QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium

Asiatic cotton(Gossypium arboreum L.) is an Old World cultivated cotton species.The sinense race was planted extensively in China.Due to the advances in spinning technology during the last century,the species was replaced by the New World allotetraploid cotton G.hirsutum L.Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs.In addition,G.arboreum serves as a model for genomic research in Gossypium.In the present study,we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 1 3 linkage groups.The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci.A population containing 1 76 F2:3 families was used to perform quantitative trait loci(QTL)mapping for 17 phenotypes using Multiple QTL Model(MQM)of MapQTL ver 5.0.Overall,108 QTLs were detected on 13 chromosomes.Thirty-one QTLs for yield and its components were detected in the F2 population.Forty-one QTLs for yield and its components were detected in the F2:3 families with a total of 43 QTLs for fiber qualities.Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F2:3.Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals.These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.     

QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium

Asiatic cotton(Gossypium arboreum L.) is an Old World cultivated cotton species.The sinense race was planted extensively in China.Due to the advances in spinning technology during the last century,the species was replaced by the New World allotetraploid cotton G.hirsutum L.Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs.In addition,G.arboreum serves as a model for genomic research in Gossypium.In the present study,we generated an A-genome...     

RFLP variation in diploid and tetraploid alfalfa

Summary Alfalfa (Medicago sativa L.) is a major forage crop throughout the world. Although alfalfa has many desirable traits, continued breeding is required to incorporate pest resistances and other traits. We conducted this study to determine the amount of restriction fragment length polymorphism (RFLP) variability present within and between diploid and tetraploid alfalfa populations, and whether or not this variability is sufficient for construction of an RFLP map. Diploid plants from M. sativa ssp. falcata, ssp. coerulea, and ssp. sativa and tetraploid spp. sativa cultivars Apollo, Florida 77, and Spredor 2 were included. A total of 19 cDNA clones was probed onto genomic Southern blots containing DNA digested by EcoRI, HindIII, or BamHI. Phylogenetic trees were produced, based on parsimony analysis of shared restriction fragments. Evidence for extensive gene duplication was found; most probes detected complex patterns of restriction fragments. Large amounts of variation are present within all diploid subspecies. M. sativa ssp. falcata plants formed clusters distinct from ssp. sativa or ssp. coerulea plants, which were not distinctly clustered. Some M. sativa ssp. falcata plants were more similar to the other groups than to other plants within ssp. falcata. Variation among tetraploid cultivars showed that Florida 77 and Apollo had more similarities than either showed with Spredor 2. All three cultivars showed large within-population variation, with Apollo being the most diverse and Spredor 2 the least. Based on these results, development of an RFLP map at the diploid level appears possible. Also, differentiation of cultivars, particularly ones of divergent origin, seems possible based on RFLP patterns.     

Location of the ethidium binding sites of high affinity in chromatin

The influence of H1 and H5 histones proteins upon the accessibility of ethidium bromide into chromatin is studied by steady-state fluorescence anisotropy in the range of r-values ([Dye]/[Phosphate]) smaller than 0.01. This corresponds to the very strong binding process. When H1 and H5 are present, the DNA segment which contains the binding sites is 25–30 base pairs long, even if H1 and H5 are digested by trypsin or by natural proteolysis, but presumably still interacting with the DNA chromatin. On the contrary, when H1 or H5 are separated from chromatin by an increase of the ionic strength, ethidium binds to a segment of DNA about 55–60 base pairs long. We may explain the results by assuming that the ethidium sites are located on a continuous segment constituting about one half of the linker, the other half interacting with H1 and H5. When chromatin is depleted from these proteins, the high affinity sites are distributed all along the linker.     

Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium)

Nuclear-encoded genes exist in families of various sizes. To further our understanding of the evolutionary dynamics of nuclear gene families we present a characterization of the structure and evolution of the alcohol dehydrogenase (Adh) gene family in diploid and tetraploid members of the cotton genus (Gossypium, Malvaceae). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members, and Southern hybridization analyses were used to document variation in gene copy number. Adh gene copy number varies among Gossypium species, with diploids containing at least seven Adh loci in two primary gene lineages. Allotetraploid Gossypium species are inferred to contain at least 14 loci. Intron lengths vary markedly between loci, and one locus has lost two introns usually found in other plant Adh genes. Multiple examples of apparent gene duplication events were observed and at least one case of pseudogenization and one case of gene elimination were also found. Thus, Adh gene family structure is dynamic within this single plant genus. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution.     

