DNA Marker Data Research Articles

Naked barley: taxonomy, breeding, and prospects of utilization.

This review surveys the current state of taxonomy, origin, and utilization prospects for naked barley. The cultivated barley Hordeum vulgare L. incorporates the covered and naked barley groups. Naked barleys are divided into six-row naked barley (convar. сoeleste (L.) A. Trof.) and two-row naked barley (convar. nudum (L.) A. Trof.). The groups include botanical varieties differing in the structural features of spikes, awns, floret and spikelet glumes, and the color of kernels. The centers of morphogenesis for naked barley are scrutinized employing archeological and paleoethnobotanical data, and the diversity of its forms. Hypotheses on the centers of its origin are discussed using DNA marker data. The main areas of its cultivation are shown, along with possible reasons for such a predominating or exclusive distribution of naked barley in highland areas. Inheritance of nakedness and mechanisms of its manifestation are considered in the context of new data in genetics. The biochemical composition of barley grain in protein, some essential and nonessential amino acids, β-glucans, vitamins, and antioxidants is described. Naked barley is shown to be a valuable source of unique combinations of soluble and insoluble dietary fibers and polysaccharides. The parameters limiting wider distribution of naked barley over the world are emphasized, and breeding efforts that could mitigate them are proposed. Pathogen-resistant naked barley accessions are identified to serve as promising sources for increasing grain yield and quality. Main stages and trends of naked barley breeding are considered and the importance of the VIR global germplasm collection as the richest repository of genetic material for the development of breeding is shown.

Developing genomic selection for dry matter yield in white clover

Genomic selection (GS) integrates DNA marker and trait data to develop a model that enables prediction of trait performance (genomic-estimated breeding values; GEBVs) based on genotype data alone. GS has been shown to improve the efficiency and effectiveness of breeding programmes, especially for complex traits such dry matter yield (DMY). DMY data were generated from a training population of 200 white clover half-sibling (HS) families assessed in multi-location field trials for two years. We generated a GS prediction model after integrating genotyping-by-sequencing marker data from parents of the HS families with the HS DMY data. We then compared two selection strategies: a conventional method where individuals were chosen randomly from the phenotypically top-ranked HS families (HSP); and another where GEBVs were used to select the best individual from the top-ranked HS families (APWFGS). The mean predicted DMY GEBVs of the selected plants, as well as the predicted response to selection, were compared with those of the base population. This study showed that, compared with conventional selection (HSP), incorporating genomic selection (APWGSHS) is predicted to double the increase in DMY and response to selection relative to the base population. Synthetic populations based on these selections have been generated and will be tested in a field trial to determine empirically the impact of genomic selection for a complex trait.

Applications of Quantitative Genetics and Statistical Analyses in Sugarcane Breeding

Sugarcane breeding programs aim to deliver new high-yielding varieties, resistant to diseases and pests, which contribute to profitability and sustainability of cane industries. These programs generally mobilize significant experimental, technological and human resources on long-term basis. Their efficiency in terms of genetic gains per unit of cost and time and their ability to release new varieties rely on the development of many breeding applications based on quantitative genetics theory and on statistical analyses of numerous experimental data from selection schemes including DNA marker data developed for some genomic breeding applications. New methodological approaches and new technologies that might better guide and support breeding research in cultivars development programs are continually sought. This paper presents an overview of the main applications developed in statistical methodology in support of the efficiency of sugarcane breeding programs. For each type of application, its conceptual and methodological framework is presented. Implementation issues are reviewed as well as the main scientific and practical achievements so far obtained.

