ThePulmonaria dacica group: Its affinities with central and south-east European allies and with the genusParaskevia (Boraginaceae)

Comparative morphological, karyological and chorological studies prove the distinctness of the SE European and Asiatic populations ofPulmonaria mollis s.l., to be treated asP. dacica (Figs. 4, 5).P. mollis s.str. is interpreted as a relatively young taxon, which probably has evolved from an older stock ofP. dacica ancestors during the Pleistocene (Figs. 6, 8) and might have migrated, perhaps with oak woodland communities, from SE to C. Europe. A similar evolution can be postulated for S—SE European dysploidP. rubra-carnica-stiriaca-vallarsae group; this may have involved still unknown tetraploids (P. carnica?, Fig. 7). This group is linked via the hypertriploid speciesP. vallarsae with theP. saccharata group and at least the eastern species of theP. australis group. The monotypic genusParaskevia apparently marks the earliest divergence from the common Tertiary ancestral stock (Fig. 8). It exhibits a tetraploid chromosome number (2n = 28) but has preserved the most primitive characters. — Some comments on the systematics and nomenclature ofP. australis andParaskevia are added.     

Salt-stress induced changes in the leaf proteome of diploid and tetraploid mandarins with contrasting Na and Cl accumulation behaviour

To understand the genotypic variation of citrus to mild salt stress, a proteomic approach has been carried out in parallel on two citrus genotypes (‘Cleopatra’ and ‘Willow leaf’ mandarins), which differ for Na⁺ and Cl⁻ accumulation, and their cognate autotetraploids (4×). Using two-dimensional electrophoresis approximately 910 protein spots were reproducibly detected in control and salt-stressed leaves of all genotypes. Among them, 44 protein spots showing significant variations at least in one genotype were subjected to mass spectrometry analysis for identification. Salt-responsive proteins were involved in several functions, including photosynthetic processes, ROS scavenging, stress defence, and signalling. Genotype factors affect the salt-responsive pattern, especially that of carbon metabolism. The no ion accumulator ‘Cleopatra’ mandarin genotype showed the highest number of salt-responsive proteins, and up-regulation of Calvin cycle-related proteins. Conversely the ion accumulator ‘Willow leaf’ mandarin showed high levels of several photorespiration-related enzymes. A common set of proteins (twelve spots) displayed higher levels in salt-stressed leaves of 2× and 4× ‘Cleopatra’ and 4× ‘Willow leaf’ mandarin. Interestingly, antioxidant enzymes and heat shock proteins showed higher constitutive levels in 4× ‘Cleopatra’ mandarin and 4× ‘Willow leaf’ mandarin compared with the cognate 2× genotype. This work provides for the first time information on the effect of 8 weeks of salt stress on citrus genotypes contrasting for ion accumulation and their cognate autotetraploids. Results underline that genetic factors have a predominant effect on the salt response, although a common stress response independent from genotype was also found.     

Development and preliminary evaluation of a 90?K Axiom? SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

Background

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.

Results

About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.

Conclusions

The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1310-1) contains supplementary material, which is available to authorized users.     

Hybridisation between oilseed rape (Brassica napus) and tetraploid Brassica rapa under field conditions

Cross-compatible relatives of crop species contribute to the uncertainty regarding the potential risk of transgene escape from genetically modified varieties. The most successful crossing partner of oilseed rape (Brassica napus L.) is diploid Brassica rapa L. Variation of ploidy level among B. rapa cultivars has, until recently, been neglected in the context of gene flow and hybridisation with oilseed rape. We estimated the extent of hybridisation between autotetraploid B. rapa varieties (female) and B. napus (pollen donor) under experimental field conditions. Morphology, variation of relative DNA amount, and microsatellite markers were used to distinguish between intraspecific offspring of tetraploid B. rapa and interspecific hybrids with B. napus. Of 517 seed progenies of tetraploid B. rapa, 45 juvenile plants showed species specific morphological traits of oilseed rape. The detection of putative hybrids based on variation in relative DNA amounts was problematic due to the occurrence of aneuploidy. In total, 84 offspring showed relative DNA amounts deviating from tetraploid B. rapa, four of which were hexaploids. Of the 205 offspring analysed at three microsatellite loci, 67 had oilseed rape alleles. Based on molecular evidence a minimum hybridisation rate of 13.0% was estimated. A few mother plants accounted for the majority of hybrids. The mean pollen viability of hybrids between B. napus and tetraploid B. rapa (80.6%) was high in comparison with mean pollen viability of triploid hybrids between B. napus and diploid B. rapa. Therefore, the occurrence of tetraploid B. rapa should be taken into consideration when estimating the likelihood of gene flow from oilseed rape to close relatives at the landscape level. Tetraploid B. rapa is a common component of several seed mixtures and establishes feral populations in northwest Germany. Assuming a similar abundance of diploid and tetraploid B. rapa, gene flow from B. napus to tetraploid may be more likely than gene flow to diploid B. rapa.     