Desynapsis in diploid and tetraploid clones of ryegrass

Desynapsis is described in diploid and tetraploid plants of perennial ryegrass. The plants were derived by repeated cloning of a single mixoploid (2n=14 and 28) detected among colchicine-treated seedlings. The diploid and tetraploid clones varied in degree of desynapsis, chiasma number, and fertility. The variation among the clones was probably environmental. The progeny of the mixoploid parent included dipoids, tetraploids, and an aneuploid. One diploid and the aneuploid were desynaptic and originated perhaps by selfing. Apparently a single recessive gene determined desynapsis. The role of synaptic genes in controlling the chemical structure and function of nucleoprotein macromolecules is discussed.     

Call degradation in diploid and tetraploid green toads

According to the 'environmental selection' hypothesis, the physical characteristics of environments influence the evolution of long-range acoustic signals by favouring those properties that decrease sound attenuation and distortion with distance. Different environments could favour different acoustic properties and therefore contribute to the intra- and interspecific variation of calls. In the present paper, we investigate whether this hypothesis could explain the differences between the advertisement calls of three taxa of central-Asian green toads: lowland diploids, highland tetraploids and lowland tetraploids. The pattern of propagation of 12 natural calls (four for each taxon) was analysed in nine localities of Kyrgyzstan and Kazakstan. We broadcast the calls and recorded them along a trasect at distances of 2, 4, 8, 16, and 32 m from the speaker, to estimate sound attenuation and propagation. Attenuation was quantified from the oscillogram (by directly calculating the SPL of calls) and from the power spectrum (by measuring the relative amplitude of the fundamental frequency) , whereas degradation was estimated by cross-correlating spectrograms of the same call at different distances. Results show that: (1) the pattern of sound propagation significantly differs among localities in relation to the different vegetation and environmental noise; (2) in most localities, call attenuation and degradation differ significantly among the three taxa ; (3) such differences are not consistent to those expected under the hypothesis of environmental selection: independent of altitude, lowland tetraploid calls fare worse than both diploid and highland tetraploid calls, whereas diploid and highland tetraploid calls show different patterns of propagation in a few localities only.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78 , 11–26.     

Isozyme gene duplication in diploid and tetraploid potatoes

Summary Isozyme techniques allow the study of gene redundancy in different ploidy levels of potato (Solanum tuberosum). In tetraploid potatoes all isozyme loci are duplicated. No sign of structural or regulatory divergence was found, as is expected due to their tetrasomic inheritance patterns. In addition to this genetic redundancy, produced by a relatively recent polyploidization event, some additional redundancy was found for at least three enzymes even in diploid groups and species. These older duplicate genes show structural and regulatory divergence, indicating they appeared by a separate polyploidization event far in the past. Their common origin is still recognizable by both their expression in the same subcellular compartment and by the dimerizing ability of the isozymes they encode. To account for the present chromosome number x = 12 of the Solanaceae family, the most frequently found among the species, a hypothetical polyploidization event is proposed.     

Analysis of the human HP1 interactome reveals novel binding partners

Heterochromatin protein 1 (HP1) has first been described in Drosophila as an essential component of constitutive heterochromatin required for stable epigenetic gene silencing. Less is known about the three mammalian HP1 isotypes CBX1, CBX3 and CBX5. Here, we applied a tandem affinity purification approach coupled with tandem mass spectrometry methodologies in order to identify interacting partners of the mammalian HP1 isotypes. Our analysis identified with high confidence about 30–40 proteins co-eluted with CBX1 and CBX3, and around 10 with CBX5 including a number of novel HP1-binding partners. Our data also suggest that HP1 family members are mainly associated with a single partner or within small protein complexes composed of limited numbers of components. Finally, we showed that slight binding preferences might exist between HP1 family members.     

