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1.
Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae)
Background and Aims
Since the advent of molecular phylogenetics, numerous attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Ideally, such inferences should be evaluated against cytogenetic data. Towards this goal, we carried out phylogenetic modelling of chromosome number change and fluorescence in situ hybridization (FISH) in a medium sized genus of Araceae to elucidate if data from chromosomal markers would support maximum likelihood-inferred changes in chromosome numbers among close relatives. Typhonium, the focal genus, includes species with 2n = 65 and 2n = 8, the lowest known count in the family.Methods
A phylogeny from nuclear and plastid sequences (96 taxa, 4252 nucleotides) and counts for all included species (15 of them first reported here) were used to model chromosome number evolution, assuming discrete events, such as polyploidization and descending or ascending dysploidy, occurring at different rates. FISH with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) was performed on ten species with 2n = 8 to 2n = 24.Key Results
The best-fitting models assume numerous past chromosome number reductions. Of the species analysed with FISH, the two with the lowest chromosome numbers contained interstitial telomeric signals (Its), which together with the phylogeny and modelling indicates decreasing dysploidy as an explanation for the low numbers. A model-inferred polyploidization in another species is matched by an increase in rDNA sites.Conclusions
The combination of a densely sampled phylogeny, ancestral state modelling and FISH revealed that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species. 相似文献2.
Background and Aims
Polyploidy is a dominant feature of flowering-plant genomes, including those of many important crop species. Arachis is a largely diploid genus with just four polyploid species. Two of them are economically important: the cultivated peanut and A. glabrata, a tropical forage crop. Even though it is usually accepted that polyploids within papilionoid legumes have arisen via hybridization and further chromosome doubling, it has been recently suggested that peanut arose through bilateral sexual polyploidization. In this paper, the polyploid nature of the recent, spontaneously originated triploid cytotype of the tropical lucerne, A. pintoi, was analysed, and thereby the mechanism by which polyploids may arise in the genus.Methods
Chromosome morphology of 2x and 3x A. pintoi was determined by the Feulgeńs technique and the rDNA sites were mapped by FISH. To investigate whether polyploidization occurred by means of unreduced gametes, a detailed analysis of the microsporogenesis and pollen grains was made.Key Results
The 2x and 3x plants presented 9m + 1sm and a satellited chromosome type 2 in each haploid genome. Physical mapping revealed a cluster of 18S–26S rDNA, proximally located on chromosome 6, and two 5S rDNA loci on chromosomes 3 and 5. Diploid plants presented 10II in meiosis while trivalents were observed in all triploids, with a maximum of 10III by cell. Diploid A. pintoi produced normal tetrads, but also triads, dyads and monads. Two types of pollen grains were detected: (1) normal-sized with a prolate shape and (2) large ones with a tetrahedral morphology.Conclusions
Karyotype and meiotic analysis demonstrate that the 3x clone of A. pintoi arose by autopolyploidy. The occurrence of unreduced gametes strongly supports unilateral sexual polyploidization as the most probable mechanism that could have led to the origin of the triploid cytotype. This mechanism of polyploidization would probably be one of the most important mechanisms involved in the origin of economically important species of Arachis, either by triploid bridge or bilateral sexual polyploidization. 相似文献3.
Karen S Aitken Meredith D McNeil Scott Hermann Peter C Bundock Andrzej Kilian Katarzyna Heller-Uszynska Robert J Henry Jingchuan Li 《BMC genomics》2014,15(1)
Background
Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids between two species with different basic chromosome numbers: Saccharum officinarum (2n = 80) with a basic chromosome number of 10 and S. spontaneum (2n = 40-128) with a basic chromosome number of 8. The first maps that were constructed utilised the single dose (SD) markers generated using RFLP, more recent maps generated using AFLP and SSRs provided at most 60% genome coverage. Diversity Array Technology (DArT) markers are high throughput allowing greater numbers of markers to be generated.Results
Progeny from a cross between a sugarcane variety Q165 and a S. officinarum accession IJ76-514 were used to generate 2467 SD markers. A genetic map of Q165 was generated containing 2267 markers, These markers formed 160 linkage groups (LGs) of which 147 could be placed using allelic information into the eight basic homology groups (HGs) of sugarcane. The HGs contained from 13 to 23 LGs and from 204 to 475 markers with a total map length of 9774.4 cM and an average density of one marker every 4.3 cM. Each homology group contained on average 280 markers of which 43% were DArT markers 31% AFLP, 16% SSRs and 6% SNP markers. The multi-allelic SSR and SNP markers were used to place the LGs into HGs.Conclusions
The DArT array has allowed us to generate and map a larger number of markers than ever before and consequently to map a larger portion of the sugarcane genome. This larger number of markers has enabled 92% of the LGs to be placed into the 8 HGs that represent the basic chromosome number of the ancestral species, S. spontaneum. There were two HGs (HG2 and 8) that contained larger numbers of LGs verifying the alignment of two sets of S. officinarum chromosomes with one set of S. spontaneum chromosomes and explaining the difference in basic chromosome number between the two ancestral species. There was also evidence of more complex structural differences between the two ancestral species.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-152) contains supplementary material, which is available to authorized users. 相似文献4.
