Outbreeding species with large, stable population sizes, such as widely distributed conifers, are expected to harbor relatively more DNA sequence polymorphism. Under the neutral theory of molecular evolution, the expected heterozygosity is a function of the product 4N e, where Ne is the effective population size and is the per-generation mutation rate, and the genomic scale of linkage disequilibrium is determined by 4N er, where r is the per-generation recombination rate between adjacent sites. These parameters were estimated in the long-lived, outcrossing gymnosperm loblolly pine (Pinus taeda L.) from a survey of single nucleotide polymorphisms across Ϸ18 kb of DNA distributed among 19 loci from a common set of 32 haploid genomes. Estimates of 4Ne at silent and nonsynonymous sites were 0.00658 and 0.00108, respectively, and both were statistically heterogeneous among loci. By Tajima's D statistic, the site frequency spectrum of no locus was observed to deviate from that predicted by neutral theory. Substantial recombination in the history of the sampled alleles was observed and linkage disequilibrium declined within several kilobases. The composite likelihood estimate of 4N er based on all two-site sample configurations equaled 0.00175. When geological dating, an assumed generation time (25 years), and an estimated divergence from Pinus pinaster Ait. are used, the effective population size of loblolly pine should be 5.6 ؋ 10 5 . The emerging narrow range of estimated silent site heterozygosities (relative to the vast range of population sizes) for humans, Drosophila, maize, and pine parallels the paradox described earlier for allozyme polymorphism and challenges simple equilibrium models of molecular evolution. N ew genetic variation within a species arises solely by the process of mutation. A new neutral variant may be lost rapidly from a population at the rate of one minus its initial frequency. If the new variant is not lost, genetic, demographic, and evolutionary processes, in addition to random genetic drift, determine its population frequency and its nonrandom association with adjacent sites (linkage disequilibrium, LD) along the segment of DNA on which it arose. Recombination is the primary genetic process that erodes LD over time. Therefore, two key parameters in simple population genetic models that govern the amount and distribution of intraspecific sequence variation are the population mutation parameter, ϭ 4N e , and the population recombination parameter, ϭ 4N e r, where N e is the effective population size, is the per-generation, per-base pair mutation rate, and r is the per-generation recombination rate between adjacent sites.Estimates of 4N e can be readily calculated from DNA sequences obtained from population samples, even with relatively small data sets. Watterson's estimate of 4N e as W (1) is based on the number of polymorphic sites in a sample of sequences drawn at random from a population. A second estimate of 4N e is nucleotide diversity, or (2), which is the average number of pairwise n...

BackgroundThe genus Actinidia (kiwifruit) consists of woody, scrambling vines, native to China, and only recently propagated as a commercial crop. All species described are dioecious, but the genetic mechanism for sex-determination is unknown, as is the genetic basis for many of the cluster of characteristics making up the unique fruit. It is, however, an important crop in the New Zealand economy, and a classical breeding program would benefit greatly by knowledge of the trait alleles carried by both female and male parents. The application of marker assisted selection (MAS) in seedling populations would also aid the accurate and efficient development of novel fruit types for the market.ResultsGene-rich female, male and consensus linkage maps of the diploid species A. chinensis have been constructed with 644 microsatellite markers. The maps consist of twenty-nine linkage groups corresponding to the haploid number n = 29. We found that sex-linked sequence characterized amplified region (SCAR) markers and the 'Flower-sex' phenotype consistently mapped to a single linkage group, in a subtelomeric region, in a section of inconsistent marker order. The region also contained markers of expressed genes, some of unknown function. Recombination, assessed by allelic distribution and marker order stability, was, in the remainder of the linkage group, in accordance with other linkage groups. Fully informative markers to other genes in this linkage group identified the comparative linkage group in the female map, where recombination ratios determining marker order were similar to the autosomes.ConclusionWe have created genetic linkage maps that define the 29 linkage groups of the haploid genome, and have revealed the position and extent of the sex-determining locus in A. chinensis. As all Actinidia species are dioecious, we suggest that the sex-determining loci of other Actinidia species will be similar to that region defined in our maps. As the extent of the non-recombining region is limited, our result supports the suggestion that the subtelomeric region of an autosome is in the early stages of developing the characteristics of a sex chromosome. The maps provide a reference of genetic information in Actinidia for use in genetic analysis and breeding programs.

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First results from two strategies aimed at elucidating the genetics of sex in the dioecious genus Actinidia Lindl. (Actinidiaceae) support the hypothesis that sex-determining genes are localized in a pair of chromosomes which, although cytologically indistinguishable, function like an XX/XY system with male heterogamety. A. chinensis Planch., a close relative of the kiwifruit [A. deliciosa (A. Chev.) CF Liang et AR Ferguson], has diploid and tetraploid races. Bulk segregant analysis to find sex-linked markers revealed two markers whose inheritance patterns in three diploid families showed X and Y linkage and indicated that the male is the heterogametic sex. Some recombination between the markers and the sex-determining loci was also demonstrated. Sex ratios in 12 progenies from controlled crosses varied around 1:1, as expected for an XX/XY system. & k w d : Key words Actinidia · Dioecism · Sex determination · Sex markers · Sex ratios& b d y :

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.