Identification of Prospective Soybean Accessions for the Creation of a Genebank Core Collection Based on High Density DNA Marker Data

Genebanks typically collect and conserve as many existing genetic variations as possible. However, a smaller core population that is representative of the whole collection but maintains as much diversity as possible is more practical for in-depth phenotypic characterization, genetic studies, and plant breeding. Here we describe genotype-based core collection development from USDA soybean germplasm collection, which contains 20,095 accessions that had been genotyped using 50,000 single nucleotide polymorphism DNA markers. Analysis using trimmed marker data and Core Hunter 3 software identified 382 accessions with maximum genetic distances from each other. Population structure analysis of the selected accessions indicated that the software favored admixed individuals instead of those with pure ancestor population genotypes. Allele frequencies of most markers are largely conserved in the core population, which indicates successful maintenance of alleles in the core population. Phenotypic variations for branch number and yield were largely similar to the original population, but slightly different for seed weight and maturity, where very high seed weight and high-latitude maturity groups were less prominent in the core collection. The resulting core population can be used as a base population for any institutions interested in utilizing worldwide soybean genetic diversity for breeding and genetic studies.

‘ND Pegasus’, a new great northern bean with upright plant architecture and high seed yield

Abstract‘ND Pegasus’ great northern bean (PVP‐201900176, Reg. no. CV‐328, PI 690448) is a new cultivar developed by the dry bean breeding program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Great northern bean is a market class of significant economic importance in the United States. In North Dakota especially, biotic and abiotic stresses are the main factors for seed yield reductions. Between 2013 and 2018, ND Pegasus, along with great northern cultivars commonly grown in the region, was tested across more than 35 environments in North Dakota and other states. Seed yield of ND Pegasus was significantly higher by 560, 414, and 571 kg ha‐1 compared with ‘Matterhorn’, ‘Aries’, and ‘Powderhorn’, respectively. However, seed yield of ND Pegasus and ‘Taurus’ were similar. ND Pegasus has an excellent upright architecture that improves the efficiency of direct harvest. Based on greenhouse and DNA marker data, ND Pegasus is resistant to Bean common mosaic virus and has improved resistance to white mold. ND Pegasus has excellent seed quality (color, shape, and size) and is larger than most commercial cultivars commonly grown in the region. ND Pegasus has acceptable canning quality based on some pilot testing. The average plant height of ND Pegasus is 71 cm, and 100‐seed weight 36.8 g. It matures in approximately 103 d. Other agronomic traits of economic importance are within commercial acceptable ranges.

Revision of the Mesobuthus caucasicus complex from Central Asia, with descriptions of six new species (Scorpiones: Buthidae)

A widespread Mesobuthus caucasicus complex, which includes some of the most common scorpions found from the Caucasus to China, is revised for the first time based on new extensive collections from Central Asia, using both morphological and DNA marker data. Mesobuthus caucasicus (Nordmann, 1840), s.str. is restricted to the Caucasus Mts. Four taxa are elevated to species rank: M. fuscus (Birula, 1897) (Tajikistan), M. intermedius (Birula, 1897) (Tajikistan), M. kaznakovi (Birula, 1904) (Tajikistan, Uzbekistan), and M. parthorum (Pocock, 1889) (Afghanistan, Iran, Turkmenistan). Six new species are described: M. brutus sp. n. (Iran), M. elenae sp. n. (Tajikistan, Uzbekistan), M. gorelovi sp. n. (Kazakhstan, Turkmenistan, Uzbekistan), M. kreuzbergi sp. n. (Tajikistan, Uzbekistan), M. mischi sp. n. (Afghanistan), and M. nenilini sp. n. (Uzbekistan). The most common species in Central Asia is a psammophilic Mesobuthus gorelovi sp. n., widespread through lowland sand deserts across Turkmenistan (Karakum), Uzbekistan (Kizylkum), and Kazakhstan (north to Baigakum and Moyinkum). A key to all studied species is provided. A DNA phylogeny based on COI and 16S rRNA markers is presented including nine Central Asian species (M. elenae sp. n., M. fuscus, M. gorelovi sp. n., M. intermedius, M. kaznakovi, M. kreuzbergi sp. n., M. mischi sp. n., M. nenilini sp. n., and M. parthorum) and M. caucasicus from Turkey. A deep phylogenetic diversity across Central Asia is revealed. Historical biogeographic scenarios for this scorpion group are discussed, including fragmentation in mountain valleys and expansion across sand deserts in Central Asia. The monotypic scorpion genus Afghanobuthus Lourenco, 2005 and its single species A. naumanni Lourenco, 2005, from Afghanistan, are demonstrated to be junior synonyms, respectively, of Mesobuthus Vachon, 1950, and M. parthorum (Pocock, 1889) from the same area.