Background
The duplication of autosomal genes onto the Y chromosome may be an important element in the evolution of sexual dimorphism.A previous cytological study reported on a putative example of such a duplication event in a dioecious tribe of Silene (Caryophyllaceae): it was inferred that the Y-linked MADS-box gene AP3Y originated from a duplication of the reportedly autosomal orthologAP3A. However, a recent study, also using cytological methods, indicated that AP3A is X-linked in Silenelatifolia.Methodology/Principal Findings
In this study, we hybridized S. latifolia and S. dioicato investigate whether the pattern of X linkage is consistent among distinct populations, occurs in both species, and is robust to genetic methods. We found inheritance patterns indicative of X linkage of AP3A in widely distributed populations of both species.Conclusions/Significance
X linkage ofAP3A and Y linkage of AP3Yin both species indicates that the genes'' ancestral progenitor resided on the autosomes that gave rise to the sex chromosomesand that neither gene has moved between chromosomes since species divergence.Consequently, our results do not support the contention that inter-chromosomal gene transfer occurred in the evolution of SlAP3Y from SlAP3A. 相似文献5.
Francisco Balao Ram��n Casimiro-Soriguer Mar��a Talavera Javier Herrera Salvador Talavera 《Annals of botany》2009,104(5):965-973
Background and Aims
Studying the spatial distribution of cytotypes and genome size in plants can provide valuable information about the evolution of polyploid complexes. Here, the spatial distribution of cytological races and the amount of DNA in Dianthus broteri, an Iberian carnation with several ploidy levels, is investigated.Methods
Sample chromosome counts and flow cytometry (using propidium iodide) were used to determine overall genome size (2C value) and ploidy level in 244 individuals of 25 populations. Both fresh and dried samples were investigated. Differences in 2C and 1Cx values among ploidy levels within biogeographical provinces were tested using ANOVA. Geographical correlations of genome size were also explored.Key Results
Extensive variation in chromosomes numbers (2n = 2x = 30, 2n = 4x = 60, 2n = 6x = 90 and 2n = 12x =180) was detected, and the dodecaploid cytotype is reported for the first time in this genus. As regards cytotype distribution, six populations were diploid, 11 were tetraploid, three were hexaploid and five were dodecaploid. Except for one diploid population containing some triploid plants (2n = 45), the remaining populations showed a single cytotype. Diploids appeared in two disjunct areas (south-east and south-west), and so did tetraploids (although with a considerably wider geographic range). Dehydrated leaf samples provided reliable measurements of DNA content. Genome size varied significantly among some cytotypes, and also extensively within diploid (up to 1·17-fold) and tetraploid (1·22-fold) populations. Nevertheless, variations were not straightforwardly congruent with ecology and geographical distribution.Conclusions
Dianthus broteri shows the highest diversity of cytotypes known to date in the genus Dianthus. Moreover, some cytotypes present remarkable internal genome size variation. The evolution of the complex is discussed in terms of autopolyploidy, with primary and secondary contact zones. 相似文献6.
Background and Aims
The sedge genus Carex, the most diversified angiosperm genus of the northern temperate zone, is renowned for its holocentric chromosomes and karyotype variability. The genus exhibits high variation in chromosome numbers both among and within species. Despite the possibility that this chromosome evolution may play a role in the high species diversity of Carex, population-level patterns of molecular and cytogenetic differentiation in the genus have not been extensively studied.Methods
Microsatellite variation (11 loci, 461 individuals) and chromosomal diversity (82 individuals) were investigated in 22 Midwestern populations of the North American sedge Carex scoparia and two Northeastern populations.Key Results
Among Midwestern populations, geographic distance is the most important predictor of genetic differentiation. Within populations, inbreeding is high and chromosome variation explains a significant component of genetic differentiation. Infrequent dispersal among populations separated by >100 km explains an important component of molecular genetic and cytogenetic diversity within populations. However, karyotype variation and correlation between genetic and chromosomal variation persist within populations even when putative migrants based on genetic data are excluded.Conclusions
These findings demonstrate dispersal and genetic connectivity among widespread populations that differ in chromosome numbers, explaining the phenomenon of genetic coherence in this karyotypically diverse sedge species. More generally, the study suggests that traditional sedge taxonomic boundaries demarcate good species even when those species encompass a high range of chromosomal diversity. This finding is important evidence as we work to document the limits and drivers of biodiversity in one of the world''s largest angiosperm genera. 相似文献7.
