A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid

Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.     

Comparative genome mapping among Picea glauca, P. mariana × P. rubens and P. abies, and correspondence with other Pinaceae

A composite linkage map was constructed from four individual maps for the conifer Picea glauca (Moench) Voss, from anonymous and gene-specific markfers (714 AFLPs, 38 SSRs, and 53 ESTPs). A total of 12 linkage groups were delineated with an average marker density of 2.7 cM. Macro-synteny and macro-colinearity comparisons with two other composite linkage maps developed for the species complex P. mariana (Mill.) B.S.P. × P. rubens Sarg., and for P. abies (L.) Karst. revealed an identical number of linkage groups and a remarkable conservation of the gene content and gene order of linkage groups over the million years since the split between these taxa. Identical gene order among taxa was observed for 10 of the 12 assembled composite linkage groups. The discovery of one breakdown in synteny between P. glauca and the other two taxa indicated the occurrence of an inter-chromosomal rearrangement involving an insertional translocation. Analysis of marker colinearity also revealed a putative segmental duplication. The combined information from these three Picea genomes validated and improved large-scale genome comparisons at the inter-generic level in the family Pinaceae by allowing for the identification of 11 homoeologous linkage groups between Picea and Pinus, and nine such groups between Picea and Pseudotsuga menziesii. Notably, the analysis of synteny among the three genera revealed a putative case of chromosomal fission and an inter-chromosomal rearrangement in the genome of P. menziesii. Both of these changes are inter-connected, indicating much instability in this part of the P. menziesii genome. Overall, the macro-structure of the Pinaceae genome was well conserved, which is notable given the Cretaceous origin of its main lineages.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Her Majesty the Queen in Right of Canada.     

A molecular linkage map with associated QTLs from a hulless × covered spring oat population

In spring-type oat (Avena sativa L.), quantitative trait loci (QTLs) detected in adapted populations may have the greatest potential for improving germplasm via marker-assisted selection. An F₆ recombinant inbred (RI) population was developed from a cross between two Canadian spring oat varieties: Terra, a hulless line, and Marion, an elite covered-seeded line. A molecular linkage map was generated using 430 AFLP, RFLP, RAPD, SCAR, and phenotypic markers scored on 101 RI lines. This map was refined by selecting a robust set of 124 framework markers that mapped to 35 linkage groups and contained 35 unlinked loci. One hundred one lines grown in up to 13 field environments in Canada and the United States between 1992 and 1997 were evaluated for 16 agronomic, kernel, and chemical composition traits. QTLs were localized using three detection methods with an experiment-wide error rate of approximately 0.05 for each trait. In total, 34 main-effect QTLs affecting the following traits were identified: heading date, plant height, lodging, visual score, grain yield, kernel weight, milling yield, test weight, thin and plump kernels, groat -glucan concentration, oil concentration, and protein. Several of these correspond to QTLs in homologous or homoeologous regions reported in other oat QTL studies. Twenty-four QTL-by-environment interactions and three epistatic interactions were also detected. The locus controlling the covered/hulless character (N1) affected most of the traits measured in this study. Additive QTL models with N1 as a covariate were superior to models based on separate covered and hulless sub-populations. This approach is recommended for other populations segregating for major genes. Marker-trait associations identified in this study have considerable potential for use in marker-assisted selection strategies to improve traits within spring oat breeding programs.Communicated by P. Langridge     

A linkage map of chickpea (Cicer arietinum L.) based on populations from Kabuli × Desi crosses: location of genes for resistance to fusarium wilt race 0