Evolutionary relations and population differentiation of Acipenser gueldenstaedtii Brandt, Acipenser persicus Borodin, and Acipenser baerii Brandt

Russian ( Acipenser gueldenstaedtii), Persian ( A. persicus) and Siberian ( A. baerii) sturgeons are closely related ‘Ponto-Caspian’ species. Investigation of their population structure is an important problem, the solution of which determines measures for conservation of these species. According to previous studies, ‘baerii-like’ mitochondrial genotypes were found in the Caspian Sea among 35% of Russian sturgeon specimens, but were not found in Persian sturgeons. This confirms genetic isolation of the Persian sturgeon from the Russian sturgeon in the Caspian Sea. However, in order to clarify the relationships of these species it is necessary to analyze nuclear DNA markers. The amplified fragment length polymorphism (method) allows estimating interpopulation and interspecific genetic distances using nuclear DNA markers. In the present study, four samples were compared: Persian sturgeons from the South Caspian Sea, Russian sturgeons from the Caspian Sea and the Sea of Azov, and Siberian sturgeons from the Ob’ River, which are close to the latter two species, but are also clearly morphologically and genetically distinct from them. For the amplified fragment length polymorphism (AFLP) method, eight pairs of selective primers were used. The analysis revealed that the Siberian sturgeon has formed a separate branch from the overall Persian-Russian sturgeons cluster, which was an expected result. In addition, the results showed that the Caspian Russian sturgeon is closer to the Persian sturgeon from the Caspian Sea than to the Russian Sturgeon from the Sea of Azov. The present DNA marker data confirm that despite the genetic isolation of the Persian sturgeon from the Russian sturgeon in the Caspian Sea, the Persian sturgeon is a young species.

Evolutionary relations and population differentiation of Acipenser gueldenstaedtii Brandt, Acipenser persicus Borodin, and Acipenser baerii Brandt

Russian ( Acipenser gueldenstaedtii), Persian ( A. persicus) and Siberian ( A. baerii) sturgeons are closely related ‘Ponto-Caspian’ species. Investigation of their population structure is an important problem, the solution of which determines measures for conservation of these species. According to previous studies, ‘baerii-like’ mitochondrial genotypes were found in the Caspian Sea among 35% of Russian sturgeon specimens, but were not found in Persian sturgeons. This confirms genetic isolation of the Persian sturgeon from the Russian sturgeon in the Caspian Sea. However, in order to clarify the relationships of these species it is necessary to analyze nuclear DNA markers. The amplified fragment length polymorphism (method) allows estimating interpopulation and interspecific genetic distances using nuclear DNA markers. In the present study, four samples were compared: Persian sturgeons from the South Caspian Sea, Russian sturgeons from the Caspian Sea and the Sea of Azov, and Siberian sturgeons from the Ob’ River, which are close to the latter two species, but are also clearly morphologically and genetically distinct from them. For the amplified fragment length polymorphism (AFLP) method, eight pairs of selective primers were used. The analysis revealed that the Siberian sturgeon has formed a separate branch from the overall Persian-Russian sturgeons cluster, which was an expected result. In addition, the results showed that the Caspian Russian sturgeon is closer to the Persian sturgeon from the Caspian Sea than to the Russian Sturgeon from the Sea of Azov. The present DNA marker data confirm that despite the genetic isolation of the Persian sturgeon from the Russian sturgeon in the Caspian Sea, the Persian sturgeon is a young species.

Evolutionary relations and population differentiation of Acipenser gueldenstaedtii Brandt, Acipenser persicus Borodin, and Acipenser baerii Brandt.