Elke Bellefroid S. Khadijah Rambe Olivier Leroux Ronald L. L. Viane 《Annals of botany》2010,106(1):157-171
Background and Aims
‘Loxoscaphoid’ Asplenium species are morphologically a remarkably distinct group of Aspleniaceae. Except for two preliminary chromosome counts of Asplenium theciferum, the cytology of this group of species has, however, been largely unstudied.Methods
Chromosome counts were obtained by acetocarmine squash preparations of one mitotic cell and several meiotic cells. Relative DNA content of gametophytic and sporophytic cells was determined by flow cytometry. The phylogenetic placement of A. loxoscaphoides, A. rutifolium s.l. and A. theciferum s.l. was investigated through an analysis of rbcL sequences.Key Results
The dysploid base number is reported to be x = 35 in Asplenium centrafricanum, A. loxoscaphoides, A. sertularioides and A. theciferum. Analysis of rbcL sequences confirms that ‘loxoscaphoids’ nest robustly within Asplenium. Several high ploidy levels exceeding the tetraploid level were found in A. theciferum s.l. and A. rutifolium s.l. All taxa proved to be sexual.Conclusions
Four base numbers are known at present for Aspleniaceae: x = 39, 38, 36 and 35. The dysploid base number x = 35 found in the ‘loxoscaphoid’ Asplenium spp. sheds a novel light on the cytoevolution of the whole family. We postulate a recurrent descending dysploid evolution within Aspleniaceae, leading to speciation at the (sub)generic and species/group level. 相似文献8.
Background
The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific regions of the Y or the Yh chromosome (MSY or HSY). Therefore, repeat composition and distribution in the sex determining region of papaya sex chromosomes would be informative to understand how these repetitive sequences might be involved in the early stages of sex chromosome evolution.Results
Detailed composition of interspersed, sex-specific, and tandem repeats was analyzed from 8.1 megabases (Mb) HSY and 5.3 Mb corresponding X chromosomal regions. Approximately 77% of the HSY and 64% of the corresponding X region were occupied by repetitive sequences. Ty3-gypsy retrotransposons were the most abundant interspersed repeats in both regions. Comparative analysis of repetitive sequences between the sex determining region of papaya X chromosome and orthologous autosomal sequences of Vasconcellea monoica, a close relative of papaya lacking sex chromosomes, revealed distinctive differences in the accumulation of Ty3-Gypsy, suggesting that the evolution of the papaya sex determining region may accompany Ty3-Gypsy element accumulation. In total, 21 sex-specific repeats were identified from the sex determining region; 20 from the HSY and one from the X. Interestingly, most HSY-specific repeats were detected in two regions where the HSY expansion occurred, suggesting that the HSY expansion may result in the accumulation of sex-specific repeats or that HSY-specific repeats might play an important role in the HSY expansion. The analysis of simple sequence repeats (SSRs) revealed that longer SSRs were less abundant in the papaya sex determining region than the other chromosomal regions.Conclusion
Major repetitive elements were Ty3-gypsy retrotransposons in both the HSY and the corresponding X. Accumulation of Ty3-Gypsy retrotransposons in the sex determining region of papaya X chromosome was significantly higher than that in the corresponding region of V. monoica, suggesting that Ty3-Gypsy could be crucial for the expansion and evolution of the sex determining region in papaya. Most sex-specific repeats were located in the two HSY expansion regions.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-335) contains supplementary material, which is available to authorized users. 相似文献9.
Background
The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements.Results
MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility.Conclusions
To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php. 相似文献10.