Syncyte formation in the microsporangium of <Emphasis Type="Italic">Chrysanthemum</Emphasis> (Asteraceae): a pathway to infraspecific polyploidy

Polyploidy, which is thought to have played an important role in plant evolution and speciation, is prevalent in Chrysanthemum (x = 9). In fact, polyploid series are known in C. zawadskii (2x, 4x, 6x, 8x, and 10x) and C. indicum (2x, 4x, and 6x), but the mechanism by which polyploidization occurs is unknown. Here we show that in diploid individuals of both C. zawadskii and C. indicum, the fusion between two adjacent pollen mother cells (PMCs) occurs at a frequency of 1.1–1.3% early in the first meiotic division. While possessing the chromosomes of both PMCs, the fused cell or syncyte undertakes subsequent meiotic division processes as a single large PMC, producing four 2n pollen grains that are able to germinate. Despite their low frequency, syncyte formation may have played a major role in the production of infraspecific polyploids in Chrysanthemum.     

Intergenomic single nucleotide polymorphisms as a tool for bacterial artificial chromosome contig building of homoeologous Brassica napus regions

Background

Homoeologous sequences pose a particular challenge if bacterial artificial chromosome (BAC) contigs shall be established for specific regions of an allopolyploid genome. Single nucleotide polymorphisms (SNPs) differentiating between homoeologous genomes (intergenomic SNPs) may represent a suitable screening tool for such purposes, since they do not only identify homoeologous sequences but also differentiate between them.

Results

Sequence alignments between Brassica rapa (AA) and Brassica oleracea (CC) sequences mapping to corresponding regions on chromosomes A1 and C1, respectively were used to identify single nucleotide polymorphisms between the A and C genomes. A large fraction of these polymorphisms was also present in Brassica napus (AACC), an allopolyploid species that originated from hybridisation of A and C genome species. Intergenomic SNPs mapping throughout homoeologous chromosome segments spanning approximately one Mbp each were included in Illumina’s GoldenGate® Genotyping Assay and used to screen multidimensional pools of a Brassica napus bacterial artificial chromosome library with tenfold genome coverage. Based on the results of 50 SNP assays, a BAC contig for the Brassica napus A subgenome was established that spanned the entire region of interest. The C subgenome region was represented in three BAC contigs.

Conclusions

This proof-of-concept study shows that sequence resources of diploid progenitor genomes can be used to deduce intergenomic SNPs suitable for multiplex polymerase chain reaction (PCR)-based screening of multidimensional BAC pools of a polyploid organism. Owing to their high abundance and ease of identification, intergenomic SNPs represent a versatile tool to establish BAC contigs for homoeologous regions of a polyploid genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-560) contains supplementary material, which is available to authorized users.     

A review of chromosome cytology in Hyacinthaceae subfamily Ornithogaloideae (Albuca, Dipcadi, Ornithogalum and Pseudogaltonia) in sub-Saharan Africa