Two recombinant inbred line (RIL) populations derived from intraspecific crosses with a common parental line (JG62) were employed to develop a chickpea genetic map. Molecular markers, flower colour, double podding, seed coat thickness and resistance to fusarium wilt race 0 (FOC-0) were included in the study. Joint segregation analysis involved a total of 160 markers and 159 RILs. Ten linkage groups (LGs) were obtained that included morphological markers and 134 molecular markers (3 ISSRs, 13 STMSs and 118 RAPDs). Flower colour (B/b) and seed coat thickness (Tt/tt) appeared to be linked to STMS (GAA47). The single-/double-podding locus was located on LG9 jointly with two RAPD markers and STMS TA80. LG3 included a gene for resistance to FOC-0 (Foc0₁/foc0₁) flanked by RAPD marker OPJ20₆₀₀ and STMS marker TR59. The association of this LG with FOC-0 resistance was confirmed by QTL analysis in the CA2139 × JG62 RIL population where two genes were involved in the resistance reaction. The STMS markers enabled comparison of LGs with preceding maps.     

A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map

The cultivated strawberry, Fragaria × ananassa, is the most economically-important soft-fruit species, but few practical molecular tools for the purpose of marker assisted selection currently exist. As a precursor to the development of such tools, a genetic linkage map was developed from a F₁ population comprising 174 seedlings derived from a cross between two F. × ananassa cultivars, ‘Redgauntlet’ × ‘Hapil’. The resultant map is composed of 315 molecular markers—218 microsatellites, 11 gene-specific markers and 86 AFLP and RAPD markers—and spans 3,116 cM. In total, 69 linkage group fragments were recovered, more than the 56 linkage groups expected for the cultivated strawberry, however, all fragments contained a transferable marker that could be associated with one of 56 linkage group scaffolds. The female (Redgauntlet) and male (Hapil) linkage maps are composed, respectively of 170 loci in 32 linkage groups covering 1,675.3 cM and 182 loci in 37 linkage groups covering 1,440.7 cM, with 37 markers common to both maps. The maximum number of markers in one linkage group was 15, the minimum was two. All linkage groups resolved contained at least one transferable marker (SSR or gene-specific) that had been mapped on the diploid Fragaria reference map (FV × FB), and therefore all linkage groups could be identified as homologous to one of the seven diploid Fragaria linkage groups. When marker order was compared to the diploid Fragaria reference map, effectively complete colinearity was observed. However, the occurrence of duplicated loci on homologues of linkage groups FG1 and FG6 provided evidence of a putative chromosomal duplication or translocation event in Fragaria. The development of this linkage map will facilitate the study and dissection of QTL associated with traits of economic importance such as disease resistance and fruit quality, and provides a foundation for the development of markers for the purpose of marker assisted breeding and selection in the cultivated strawberry, F. × ananassa.     

A new broccoli × broccoli immortal mapping population and framework genetic map: tools for breeders and complex trait analysis

A unique broccoli × broccoli doubled haploid (DH) population has been created from the F₁ of a cross between two DH broccoli lines derived from cultivars Green Duke and Marathon. We genotyped 154 individuals from this population with simple sequence repeat and amplified fragment length polymorphism markers to create a B. oleracea L. var. italica ‘intra-crop’ specific framework linkage map. The map is composed of nine linkage groups with a total length of 946.7 cM. Previous published B. oleracea maps have been constructed using diverse crosses between morphotypes of B. oleracea; this map therefore represents a useful breeding resource for the dissection of broccoli specific traits. Phenotype data have been collected from the population over five growing seasons; the framework linkage map has been used to locate quantitative trait loci for agronomically important broccoli traits including head weight (saleable yield), head diameter, stalk diameter, weight loss and relative weight loss during storage, as well as traits for broccoli leaf architecture. This population and associated linkage map will aid breeders to directly map agronomically important traits for the improvement of elite broccoli cultivars.     