Russian ( Acipenser gueldenstaedtii), Persian ( A. persicus) and Siberian ( A. baerii) sturgeons are closely related 'Ponto-Caspian' species. Investigation of their population structure is an important problem, the solution of which determines measures for conservation of these species. According to previous studies, 'baerii-like' mitotypes were found in the Caspian Sea among 35% of Russian sturgeon specimens, but were not found in Persian sturgeons. This confirms genetic isolation of the Persian sturgeon from the Russian sturgeon in the Caspian Sea. However, in order to clarify the relationships of these species it is necessary to analyze nuclear DNA markers. The amplified fragment length polymorphism (method) allows estimating interpopulation and interspecific genetic distances using nuclear DNA markers. In the present study, four samples were compared: Persian sturgeons from the South Caspian Sea, Russian sturgeons from the Caspian Sea and the Sea of Azov, and Siberian sturgeons from the Ob' River, which are close to these two species, but are also clearly morphologically and genetically distinct from them. For the AFLP method, eight pairs of selective primers were used. The analysis revealed that the Siberian sturgeon has formed a separate branch from the overall Persian-Russian sturgeons cluster, which was an expected result. In addition, the results showed that the Caspian Russian sturgeon is closer to the Persian sturgeon from the Caspian Sea than to the Russian Sturgeon from the Sea of Azov. The present DNA marker data confirm that despite the genetic isolation of the Persian sturgeon from the Russian sturgeon in the Caspian Sea, the Persian sturgeon is a young species.

Kinship and inbreeding estimates based on microsatellite markers in breeding of Japanese pear (Pyrus pyrifolia Nakai)

The degree of inbreeding should ideally be determined across the entire genome, but is instead widely measured using the pedigree-based coefficients of kinship (f) for pairs of individuals and of inbreeding (F) for individuals. For fruit trees, this biases the estimates for pairs of cross-parents and crossbred accessions, because f and F do not account for any latent kinship among the parents, particularly when these are local cultivars. Local cultivars are often important genetic resources but usually have an unknown pedigree. Several estimators have been developed for estimating kinship and inbreeding from DNA marker data. Among these, we selected the kinship estimator of Wang (Genet Res 89: 135; 2007) and the inbreeding estimator of Leutenegger et al. (Am J Hum Genet 73: 516; 2003), using 207 simple sequence repeat markers in 73 Japanese pear (Pyrus pyrifolia Nakai) and 3 Chinese pear (Pyrus ussuriensis Maxim.) accessions with high potential as cross-parents in breeding of Japanese pear. Pedigree-based coefficients calculated from accessions with all known great-grandparents were used to compare the performance (measured by root mean square errors and correlations) of the estimators. Most marker kinship estimates matched the expected values for parent–offspring and full-sibling pairs, and indicated latent inbreeding, especially among accessions with f = 0, including local cultivars. Marker estimators highlighted latent inbreeding early in the breeding program. The data presented here will help breeders identify the degree of inbreeding in breeding populations and avoid inbreeding during crossbreeding of Japanese pear.

Extensive dispersal of Roanoke logperch (Percina rex) inferred from genetic marker data

AbstractThe dispersal ecology of most stream fishes is poorly characterised, complicating conservation efforts for these species. We used microsatellite DNA marker data to characterise dispersal patterns and effective population size (Ne) for a population of Roanoke logperch Percina rex, an endangered darter (Percidae). Juveniles and candidate parents were sampled for 2 years at sites throughout the Roanoke River watershed. Dispersal was inferred via genetic assignment tests (ATs), pedigree reconstruction (PR) and estimation of lifetime dispersal distance under a genetic isolation‐by‐distance model. Estimates of Ne varied from 105 to 1218 individuals, depending on the estimation method. Based on PR, polygamy was frequent in parents of both sexes, with individuals spawning with an average of 2.4 mates. The sample contained 61 half‐sibling pairs, but only one parent–offspring pair and no full‐sib pairs, which limited our ability to discriminate natal dispersal of juveniles from breeding dispersal of their parents between spawning events. Nonetheless, all methods indicated extensive dispersal. The AT indicated unrestricted dispersal among sites ≤15 km apart, while siblings inferred by the PR were captured an average of 14 km and up to 55 km apart. Model‐based estimates of median lifetime dispersal distance (6–24 km, depending on assumptions) bracketed AT and PR estimates, indicating that widely dispersed individuals do, on average, contribute to gene flow. Extensive dispersal of P. rex suggests that darters and other small benthic stream fishes may be unexpectedly mobile. Monitoring and management activities for such populations should encompass entire watersheds to fully capture population dynamics.