The chromosome cytology of Hyacinthaceae subfamily Ornithogaloideae is reviewed within the framework of a recent molecular-based classification, with particular emphasis on its center of diversity in sub-Saharan Africa. We also provide new chromosome counts for sections that are unknown or poorly known cytologically. Albuca subgen. Namibiogalum (9 spp.) probably has an ancestral base number of x = 10 but subgen. Albuca (± 70 spp), subgen. Monarchos (9 spp.) and subgen. Osmyne (36 spp.) have x = 9. The pattern in subgen. Urophyllon (3 spp.) is remarkable: although x = 6 is likely, the species in the section exhibit a range of 2n = 12, 10, 8, 6 and 4 (exclusive of polyploidy). All karyotypes have three large chromosome pairs and a variable number of small chromosomes. Pseudogaltonia (2 spp.) has x = 9 and Dipcadi (26 spp.) possibly x = 9 in series Uropetalum and x = 6 in series Dipcadi, which exhibits a pattern of descending dysploidy leading to n = 3 in D. marlothii. In Ornithogalum (± 130 spp.) chromosome numbers are known for only 24 of the ± 84 sub-Saharan species, mostly from subgen. Aspasia and subgen. Ornithogalum sect. Linaspasia, both of which have x = 6, and from subgen. Galtonia, which has x = 8. In contrast, x = 7 is basic for the Eurasian sects. Honorius and Melophis, and x = 18 seems likely for sect. Cathissa. Sect. Ornithogalum, the cytology of which we does not examine in detail, may have x = 9. Polyploidy is apparently rare in the sub-Saharan African ornithogaloids, in marked contrast to the high frequency of polyploidy among Eurasian species. In Albuca just 3 or possibly 4 sub-Saharan species (9% or 13% of those counted) are exclusively polyploid and 5 more have diploid and polyploid races; and in sub-Saharan Ornithogalum, only the tropical O. gracillimum is exclusively polyploid, and the western southern African O. hispidum has diploid and polyploid races.     

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers

Sugarcane cultivars are polyploid, aneuploid clones derived from interspecific hybridization between Saccharum officinarum and S. spontaneum. Their genome has recently started to be unravelled as a result of the development of molecular markers. We constructed an AFLP genetic map based on a selfing population of a specific cultivar, R570.Using 37 AFLP primer pairs, we detected 1,185 polymorphic markers of which 939 were simplex (segregated 3:1); these were used to construct the map. Of those 939, 887 were distributed on 120 cosegregation groups (CGs) based on linkages in coupling, while 52 remained unlinked. The cumulative length of all the groups was 5,849 cM, which is probably around one-third of the total genome length. Comparison with reference S. officinarum clones enabled us to assign 11 and 79 CGs to S. spontaneum and S. officinarum,respectively, whereas 11 CGs were probably derived from recombination between chromosomes of the two ancestral species. The patchy size of the groups, which ranges from 1 to 232 cM, illustrates the difficulty to access large portions of chromosomes, particularly those inherited from S. officinarum. Repulsion phase linkages suggested a high preferential pairing for 13 CG pairs. Out of the 120 CGs, 34 could be assigned to one of the 10 homo(eo)logy groups already defined in a previous RFLP map owing to the use of a small common marker set. The genome coverage was significantly increased in the map reported here. Implications for quantitative trait loci (QTL) research and marker-assisted breeding perspectives are discussed. Received: 31 August 2000 / Accepted: 16 October 2000     

Transferability of wheat microsatellites to diploid Triticeae species carrying the A, B and D genomes

Hexaploid wheat (Triticum aestivum L em Thell) is derived from a complex hybridization procedure involving three diploid species carrying the A, B and D genomes. In this study, we evaluated the ability of microsatellite sequences from T. aestivum to be revealed on different ancestral diploid species more or less closely related, i.e. to test for their transferability. Fifty five primer pairs, evenly distributed all over the genome, were investigated. Forty three of them mapped to single loci on the hexaploid wheat genetic map although only 20 (46%) gave single PCR products; the 23 others (54%) gave more than one band with either only one being polymorphic, the others remaining monomorphic, or with several co-segregating polymorphic bands. The other 12 detected two (9) or three (3) different loci. From the 20 primer pairs which gave one amplification pro- duct on hexaploid wheat, nine (45%) also amplified products on only one of the diploid species, and seven (35%) on more than one. Four microsatellites (20%) which mapped to chromosomes from the B genome of wheat, did not give any amplification signal on any of the diploid species. This suggests that some regions of the B genome have evolved more rapidly compared to the A or D genomes since the emergence of polyploidy, or else that the donor(s) of this B genome has(have) not yet been identified. Our results confirm that Triticum monococcum ssp. urartu and Triticum tauschii were the main donors of the A and D genomes respectively, and that Aegilops speltoides is related to the ancestor(s) of the wheat polyploid B genome. Received: 21 June 2000 / Accepted: 15 November 2000