A microsatellite linkage map for the cultivated strawberry (Fragaria?×?ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection

The linkage maps of the cultivated strawberry, Fragaria × ananassa (2n = 8x = 56) that have been reported to date have been developed predominantly from AFLPs, along with supplementation with transferrable microsatellite (SSR) markers. For the investigation of the inheritance of morphological characters in the cultivated strawberry and for the development of tools for marker-assisted breeding and selection, it is desirable to populate maps of the genome with an abundance of transferrable molecular markers such as microsatellites (SSRs) and gene-specific markers. Exploiting the recent release of the genome sequence of the diploid F. vesca, and the publication of an extensive number of polymorphic SSR markers for the genus Fragaria, we have extended the linkage map of the ‘Redgauntlet’ × ‘Hapil’ (RG × H) mapping population to include a further 330 loci, generated from 160 primer pairs, to create a linkage map for F. × ananassa containing 549 loci, 490 of which are transferrable SSR or gene-specific markers. The map covers 2140.3 cM in the expected 28 linkage groups for an integrated map (where one group is composed of two separate male and female maps), which represents an estimated 91% of the cultivated strawberry genome. Despite the relative saturation of the linkage map on the majority of linkage groups, regions of apparent extensive homozygosity were identified in the genomes of ‘Redgauntlet’ and ‘Hapil’ which may be indicative of allele fixation during the breeding and selection of modern F. × ananassa cultivars. The genomes of the octoploid and diploid Fragaria are largely collinear, but through comparison of mapped markers on the RG × H linkage map to their positions on the genome sequence of F. vesca, a number of inversions were identified that may have occurred before the polyploidisation event that led to the evolution of the modern octoploid strawberry species.     

Interactions of two species of the genusChenopodium with two production plants—Sugar beet and spring wheat

TwoChenopodium species (C. album L.,C. suecicum J. Murr) were grown under field conditions with sugar beet to assess the weed-caused crop loss, and with spring wheat in a replacement series experiment. The weeds strongly reduced the growth of sugar beet. Dew's competition indexes for the regressions of sugar beet yield on weed density were 6.81 and 3.78 forC. suecicum andC. album respectively. On the other hand, the yield of spring wheat was not affected by the twoChenopodium species owing to early shading of the weeds by the faster growing crop stand.     

An update of the Courtot × Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat

We made an update of the intervarietal molecular marker linkage map of the wheat genome developed using a doubled-haploid (DH) population derived from the cross between the cultivars "Courtot" and "Chinese Spring". This map was constructed using 187 DH lines and 659 markers. The genome was well covered (more than 95%) except for chromosomes from homoeologous group 4 and chromosomes 5D and 7D, which had gaps slightly larger than 50 cM. A core-map based on a set of 200 anchor loci (one marker each 18.4 cM) was developed. The total length of this map was 3,685 cM which is similar to the size of the international reference map of the ITMI population (3,551 cM). Map coverage was identical for the three genomes (A, B and D) and for the number of anchor loci, as well as for the size of the map. Using this map, QTLs for several agronomic traits were detected on phenotypic data from the population grown in Clermont-Ferrand (France) under natural field conditions over 6 years, and in Norwich (UK) in controlled conditions and under natural field conditions in 1 year. Almost all of the 21 chromosomes were involved in at least one trait. However, several regions seemed to contain gene clusters either for grain traits (and thus bread-making quality) or plant development traits.     

A DNA marker assay based on high-resolution melting curve analysis for distinguishing species of the Festuca–Lolium complex

The grass breeding industry is interested in a fast and cheap method of identifying contamination in seeds of Italian and perennial ryegrass (Lolium perenne L. and L. multiflorum Lam., respectively). This study shows that high-resolution melting curve analysis in combination with an unlabelled probe assay is an effective method of detecting single nucleotide polymorphisms (SNPs) in diverse Italian and perennial ryegrass backgrounds. This method proved efficient in differentiating ryegrass species and reducing the effect of additional DNA sequence polymorphisms close to the target SNP on the melting curve profiles. For the identification of contamination in Italian and perennial ryegrass seed production, high-resolution melting curve analysis shows great potential, as it is a single closed-tube PCR reaction with an easy workflow, providing results in <2 h after DNA extraction.     