Molecular and morphometric analyses reveal discrete grouping of pomegranate (Punica granatum) genebank accessions away from cultivars

Management of germplasm in the field genebanks is greatly assisted by genetic analysis. Estimation of genetic diversity and assessment of genetic relationships among 45 accessions of pomegranate (Punica granatum L.) that included cultivars and germplasm collections were carried out using nine morphometric, 241 ISSR and six SSR markers. The average genetic distance values based on ANOVA sum of squares (Ward) were 3.94 and 5.10 for morphometric and DNA markers respectively. Hierarchical clustering based on genetic distances grouped the accessions into at least three distinct clusters; the two-way clustering showing the contribution of individual markers in genetic grouping. Discrete grouping of field genebank accessions (with IC numbers) away from cultivars was evident based both on quantitative traits data as well as DNA marker data. The findings suggested the possibility of broadening genetic base of cultivated varieties by augmenting the breeding programmes in India with diverse as well as trait- specific pomegranate germplasm.

Isozyme variation and differentiation of morphologically cryptic species in the Brachypodium distachyon complex

Isozyme variation of nine enzymes among three morphologically cryptic species of the Brachypodium distachyon complex was studied with PAGE. Aspartate aminotransferase isozymes AAT-A and AAT-C, aryl alcohol dehydrogenase AAD-B, malate dehydrogenase MDH-A and leucine aminopeptidase LAP-A in the allotetraploid B. hybridum display fixed heterozygosities with codominant expression of homoeozymes corresponding to divergent orthozymes of diploids B. distachyon and B. stacei. The multilocus isozyme genotype inherent to most accessions of B. hybridum combines two divergent multilocus isozyme genotypes characteristic of most accessions of B. distachyon and B. stacei. The maternally inherited chloroplast-encoded RUBISCO isozymes show that B. stacei is a maternal progenitor of B. hybridum, whereas the nuclear-encoded isozymes AAD-B, AAT-A, AAT-C, LAP-A, and MDH-A confirm that B. distachyon is the paternal progenitor. These data provide a new isozyme-based support to the karyological and DNA marker data on the allotetraploid nature of B. hybridum and its origin from diploids B. distachyon and B. stacei.

Genetic diversity of Zimbabwean and exotic flue-cured tobacco varieties based on phenotypic traits and simple sequence repeats

Determination of genetic diversity among Zimbabwean and exotic flue-cured tobacco varieties is important for variety identification and for rational use of germplasm in breeding programs. This research investigated genetic diversity among Zimbabwean and exotic flue-cured tobacco varieties using phenotypic traits and simple sequence repeats markers. A total of twenty eight flue-cured cultivars (sixteen from China, six from Brazil, two from South Africa and four from Zimbabwe) were studied. Phenotypic data for tobacco descriptor traits were collected from a field experiment carried out using standard cultural practices for flue-cured tobacco in Zimbabwe. A sample of fifteen cultivars was genotyped with simple sequence repeats markers. Low levels of diversity were detected among the cultivars using analysis of either phenotypic or DNA marker data. Pair wise genetic similarities ranged from 0.80 to 0.99. Genetic distances determined were all less than 0.4. The study suggests the need for conservation of germplasm used in Zimbabwe to avoid further genetic erosion. Key words: Fingerprinting, genetic erosion, genetic conservation, Nicotiana tabacum.

A novel and efficient strategy for practical identification of tomato (Solanum lycopersicon) varieties using modified RAPD fingerprints

Tomato breeding and variety development have led to the generation of a large number of varieties in many countries worldwide. This has created a growing and urgent need for an improved strategy for genotyping and identification since the traditional methods based on phenotype are growing unreliable. DNA markers could provide distinct benefits in tomato variety identification; however, DNA fingerprint analyses have not made DNA marker data readily usable for identification of varieties in tomato and other crops. A manual cultivar and/or variety identification diagram (MCID) strategy has been developed and has been found to make DNA markers more usable for the identification of genotyped plant individuals. We adopted this strategy, using modified RAPD markers to identify 42 tomato varieties from different geographical origins and seed merchants. All of the varieties were clearly separated and individually identified by reproducible fingerprints of only 6 RAPD primers. The tomato MCID that is generated is usable for the identification of any two or more tomato varieties. In addition, fewer primers can be used to make a distinction between varieties using this approach, since the selected fingerprints from each primer are used after they have been generated. The information in this first version of the tomato MCID can be enriched through identification and incorporation of more varieties and adaptation to other molecular markers in order to provide a more comprehensive tomato variety identification service for the horticultural industry.

