unknown parental origins-likely reflecting reticulate processes such as hybridization, introgression, and associated backcrossing events. Prior analyses have been unable to disentangle these processes, leaving the mechanisms underlying reticulate evolution in the Morelloid clade poorly understood. Here, we use genome skimming to produce a well-supported maximum likelihood plastid phylogeny from complete circularized plastomes and a coalescent-based species tree from combined Angiosperms353 and conserved ortholog set nuclear markers. Our dataset, composed of previously published data and deep genome skimming from herbarium samples, spans 26 Morelloid species. To investigate phylogenetic discordance, we used a nuclear phylogenetic network, multispecies coalescent simulations, a fused rooted nuclear chloroplast tree, and quantification of nuclear gene tree concordance. We show that incongruence between nuclear and plastid trees is pervasive and cannot be explained by incomplete lineage sorting alone. Instead, our results demonstrate that events consistent with repeated chloroplast capture have shaped the reticulate evolutionary history of the clade, especially among African polyploid and Pan-American diploid lineages.

Phylogeny↗
PubMed2004

The development of lettuce backcross inbred lines (BILs) for exploitation of the Lactuca saligna (wild lettuce) germplasm.

Backcross inbred lines (BILs) were developed in which chromosome segments of Lactuca saligna (wild lettuce) were introgressed into L. sativa (lettuce). These lines were developed by four to five backcrosses and one generation of selfing. The first three generations of backcrossing were random. Marker-assisted selection began in the BC(4) generation and continued until the final set of BILs was reached. A set of 28 lines was selected that together contained 96% of the L. saligna genome. Of these lines, 20 had a single homozygous introgression (BILs), four had two homozygous introgressions (doubleBILs) and four lines had a heterozygous single introgression (preBILs). Segregation ratios in backcross generations were compared to distorted segregation ratios in an F(2) population, and the results indicated that most of the distorted segregations can be explained by genetic effects on pollen- or egg-cell fitness. By means of BIL association mapping we were able to map 12 morphological traits and hundreds of additional amplified fragment length polymorphic (AFLP) markers. The total AFLP map now comprises 757 markers. This set of BILs is very useful for future genetic studies.

Chromosome Mapping↗
PubMed2003

A model for chloroplast capture.

Chloroplast capture, the introgression of a chloroplast from one species into another, has been frequently suggested as the explanation for inconsistencies between gene trees based on nuclear and cytoplasmic markers in plants. We use a genetic model to determine the conditions for capture to occur, and we find that they are somewhat more general than those given in earlier verbal arguments. Chloroplast capture can occur if cytoplasm substitution provides an advantage in seed production. This can happen through reallocation to the female function when cytonuclear incompatibilities cause partial male sterility, but also under more general conditions. Capture is promoted by nuclear incompatibilities between the two genomes (or a low heterosis in F1 hybrids) and by partial selfing when hybridization causes a decrease in the selfing rate and inbreeding depression is strong. We discuss empirical predictions that can be used to test this mechanism.

Biological Evolution↗
PubMedDate not supplied

[Polymorphism of Phaseolus vulgaris var. aborigineus (fabaceae). Evidences of natural hibridation].