Length–weight relationships for five species of Chimaerids and two species of Rhinochimaerids to the west of Ireland

Length–weight regressions for five chimaerid species, Chimaera monstrosa Linnaeus, 1758, Chimaera opalescens Luchetti, Iglesias & Sellos, 2011, Hydrolagus affinis de Brito Capello, 1868, Hydrolagus pallidus Hardy & Stehmann, 1990 and Hydrolagus mirabilis Collett, 1904, and two Rhinochimaerid species, Rhinochimaera atlantica Holt & Byrne, 1909 and Harriotta raleighana Goode & Beane, 1895, are calculated from data collected during a series of deepwater surveys conducted by the Irish Marine Institute from 2006 to 2009. This work was carried out on the continental slope to the west and northwest of Ireland and the northern slope of the Porcupine bank. Samples were measured fresh at the end of each haul. Due to the fragility of the tails of many of these species, length measurements for Chimaerids were made to the pre supra caudal fin, while for Rhinochimaerids they were made to the second dorsal fin. Lengths were measured to the nearest centimetre below and weights were recorded to the nearest gram. Outliers were removed from the dataset according to difference in fits (DFFITS) (Belsley et al., Regression diagnostics: Identifying influential data and sources of collinearity, John Wiley & Sons; 1980). b values for the Chimaeridae ranged from 2.915 to 3.075, while r² values ranged from .981 to .995. b values for H. raleighana and R. atlantica were 2.764 and 3.505 and r² values were .977 and .976 respectively.     

Are Mojave Desert annual species equal? Resource acquisition and allocation for the invasive grass Bromus madritensis subsp. rubens (Poaceae) and two native species

Abundance of invasive plants is often attributed to their ability ot outcompete native species. We compared resource acquisition and allocation of the invasive annual grass Bromus madritensis subsp. rubens with that of two native Mojave Desert annuals, Vulpia octoflora and Descurainia pinnata, in a glasshouse experiment. Each species was grown in monoculture at two densities and two levels of N availability to compare how these annuals capture resources and to understand their relative sensitivities to environmental change. During >4 mo of growth, Bromus used water more rapidly and had greater biomass and N content than the natives, partly because of its greater root-surface area and its exploitation of deep soils. Bromus also had greater N uptake, net assimilation and transpiration rates, and canopy area than Vulpia. Resource use by Bromus was less sensitive to changes in N availability or density than were the natives. The two native species in this study produced numerous small seeds that tended to remain dormant, thus ensuring escape of offspring from unfavorable germination conditions; Bromus produced fewer but larger seeds that readily germinated. Collectively, these traits give Bromus the potential to rapidly establish in diverse habitats of the Mojave Desert, thereby gaining an advantage over coexisting native species.     

New genetic map of rye composed of PCR-based molecular markers and its alignment with the reference map of the DS2 × RXL10 intercross

A new genetic map of rye, developed by using the 541 x Ot1-3 F2 intercross, consists of 148 marker loci, including 99 RAPDs, 18 SSRs, 14 STSs, 9 SCARs and 7 ISSRs, and spans the distance of 1401.4 cM. To the 7 rye chromosomes, 8 linkage groups were assigned and compared with the reference map of the DS2 x RXL10 F2 intercross by using 24 common markers. The 2 combined maps contain altogether 611 marker loci (70-109 per chromosome) and constitute a substantial source of information useful for further genomic studies in rye. From 21 to 37 RAPD marker loci are distributed randomly along each chromosome length and their total number for all 7 rye chromosomes is 177. This abundance of RAPD marker loci in the rye genetic map can be exploited for development of SCARs in regions containing important genes or QTL.     