Tom Dierschke Terezie Mand��kov�� Martin A. Lysak Klaus Mummenhoff 《Annals of botany》2009,104(4):681-688
Background and Aims
Incongruence between chloroplast and nuclear DNA phylogenies, and single additive nucleotide positions in internal transcribed spacer (ITS) sequences of polyploid Australian/New Zealand (NZ) Lepidium species have been used to suggest a bicontinental hybrid origin. This pattern was explained by two trans-oceanic dispersals of Lepidium species from California and Africa and subsequent hybridization followed by homogenization of the ribosomal DNA sequence either to the Californian (C-clade) or to the African ITS-type (A-clade) in two different ITS-lineages of Australian/NZ Lepidium polyploids.Methods
Genomic in situ hybridization (GISH) was used to unravel the genomic origin of polyploid Australian/NZ Lepidium species. Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) probes was applied to test the purported ITS evolution, and to facilitate chromosome counting in high-numbered polyploids.Key Results
In Australian/NZ A-clade Lepidium polyploids, GISH identified African and Australian/NZ C-clade species as putative ancestral genomes. Neither the African nor the Californian genome were detected in Australian/NZ C-clade species and the Californian genome was not detected in Australian/NZ A-clade species. Five of the eight polyploid species (from 7x to 11x) displayed a diploid-like set of rDNA loci. Even the undecaploid species Lepidium muelleriferdinandi (2n = 11x = 88) showed only one pair of each rDNA repeat. In A-clade allopolyploids, in situ rDNA localization combined with GISH corroborated the presence of the African ITS-type.Conclusions
The nuclear genomes of African and Australian/NZ C-clade species were detected by GISH in allopolyploid Australian/NZ Lepidium species of the A-clade, supporting their hybrid origin. The presumed hybrid origin of Australian/NZ C-clade taxa could not be confirmed. Hence, it is assumed that Californian ancestral taxa experienced rapid radiation in Australia/NZ into extant C-clade polyploid taxa followed by hybridization with African species. As a result, A-clade allopolyploid Lepidium species share the Californian chloroplast type and the African ITS-type with the C-clade Australian/NZ polyploid and African diploid species, respectively.Key words: Lepidium, Brassicaceae, FISH, GISH, hybridization, polyploidy, long-distance dispersal, ITS, rDNA, Australia, New Zealand 相似文献11.
Romain Philippe Etienne Paux Isabelle Bertin Pierre Sourdille Fréderic Choulet Christel Laugier Hana ?imková Jan ?afá? Arnaud Bellec Sonia Vautrin Zeev Frenkel Federica Cattonaro Federica Magni Simone Scalabrin Mihaela M Martis Klaus FX Mayer Abraham Korol Hélène Bergès Jaroslav Dole?el Catherine Feuillet 《Genome biology》2013,14(6):R64
Background
As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.Results
Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.Conclusions
Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. 相似文献12.
Background and Aims Dioscorea alata
is a polyploid species with a ploidy level ranging from diploid (2n = 2x = 40) to tetraploid (2n = 4x = 80). Ploidy increase is correlated with better agronomic performance. The lack of knowledge about the origin of D. alata spontaneous polyploids (triploids and tetraploids) limits the efficiency of polyploid breeding. The objective of the present study was to use flow cytometry and microsatellite markers to understand the origin of D. alata polyploids.Methods
Different progeny generated by intracytotype crosses (2x × 2x) and intercytotype crosses (2x × 4x and 3x × 2x) were analysed in order to understand endosperm incompatibility phenomena and gamete origins via the heterozygosity rate transmitted to progeny.Results
This work shows that in a 2x × 2x cross, triploids with viable seeds are obtained only via a phenomenon of diploid female non-gametic reduction. The study of the transmission of heterozygosity made it possible to exclude polyspermy and polyembryony as the mechanisms at the origin of triploids. The fact that no seedlings were obtained by a 3x × 2x cross made it possible to confirm the sterility of triploid females. Flow cytometry analyses carried out on the endosperm of seeds resulting from 2x × 4x crosses revealed endosperm incompatibility phenomena.Conclusions
The major conclusion is that the polyploids of D. alata would have appeared through the formation of unreduced gametes. The triploid pool would have been built and diversified through the formation of 2n gametes in diploid females as the result of the non-viability of seeds resulting from the formation of 2n sperm and of the non-viability of intercytotype crosses. The tetraploids would have appeared through bilateral sexual polyploidization via the union of two unreduced gametes due to the sterility of triploids. 相似文献13.