A polymorphic population of Phaseolus vulgaris var. aborigineus growing at the Northwest of Argentina was studied. In order to know the origin of this polymorphism, some plants belonging to the var. aborigineus, other plants showing floral dimorphism and other individuals with particular characters were collected. Their seeds, obtained after field-work treatments of autogamy and free pollination, were sown in a greenhouse, isolated of the access of pollinators. The growth of each plant was followed until its fructification, and the number of plants that died due to infections was recorded. The number of plants that flowered and fructified was registered in order to study their reproductive success. The floral, fruit and seed qualitative and quantitative characters were documented. With the results obtained, the authors concluded that those individuals that showed floral dimorphism are probably a result of hybridization and introgression between the var. aborigineus and "old cultivars". This hypothesis is supported by the presence of divergent segregation, observed in the offspring of the plants with this segregation. Other crops should allow the genic flow between the parental entities, with the consequence of the establishment of an hybrid population coexistent with their ancestors. Perhaps, as a result of introgression, the stabilized lines exhibit characters different from their parental varieties. The results of autopollination and free pollination in those individuals assigned to var. aborigineus, showed that free pollination brings a great genetic plasticity, because next generations can persist and resist infections. The offspring of the F1 was followed. The plants that belonged to var. aborigineus, product of free pollination, exhibited fast growth and were healthy, while the descendant of the individuals with the floral dimorphism showed characteristics that allowed to conclude the possible existence of degeneration of the hybrid progeny; this characteristics were: curled radicles with cotyledons that never emerge, plantule's apex that soon die with the following development of branches from the cotyledon's axil, and death after some weeks. This degeneration indicates that an unwanted gene flow in the area could lead to a decline in the wild bean population. The vigor, high reproductive success and resistance to illnesses of the individuals corresponding to the var. vulgaris, whose progenitor was treated for free fecundation, and the offspring of the plants with cultivated characteristics, are indicative of the necessity of preserving this germplasm to evaluate its agronomic potential to brief term. The DNA analyses already initiated, will allow the confirmation of the hypotheses outlined in this work.

Argentina↗
PubMed2003

Resistance to rust ( Puccinia psidii Winter) in eucalyptus: mode of inheritance and mapping of a major gene with RAPD markers.

Rust is one of the most-damaging eucalypt diseases in Brazil and is considered a potential threat to eucalypt plantations worldwide. To determine the mode of inheritance of resistance in the Eucalyptus grandis- Puccinia psidii pathosystem, ten full-sib families, generated from crosses between susceptible and resistant trees, were inoculated with a single-pustule isolate of the pathogen and rust severity was scored. The observed segregation ratios in segregating families suggested major gene control of rust resistance, although clearly incomplete penetrance, variable expressivity and minor genes are also involved in the global rust-resistance response. To identify markers linked to the resistance locus, screening of RAPD polymorphisms was conducted using bulked segregant analysis in a large full-sib family. A linkage group was built around the Ppr1 gene ( P. psidii resistance gene 1) encompassing six RAPD markers, with a genetic window spanning 5 cM with the two most-closely linked flanking markers. Besides these two flanking markers, RAPD marker AT9/917 co-segregated with Ppr1 without a single recombinant in 994 meioses. This tightly linked marker should prove useful for marker-assisted introgression and will provide an initial lead for a positional cloning effort of this resistance allele. This is the first report of a disease resistance gene identified in Eucalyptus, and one of the few examples of the involvement of a major gene in a non-coevolved pathosystem.

Basidiomycota↗
PubMed2004

Use of the Serial Analysis of Gene Expression (SAGE) method in veterinary research: A concrete application in the study of the bovine trypanotolerance genetic control.

New postgenomic biotechnologies, such as transcriptome analyses, are now able to characterize the full complement of genes involved in the expression of specific biological functions. One of these is the Serial Analysis of Gene Expression (SAGE) technique, which consists of the construction of transcripts libraries for a quantitative analysis of the entire gene(s) expressed or inactivated at a particular step of cellular activation. Bioinformatic comparisons in the bovine genomic databases allow the identification of several up- and downregulated genes, expressed sequence tags, and unknown functional genes directly involved in the genetic control of the studied biological mechanism. We present and discuss the preliminary results in comparing the expressed genes in two total mRNA transcripts libraries obtained during an experimental Trypanosoma congolense infection in one trypanotolerant N'Dama animal cow. Knowing all the functional genes involved in the trypanotolerance control will permit validation of some results obtained with the quantitative trait locus approach, to set up specific microarrays sets for further metabolic and pharmacological studies, and to design field marker-assisted selection by introgression programs.

Animals↗
PubMed2005

Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length.