Are lice good proxies for host history? A comparative analysis of the Australian magpie, Gymnorhina tibicen, and two species of feather louse

Parasites have been recently advocated as useful proxies for unravelling a complex evolutionary history of a host. In the present study, two species of feather lice, Brueelia semiannulata and Philopterus sp. were analysed for mitochondrial variation and compared to mitochondrial and nuclear variation in their host, the Australian magpie Gymnorhina tibicen. Phylogenies constructed using maximum likelihood methods revealed geographic structuring for both species of feather lice and host. Our genetic analysis shows concordance of east-west structure between host and Philopterus sp. indicating that it is an informative proxy for host history. Analysis of the Philopterus sp. phylogeny also suggested cryptic structuring within the eastern magpie population that had not been previously realized through genetic analysis of the host. B. semiannulata however, did not show congruent phylogeographic structuring with the host. Rather than showing an east-west split between lineages, the phylogeny of B. semiannulata showed north-south geographic structuring. It is postulated that this incongruence may be due to ecological habitat differences and/or the dispersal ability of B. semiannulata.     

Phylogenetic analysis of the polymorphic 4× species complex Lonicera caerulea (Caprifoliaceae) using RAPD markers and noncoding chloroplast DNA sequences

The blue-berried honeysuckle (Lonicera caerulea L.) is one of the most representative species of the genus Lonicera L. in horticulture. This article presents the results of research on the taxonomy of blue-fruited honeysuckles, which is quite complicated due to the phenotypic plasticity, ability to hybridize and distribution across different ecological zones. We used the random amplified polymorphic DNA (RAPD) markers and sequencing of seven chloroplast DNA (cpDNA) regions (trnH-psbA, rpS12-rpL20, trnL-trnF, trnS-trnG, trnG, rpS16 and trnS-psbZ) to assess the phylogenetic relationships among the taxa within the polymorphic 4 × species complex L. caerulea and to determine the position of Lonicera boczkarnikowae Plekh. and Lonicera venulosa Maxim. within this complex. Lonicera chrysantha Turcz. ex Ledeb., L. orientalis Lam. and L. xylosteum L. were used as the outgroup species. The RAPD and cpDNA analyses both indicated that all of the studied taxa of the blue-fruited honeysuckle form a single cluster consisting of two subclusters. A second cluster includes the outgroup species. According to the cpDNA analysis, L. boczkarnikowae and L. venulosa belong to the subcluster that includes the taxa of the polymorphic tetraploid complex L. caerulea. A separate subcluster within the cluster of blue-fruited honeysuckles contains L. altaica and L. edulis.     

Did Pleistocene glaciations shape genetic patterns of European ostracods? A phylogeographic analysis of two species with asexual reproduction

Nested clade analyses (NCA) and likelihood mapping were applied to DNA sequence data of the ribosomal ITS1 and mitochondrial COI region from two non-marine ostracod species. The aim was to test whether Pleistocene glaciations may have shaped genetic and geographic patterns. According to the results from both types of analyses, evidence was lacking for any kind of geographic grouping of European (and one African) population from the putatively ancient asexual ostracod, Darwinula stevensoni. This counters the possibility that a recent selective sweep could have caused the low intraspecific, genetic diversity observed in this species. One of the most cited hypotheses to explain geographic parthenogenesis invokes faster, postglacial colonization by asexual lineages. However, no evidence for northern ‘range expansion’ of asexual haplotypes was found for Eucypris virens, a species with geographic parthenogenesis. Rather, the outcome of the NCA reveals that phylogeographic relationships are characterized by ‘restricted dispersal with isolation by (geographic) distance’. This result suggests that either no faster, postglacial range expansion of asexuals occurred in E. virens or, that patterns of subsequent colonization became ‘overwritten’ by more recent dispersal events. Likelihood mapping provides evidence for the second scenario because genetic instead of geographic clustering was statistically supported. Handling editor: K. Martens     

Is the pollination biology of Bathysa and Schizocalyx consistent with their segregation? A first approach for two sympatric species in southeastern Brazil