Jana Krej?íková Radka Sudová Magdalena Lu?anová Pavel Trávní?ek Tomá? Urfus Petr Vít Hanna Weiss-Schneeweiss Bo?ena Kolano Kenneth Oberlander Leanne L. Dreyer Jan Suda 《Annals of botany》2013,111(4):641-649
Background and Aims
Genome duplication is widely acknowledged as a major force in the evolution of angiosperms, although the incidence of polyploidy in different floras may differ dramatically. The Greater Cape Floristic Region of southern Africa is one of the world''s biodiversity hotspots and is considered depauperate in polyploids. To test this assumption, ploidy variation was assessed in a widespread member of the largest geophytic genus in the Cape flora: Oxalis obtusa.Methods
DNA flow cytometry complemented by confirmatory chromosome counts was used to determine ploidy levels in 355 populations of O. obtusa (1014 individuals) across its entire distribution range. Ecological differentiation among cytotypes was tested by comparing sets of vegetation and climatic variables extracted for each locality.Key Results
Three majority (2x, 4x, 6x) and three minority (3x, 5x, 8x) cytotypes were detected in situ, in addition to a heptaploid individual originating from a botanical garden. While single-cytotype populations predominate, 12 mixed-ploidy populations were also found. The overall pattern of ploidy level distribution is quite complex, but some ecological segregation was observed. Hexaploids are the most common cytotype and prevail in the Fynbos biome. In contrast, tetraploids dominate in the Succulent Karoo biome. Precipitation parameters were identified as the most important climatic variables associated with cytotype distribution.Conclusions
Although it would be premature to make generalizations regarding the role of genome duplication in the genesis of hyperdiversity of the Cape flora, the substantial and unexpected ploidy diversity in Oxalis obtusa is unparalleled in comparison with any other cytologically known native Cape plant species. The results suggest that ploidy variation in the Greater Cape Floristic Region may be much greater than currently assumed, which, given the documented role of polyploidy in speciation, has direct implications for radiation hypotheses in this biodiversity hotspot. 相似文献14.
Background and Aims
In the genus Anemone two small groups of taxa occur with the highest ploidy levels 2n = 6x = 48, belonging to the closely related clades: the montane/alpine Baldensis clade and the more temperate Multifida clade. To understand the formation of polyploids within these groups, the evolution of allohexaploid A. baldensis (AABBDD, 2n = 6x = 48) from Europe and allotetraploid Anemone multifida (BBDD, 2n = 4x = 32) from America was analysed.Methods
Internal transcribed spacer and non-transcribed spacer sequences were used as molecular markers for phylogenetic analyses. Cytogenetic studies, including genomic in situ hybridization with genomic DNA of potential parental species as probe, fluorescence in situ hybridization with 5S and 18S rDNA as probes and 18S rDNA restriction analyses, were used to identify the parental origin of chromosomes and to study genomic changes following polyploidization.Key Results
This study shows that A. multifida (BBDD, 2n= 4x = 32) and A. baldensis (AABBDD, 2n = 6x = 48) are allopolyploids originating from the crosses of diploid members of the Multifida (donor of the A and B subgenomes) and Baldensis groups (donor of the D subgenome). The A and B subgenomes are closely related to the genomes of A. sylvestris, A. virginiana and A. cylindrica, indicating that these species or their progeny might be the ancestral donors of the B subgenome of A. multifida and A and B subgenomes of A. baldensis. Both polyploids have undergone genomic changes such as interchromosomal translocation affecting B and D subgenomes and changes at rDNA sites. Anemone multifida has lost the 35S rDNA loci characteristic of the maternal donor (B subgenome) and maintained only the rDNA loci of the paternal donor (D subgenome).Conclusions
It is proposed that A. multifida and A. baldensis probably had a common ancestor and their evolution was facilitated by vegetation changes during the Quaternary, resulting in their present disjunctive distribution. 相似文献15.
Andrew Gallagher 《PloS one》2008,3(12)
Background
Recent discoveries on Palau are claimed to represent the remains of small-bodied humans that may display evidence insular size reduction. This claim has yet to be statistically validatedMethodology/Principal Findings
Published postcranial specimens (n = 16) from Palau were assessed relative to recent small-bodied comparative samples. Resampling statistical approaches were employed to test specific hypotheses relating to body size in the Palau sample. Results confirm that the Palau postcranial sample is indisputably small-bodied.Conclusions/Significance
A single, homogenous body size morph is represented in early prehistoric postcrania from Palau. Small body size in early Palauans is an ancestral characteristic and was likely not a consequence of in-situ size reduction. Specimens from Palau have little bearing upon hypothesised insular size reduction in the ancestral lineage of Homo floresiensis. 相似文献16.
17.