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing 15 parameters that reflect fiber length. Applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC(3)F(2) plants from 24 independently derived BC(3) families, we detected 28, nine, and eight quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content, respectively. For eight, six, and two chromosomal regions containing quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content (respectively), two-way analysis of variance showed a significant (P<0.001) among-family genotypic effect. A total of 13, two, and four loci showed genotype x family interaction, illustrating some of the complexities that are likely to be faced in introgression of exotic germplasm into the gene pool of cultivated cotton. Co-location of many QTLs for fiber length, length uniformity, and short fiber content accounted for correlations among these traits, while the discovery of many QTLs unique to each trait suggests that maximum genetic gain will require breeding efforts that target each trait (or an index including all three). The availability of DNA markers linked to G. barbadense QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development.

Analysis of Variance↗
PubMed2006

Late Quaternary climate change and spatial genetic structure in the shrub Banksia hookeriana.

Spatial genetic variation within species is influenced by both contemporary and historical factors. We attempted to assess the impact of increased aridity and lower temperatures associated with the last glacial maximum on possible refugia and the structuring of genetic variation in Banksia hookeriana, a shrub species restricted to deep sands on the Eneabba sandplain and adjacent Gingin Scarp/Dandaragan Plateau, centred 300 km north of Perth, Western Australia. We used optically stimulated luminescence (OSL) dating to estimate the last time these sands were mobile, as well as amplified fragment length polymorphisms (AFLP) to infer spatial patterns and the phylogeographical history of genetic variation among 15 populations of B. hookeriana. While genetic variation at the species level was high, with 96.6% of 238 AFLP markers polymorphic, average within population gene diversity was low (H(pop) = 0.16). Of the total genetic variation, an analysis of molecular variance (amova) partitioned 70% within populations, 24% among populations within substrate and 6% between substrates. There was an isolation-by-distance effect among populations within the same substrate, but not across substrates, and ordination highlighted genetic differentiation between the sandplain and scarp/plateau populations. A neighbour-joining tree identified the sandplain populations as a distinct clade, with the exception of the most northern sandplain population, which clustered with two northern and eastern plateau populations. The most southern plateau populations formed a clade sister to the sandplain clade. OSL dating of sand at six extant populations suggested that dunes were last mobile 15,000-35,000 years ago, with no clear difference in the ages of sandplain and plateau dunes. These data are consistent with a historical scenario of (re)colonization from isolated refugia of smaller populations either within the patchily vegetated sandplain and/or refugia at the northern, eastern and southern sandplain/scarp margins following postglacial climate amelioration and dune stabilization. Historic interpretations were confounded by the possible effects of long-distance dispersal, natural selection by substrate, and weak and/or ancient introgression with the sister species, Banksia prionotes.

Analysis of Variance↗
PubMed1986

The ecological genetics of introduced populations of the giant toad, Bufo marinus. IV. Gene flow estimated from admixture in Australian populations.

Allele frequency variation is described at nine polymorphic enzyme loci in 21 samples from populations of the introduced Giant Toad, Bufo marinus, in the region of Townsville in north Queensland, Australia. Some of these populations appear to have been established through the introgression of other populations that previously had been isolated. Comparisons of allele frequencies at three polymorphic loci between the introgressed populations and the original populations are used to obtain admixture estimates. These are used to estimate a rate of gene flow among the populations of approximately 2 km/year. This is consistent with an estimate based on the rate at which Bufo marinus has colonised new areas in Australia when discontinuities in the pattern of this colonisation are taken into account. The estimate of gene flow is combined with published data on population density to estimate neighbourhood size. The estimate obtained is substantially greater than the effective population size estimate determined previously from data on allele frequency variances in other populations. This discrepancy is most likely due to inaccuracies in the population density estimates, to underestimates of the extent of offspring number variance and perhaps to occasional departures from sex ratio parity. It has important implications for the study of the genetic structure of populations which are discussed.

Alleles↗