Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting peak ratios) method

Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting¿peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships. We report here the application of MAC-PR for the first time to random samples of unknown pedigrees. We analysed six microsatellite loci using a set of tetraploid ornamental rose (Rosa x hybrida L.) varieties. For each locus, all alleles were analysed in pairwise combinations in order to determine their copy number in the individual samples. This was accomplished by calculating the ratios between the peak areas for two alleles in all of the samples where these two alleles occurred together. The allele peak ratios observed were plotted in a histogram, and those histograms that produced at least two well-separated groups were selected for further analysis. Mean allelic peak ratio values for these groups were compared to the relationships expected between alleles in hypothetical configurations of the locus investigated. Using this approach, we were able to assign precise allelic configurations (the actual genotype) to almost all of the varieties analysed for five of the six loci investigated. MAC-PR also appears to be a very effective tool for detecting null alleles in polyploid specie

Sexual preferences linked to rose taxonomy and cytology

The genus Rosa is usually subdivided into four subgenera, the largest of these is subgenus Rosa with 10 sections. Most of the genetically analysed rose species appear to be sexual and diploid (2n = 14) or tetraploid (2n = 28) although there are a few triploid (2n = 21), hexaploid (2n = 42) and octaploid species (2n = 56). The diploid species are usually self-incompatible whereas the polyploids are self-fertile. Pollen stainability is usually high in all species with even ploidy levels, i.e. 2x, 4x or 6x. Rose species are usually sexual and have a regular meiosis but there is one deviating section, Caninae, which harbours the so-called dogroses. Most of these are 5x but there are some taxa with 4x and 6x. Only seven chromosomes (derived from seven bivalents) are transmitted through the pollen grains, whereas egg cells contain 21, 28 or 35 chromosomes (derived from seven bivalents and 14, 21 or 28 univalents) depending on the ploidy level. Apomixis occurs occasionally in the dogroses and genetic selfing is probably common since these taxa are self-fertile. Interspecific hybridization takes place spontaneously among rose species at all ploidy levels and is used as a potent tool in plant breeding. Information about compatibility, breeding system, pollen viability, chromosome number and inheritance is important for optimal utilization of crosses in rose breedin

Isolation and characterization of trinucleotide repeat microsatellite markers for Plutella xylostella L.

Thirteen microsatellite markers generating high quality patterns have been developed and characterized for diamondback moth (Plutella xylostella L.), of which 11 are based on trinucleotide repeats. These markers are polymorphic, generating up to 15 alleles in a test set of 12 caterpillars. The markers will be useful to assess the differentiation of P. xylostella populations and the exchange of pest populations between sites with crops, green manure crops and weed

Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses, Rosa sect.Caninae.

An allopolyploid complex with high genomic integrity has been studied. Dogroses transmit only seven chromosomes (from seven bivalents) through the pollen, whereas 21, 28 or 35 chromosomes (from seven bivalents and 14, 21 or 28 univalents) come from the egg cells. Seedlings derived from two interspecific crosses were analysed with flow cytometry and molecular markers to determine ploidy level, mode of reproduction and genomic constitution. Evidence was obtained for the formation of unreduced male and female gametes, which can take part in fertilization (producing seedlings with higher ploidy than the parental plants) or in apomictic reproduction. Random amplified polymorphic DNA (RAPD) and microsatellite analyses indicated that three seedlings (5%) were derived through apomixis, whereas the other 49 were hybrids. Bivalent formation appears to involve chromosomes that consistently share the same microsatellite alleles. Allele-sharing between the maternally transmitted and highly conserved univalent-forming chromosomes reflected the taxonomic distance between different genotypes. The frequently recombining bivalent-forming chromosomes were taxonomically less informativ

Isolation of polymorphic microsatellite loci from the flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae)

Ten microsatellite markers for the flea beetle Phyllotreta nemorum were developed using di- and trinucleotide repeat-enriched libraries. Each of these primer pairs were characterized on 96 individuals. Expected heterozygosities ranged between 0.11 and 0.84 and the number of alleles ranged between two and 14 per locus. These microsatellite markers are the first published for any Phyllotreta specie

Isolation and characterization of six microsatellite loci in the larch budmoth Zeiraphera diniana (Lepidoptera: Tortricidae)

Six microsatellite markers were developed for the larch budmoth Zeiraphera diniana Guénée 1845, using two enrichment protocols. The number of alleles ranged from 3 to 15 per locus and observed heterozygosities ranged from 0.09 to 0.98 for the 69 individuals genotyped. Using these markers significant genetic differentiation between one population from Poland and samples from Alpine populations in France and Switzerland (overall FST = 0.0298) was detected. However, the two Alpine samples did not differ significantly. These microsatellite markers are valuable tools for studying the population genetics of Zeiraphera diniana

Development of microsatellite markers in Gonystylus bancanus (Ramin) useful for tracing and tracking of wood of this protected species

Ten polymorphic microsatellite markers have been developed for Gonystylus bancanus (Ramin), a protected tree species of peat swamp forests in Malaysia and Indonesia. Eight markers were also shown to be polymorphic in other Gonystylus species. The markers will enable assessing the amount of genetic variation within and among populations and the degree of population differentiation, such that donor populations can be selected for reforestation projects. They may be used for tracing and tracking of wood in the production chain, so that legal trade in this Convention on International Trade in Endangered Species of Wild Fauna and Flora-protected timber species, derived from specifically described origins, can be distinguished from illegally logged timber

Development of microsatellite markers in Gonystylus bancanus (Ramin) useful for tracing and tracking of wood of this protected species

Ten polymorphic microsatellite markers have been developed for Gonystylus bancanus (Ramin), a protected tree species of peat swamp forests in Malaysia and Indonesia. Eight markers were also shown to be polymorphic in other Gonystylus species. The markers will enable assessing the amount of genetic variation within and among populations and the degree of population differentiation, such that donor populations can be selected for reforestation projects. They may be used for tracing and tracking of wood in the production chain, so that legal trade in this Convention on International Trade in Endangered Species of Wild Fauna and Flora-protected timber species, derived from specifically described origins, can be distinguished from illegally logged timber

Genetic diversity and genetic similarities between Iranian rose species

Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified alleles in all species, even if they were from different sections within the genus. An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main Groups. The data showed no support for any distinction between R. canina and R. iberica, as all the accessions were placed in one Group, and accessions of these two species were more closely-related to each other within a Province than to accessions of the same species in other Provinces. Accessions of sect. Pimpinellifoliae were combined with plants from sect. Rosa and Cinnamomeae in two different Groups. Genetically, R. persica clustered distinctly from all others, with few alleles shared with the other taxa. We discuss the use of SSR markers for phylogenetic analysis when these markers are amplified in all species of a genu