Background
Next-generation sequencing techniques, such as genotyping-by-sequencing (GBS), provide alternatives to single nucleotide polymorphism (SNP) arrays. The aim of this work was to evaluate the potential of GBS compared to SNP array genotyping for genomic selection in livestock populations.Methods
The value of GBS was quantified by simulation analyses in which three parameters were varied: (i) genome-wide sequence read depth (x) per individual from 0.01x to 20x or using SNP array genotyping; (ii) number of genotyped markers from 3000 to 300 000; and (iii) size of training and prediction sets from 500 to 50 000 individuals. The latter was achieved by distributing the total available x of 1000x, 5000x, or 10 000x per genotyped locus among the varying number of individuals. With SNP arrays, genotypes were called from sequence data directly. With GBS, genotypes were called from sequence reads that varied between loci and individuals according to a Poisson distribution with mean equal to x. Simulated data were analyzed with ridge regression and the accuracy and bias of genomic predictions and response to selection were quantified under the different scenarios.Results
Accuracies of genomic predictions using GBS data or SNP array data were comparable when large numbers of markers were used and x per individual was ~1x or higher. The bias of genomic predictions was very high at a very low x. When the total available x was distributed among the training individuals, the accuracy of prediction was maximized when a large number of individuals was used that had GBS data with low x for a large number of markers. Similarly, response to selection was maximized under the same conditions due to increasing both accuracy and selection intensity.Conclusions
GBS offers great potential for developing genomic selection in livestock populations because it makes it possible to cover large fractions of the genome and to vary the sequence read depth per individual. Thus, the accuracy of predictions is improved by increasing the size of training populations and the intensity of selection is increased by genotyping a larger number of selection candidates.Electronic supplementary material
The online version of this article (doi:10.1186/s12711-015-0102-z) contains supplementary material, which is available to authorized users. 相似文献18.
Koehler S Cabral JS Whitten WM Williams NH Singer RB Neubig KM Guerra M Souza AP Amaral Mdo C 《Annals of botany》2008,102(4):491-507
Background and Aims
Species'' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species'' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species'' identification.Methods
Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes.Key Results
Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species'' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands.Conclusions
The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.Key words: Chromosome number, Christensonella, Cymbidieae, cytotaxonomy, fluorochrome staining, Maxillaria, Maxillariinae, molecular phylogenetics, species delimitation 相似文献19.
Karol Marhold Hiroshi Kudoh Jae-Hong Pak Kuniaki Watanabe Stanislav ?paniel Judita Lihová 《Annals of botany》2010,105(2):249-264
Background and Aims
Intraspecific ploidy-level variation is an important aspect of a species'' genetic make-up, which may lend insight into its evolutionary history and future potential. The present study explores this phenomenon in a group of eastern Asian Cardamine species.Methods
Plant material was sampled from 59 localities in Japan and Korea, which were used in karyological (chromosome counting) and flow cytometric analyses. The absolute nuclear DNA content (in pg) was measured using propidium iodide and the relative nuclear DNA content (in arbitrary units) was measured using 4,6-diamidino-2-phenylindole fluorochrome.Key Results
Substantial cytotype diversity was found, with strikingly different distribution patterns between the species. Two cytotypes were found in C. torrentis sensu lato (4x and 8x, in C. valida and C. torrentis sensu stricto, respectively), which displays a north–south geographical pattern in Japan. Hypotheses regarding their origin and colonization history in the Japanese archipelago are discussed. In Korean C. amaraeiformis, only tetraploids were found, and these populations may in fact belong to C. valida. C. yezoensis was found to harbour as many as six cytotypes in Japan, ranging from hexa- to dodecaploids. Ploidy levels do not show any obvious geographical pattern; populations with mixed ploidy levels, containing two to four cytotypes, are frequently observed throughout the range. C. schinziana, an endemic of Hokkaido, has hexa- and octoploid populations. Previous chromosome records are also revised, showing that they are largely based on misidentified material or misinterpreted names.Conclusions
Sampling of multiple populations and utilization of the efficient flow cytometric approach allowed the detection of large-scale variation in ploidy levels and genome size variation attributable to aneuploidy. These data will be essential in further phylogenetic and evolutionary studies. 相似文献20.
Sebastian Haller Juliane Spiegler Claudia Hemmelmann Helmut Küster Matthias Vochem Jens M?ller Dirk Müller Angela Kribs Thomas Hoehn Christoph H?rtel Egbert Herting Wolfgang G?pel the German Neonatal Network 《PloS one》2013,8(6)