The k Partition-Distance Problem

Many applications of data partitioning (clustering) have been well studied in bioinformatics. Consider, for instance, a set N of organisms (elements) based on DNA marker data. A partition divides all elements in N into two or more disjoint clusters that cover all elements, where a cluster contains a non-empty subset of N. Different partitioning algorithms may produce different partitions. To compute the distance and find the consensus partition (also called consensus clustering) between two or more partitions are important and interesting problems that arise frequently in bioinformatics and data mining, in which different distance functions may be considered in different partition algorithms. In this article, we discuss the k partition-distance problem. Given a set of elements N with k partitions of N, the k partition-distance problem is to delete the minimum number of elements from each partition such that all remaining partitions become identical. This problem is NP-complete for general k > 2 partitions, and no algorithms are known at present. We design the first known heuristic and approximation algorithms with performance ratios 2 to solve the k partition-distance problem in O(k · ρ · |N|) time, where ρ is the maximum number of clusters of these k partitions and |N| is the number of elements in N. We also present the first known exact algorithm in O(ℓ · 2(ℓ)·k(2) · |N|(2)) time, where ℓ is the partition-distance of the optimal solution for this problem. Performances of our exact and approximation algorithms in testing the random data with actual sets of organisms based on DNA markers are compared and discussed. Experimental results reveal that our algorithms can improve the computational speed of the exact algorithm for the two partition-distance problem in practice if the maximum number of elements per cluster is less than ρ. From both theoretical and computational points of view, our solutions are at most twice the partition-distance of the optimal solution. A website offering the interactive service of solving the k partition-distance problem using our and previous algorithms is available (see http://mail.tmue.edu.tw/~yhchen/KPDP.html).

Genetic diversity of Pistacia khinjuk Stocks. using RAPD markers and leaf morphological characters

The aim of this research was to study the genetic diversity of Pistacia khinjuk Stocks. and also to reveal the genetic relationships. Leaf morphological characters of 16 genotypes together with Randomly Amplified Polymorphic DNA (RAPD) marker data were used for this purpose. Leaf morphological characters were used for factor analysis, which determined four main factors. Grouping of genotypes by these factors was performed by Ward’s method. Fifteen primers produced a total of 146 fragments, with an average of 9.73 fragments per primer, of which 129 were polymorphic. The unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to RAPD data, genotypes were separated into three groups. The first contained the genotypes with round leaflets. Genotypes with three lanceolate leaflets were located in the second and third groups, respectively. This study revealed that high diversity exists among genotypes of P. khinjuk, like in P. vera. Also it could be postulated that genotypes of P. khinjuk with oblique and lanceolate leaflets are probably descendents of the genotypes with acuminate and roundish leaflets.

Three new teosintes (Zea spp., Poaceae) from México

Teosinte species are the closest relatives of maize and represent an important but increasingly rare genetic resource for maize improvement and the study of evolution by domestication. Three morphologically and ecologically distinct teosinte populations were recently discovered in México. The taxonomic status of these rare and endangered populations was investigated by detailed comparisons to previously characterized wild Zea species. • Three new teosinte populations were compared to known teosinte taxa on the basis of morphological, ecogeographic, cytological, and molecular characteristics. Phenetic and phylogenetic analyses were performed using morphological and molecular data, respectively. • The newly discovered populations are distinct from each other and from other Zea species to represent three new entities based on their unique combinations of morphological, ecological, ploidy, and DNA markers. A perennial diploid population from Nayarit is distinguished by early maturing plants, and having male inflorescences with few tassel branches and long spikelets. A perennial tetraploid population from Michoacán is characterized by tall and late maturing plants, and having male inflorescences with many branches. An annual diploid population from Oaxaca is characterized by having male inflorescences with fewer branches and longer spikelets than those found in the sister taxa Z. luxurians and Z. nicaraguensis, plants with high thermal requirements, and very long seed dormancy. • Evidence from multiple independent sources suggests placement of the three new populations of teosinte as distinct entities within section Luxuriantes of the genus Zea. However, more extensive DNA marker or sequence data are required to resolve the taxonomy of this genus.