Tribe Condamineeae appears to be well supported in recent phylogenetic studies. However, the species of Bathysa were divided into two clades, leading to restoration of Schizocalyx. We studied the reproductive biology of one species from each clade, which occur sympatrically in the montane Brazilian Atlantic forest. Flowering overlap was short (from December to March in B. australis and from February to June in S. cuspidatus). The flowers of both species are protogynous and homostylous and last for about 3 days. The unit of pollination in B. australis is the inflorescence. Its flowers have a greenish hypocrateriform corolla (tube about 5 mm long) and were mainly pollinated by bees and wasps in search of nectar. Schizocalyx cuspidatus has white flowers with an infundibuliform corolla (tube about 8 mm long), and its main pollinators were stingless bees in search of pollen. The pollination systems of the two species did not correspond to their pollination syndromes. Morphological differences between Bathysa and Schizocalyx were reflected in their pollination systems, with greater phenotypic specialization in S. cuspidatus, the flowers of which offer pollen as the main resource, an unusual feature within Rubiaceae. Schizocalyx cuspidatus showed higher reproductive capacity by having more inflorescences per plant, more ovules per flower, and twice the proportion of flowering individuals. However, the reproductive efficiency (fruit set, seed/ovule ratio) did not differ between the species, despite the higher frequency of visits by pollinators to S. cuspidatus. Self-compatibility in B. australis and self-incompatibility in S. cuspidatus seem to explain these results.     

A sialidase complex from chicken liver: Characterization of a multienzyme complex with β-galactosidase and carboxypeptidase

Mammalian lysosomal sialidase exists as an enzyme complex with β-galactosidase and carboxypeptidase, so-called “protective protein.” In this article, we report that chicken sialidase also occurs as a complex with β-galactosidase and protective protein. The purified sialidase complex had a molecular weight > 700 kDa on gel filtration and showed four protein components of 76, 65, 54 and 48 kDa on SDS-PAGE under nonreducing conditions. N-Terminal sequences of the 65- and 48-kDa proteins were homologous to human lysosomal β-galactosidase and protective protein precursor, respectively. The purified sialidase complex also had carboxypeptidase activity. Both sialidase and carboxypeptidase activities were precipitated together by an antibody against chicken β-galactosidase. The complex reversibly dissociated into 120-kDa β-galactosidase dimer and 100-kDa carboxypeptidase dimer at pH 7.5, but the sialidase irreversibly inactivated during the depolymerization. These findings indicate that chicken sialidase exists as a multienzyme complex, by which the sialidase activity appears to be stabilized.     

Comparative analyses of linkage maps and segregation distortion of two F₂ populations derived from japonica crossed with indica rice

To facilitate genetic research, we constructed two linkage maps by employing two F? populations derived from rice inter-subspecific crosses, japonica Tainung 67 (TNG67)/indica Taichung Sen 10 (TCS10) and japonica TNG67/indica Taichung Sen 17 (TCS17). We established linkage map lengths of 1481.6 cM and 1267.4 cM with average intervals of 13.8 cM and 14.4 cM by using 107 and 88 PCR markers for coverage of 88% of the rice genome in TNG67/TCS10 and TNG67/TCS17, respectively. The discrepancy in genetic maps in the two populations could be due to different cross combinations, crossing-over events, progeny numbers and/or markers. The most plausible explanation was segregation distortion; 18 markers (16.8%) distributed at nine regions of seven chromosomes and 10 markers (11.4%) at four regions of four chromosomes displayed severe segregation distortion (p < 0.01)in TNG67/TCS10 and TNG67/TCS17, respectively. All segregation-distorted markers in these two populations corresponded to reported reproductive barriers, either gametophytic or zygotic genes but not to hybrid breakdown genes. The observed recombination frequency, which was higher or lower than the intrinsic frequency, revealed the association of segregation distortion skewed to the same or different genotypes at the consecutive markers. The segregation distortion, possibly caused by reproductive barriers, affects the evaluation recombination frequencies and consequently the linkage analysis of QTLs and positional cloning.