Plastid and nuclear DNA marker data support the recognition of four tetraploid marsh orchids (Dactylorhiza majalis s.l., Orchidaceae) in Britain and Ireland, but require their recircumscription

Relationships among allotetraploid marsh orchids collectively assignable to Dactylorhiza majalis s.l. are exceptionally complex because of multiple origins, secondary hybridization with each other, and with their parental lineages, local adaptation, and genomic reorganization processes, all extending through time and space. We sampled 34 populations from Britain and Ireland in an attempt to simultaneously interpret patterns of genetic differentiation within and between populations. The material analysed consisted of 250 individuals that were examined for variation at five nuclear microsatellite loci, internal transcribed spacer (ITS), and plastid DNA. Once integrated, patterns of differentiation in the three molecular data sets show that the British and Irish members of the D. majalis s.l. complex should be assigned to a minimum of four genetically differentiated subgroups of equal status (either species or subspecies), broadly corresponding to the traditional D. majalis ssp. praetermissa, ssp. purpurella, ssp. occidentalis, and ssp. traunsteinerioides. UK plants previously attributed to 'Dactylorhiza lapponica' and given high conservation status have been shown to be genetically identical to ssp. traunsteinerioides. The endemic Hebridean marsh orchid, D. majalis ssp. ebudensis, genetically resembles ssp. traunsteinerioides. Dactylorhiza majalis 'ssp. cambrensis' could readily be accommodated within ssp. purpurella. Together, these observations reinforce a recent assertion that anthocyanin content has been over-weighted in previous morphologically based classifications of Dactylorhiza. Several study populations showed signs of hybridization and introgression with other allotetraploids, or their parental lineages, especially with D. incarnata s.l. However, ssp. praetermissa and ssp. traunsteinerioides were better separated than anticipated: southern populations widely regarded as mixed populations of the two taxa are arguably better treated as containing an unusually narrow-leaved, ecologically specialized form of ssp. praetermissa. Accepting this recircumscription means that the southern margins of the distributions of ssp. purpurella and ssp. traunsteinerioides now coincide, stretching from mid-Wales to the Humber Estuary of Yorkshire, and together indicating a significant genetic transition zone. Plastid haplotype data confirm that ssp. traunsteinerioides and ssp. praetermissa are relatively old polyploids derived from the Continental D. majalis s.l. complex, whereas ssp. purpurella and ssp. occidentalis may have more recent (most likely postglacial) origins within their current distributions. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 107-128. (Less)

RAPD-based assessment of genetic diversity among annual caraway (Carum carvi) populations

For the first time, genetic variability and differentiation among five annual caraway (Carum carvi) populations originating from Tunisia, Germany and Egypt were examined. Random Amplified Polymorphic DNA (RAPD) marker data were obtained and analysed with respect to genetic diversity, population structure and gene flow. Fourteen primers generated a total of 136 discernible and reproducible bands across the analyzed populations, out of which 56 were polymorphic. The UPGMA cluster analysis permitted the discrimination of all the genotypes and their sorting into 3 main groups. Tunisian caraway populations diverged significantly from German and Egyptian ones. Population clustering was made dependently from geographic origin. This has been further explained at the DNA level as we were able to select a set of RAPD fingerprints unique to each of the studied populations. Furthermore, dimensional graph derived from factorial analysis of RAPD frequency data, allowed significant grouping of the genotypes into five sub-plots, representing each one population. Shannon's index values showed that variation ranks between rather than within populations. These results indicated that considerable genetic differences among C. carvi populations were registered.