Correspondence of trichome mutations in diploid and tetraploid cottons

Quantitative variation for leaf trichome number is observed within and among Gossypium species, varying from glabrous to densely pubescent phenotypes. Moreover, economically important cotton lint fibers are modified trichomes. Earlier studies have mapped quantitative trait loci (QTLs) affecting leaf pubescence in Gossypium using allotetraploids. In this study, we mapped genes responsible for leaf trichome density in a diploid A genome cross. We were able to map 3 QTLs affecting leaf pubescence based on trichome counts obtained from young leaves (YL) and mature leaves (ML). When the F(2) progeny were classified as pubescent versus glabrous, their ratio did not deviate significantly from a 3:1 model, suggesting that glabrousness is inherited in a simple Mendelian fashion. The glabrous mutation mapped to linkage group A3 at the position of major QTL YL1 and ML1 and appeared orthologous to the t1 locus of the allotetraploids. Interestingly, a fiber mutation, sma-4(ha), observed in the same F(2) population cosegregated with the glabrous marker, which indicates either close linkage or common genetic control of lint fiber and leaf trichomes. Studies of A genome diploids may help to clarify the genetic control of trichomes and fiber in both diploid and tetraploid cottons.     

Triploid and tetraploid hybrids from diploid x tetraploid crosses in Grindella (compositae)

Crosses between the diploids G. oxylepis var. eligulata Steyermark (Mexico) and G. havardii Steyermark (New Mexico) and the tetraploid G. aphanactis Rydb. (New Mexico) were made. With G. aphanactis as the pistillate parent and G. havardii as the pollen parent a triploid hybrid was obtained in which the maximum meiotic configuration observed was 6m. The plant was 10 % fertile. Two triploid hybrid plants were also obtained when G. aphanactis was used as the pistillate parent and G. oxylepis var. eligulata was the pollen parent. One plant was about 20 % fertile and the other had a maximum configuration of 3_II + 4_III. The reciprocal cross produced a tetraploid which had a maximum configuration of 6_II + 3_IV and was 8 % fertile. The tetraploid plant undoubtedly resulted from the union of an unreduced gamete from the 2n parent and a normally reduced gamete from the tetraploid. Morphology of the hybrids was usually intermediate when compared with the parental species, although some characters in the triploids were those of the diploid parent. Chromosome end arrangements of the respective genomes and putative pairing relationships are presented and phylogenetic implications are discussed. It is concluded that G. aphanactis is more closely related to G. havardii than to G. oxylepis var. eligulata.     

High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.     

Quantitative phosphoproteomics reveals novel roles of cAMP in plants

3′,5′-cyclic adenosine monophosphate (cAMP) is finally recognized as an essential signaling molecule in plants where cAMP-dependent processes include responses to hormones and environmental stimuli. To better understand the role of 3′,5′-cAMP at the systems level, we have undertaken a phosphoproteomic analysis to elucidate the cAMP-dependent response of tobacco BY-2 cells. These cells overexpress a molecular “sponge” that buffers free intracellular cAMP level. The results show that, firstly, in vivo cAMP dampening profoundly affects the plant kinome and notably mitogen-activated protein kinases, receptor-like kinases, and calcium-dependent protein kinases, thereby modulating the cellular responses at the systems level. Secondly, buffering cAMP levels also affects mRNA processing through the modulation of the phosphorylation status of several RNA-binding proteins with roles in splicing, including many serine and arginine-rich proteins. Thirdly, cAMP-dependent phosphorylation targets appear to be conserved among plant species. Taken together, these findings are consistent with an ancient role of cAMP in mRNA processing and cellular programming and suggest that unperturbed cellular cAMP levels are essential for cellular homeostasis and signaling in plant cells.     

Introgression of A- and B-genome of tetraploid triticale chromatin into tetraploid rye

An improvement of rye is one of the mainstream goals of current breeding. Our study is concerned with the introduction of the tetraploid triticale (ABRR) into the 4x rye (RRRR) using classical methods of distant crossing. One hundred fifty BC₁F₉ hybrid plants [(4x rye?×?4x triticales)?×?4x rye] obtained from a backcrossing program were studied. The major aim of this work was to verify the presence of an introgressed A- and B- genome chromatin of triticale in a collection of the 4x rye-tiritcale hybrids and to determine their chromosome compositions. In the present study, karyotypes of the previously reported BC₁F₂s and BC₁F₃s were compared with that of the BC₁F₉ generation as obtained after several subsequent open pollinations. The genomic in situ hybridisation (GISH) allowed us to identify 133 introgression forms in which chromosome numbers ranged between 26 and 32. Using four DNA probes (5S rDNA, 25S rDNA, pSc119.2 and pAs1), the fluorescence in situ hybridisation (FISH) was carried out to facilitate an exact chromosome identification in the hybrid plants. The combination of the multi-colour GISH with the repetitive DNA FISH singled out five types of translocated chromosomes: 2A.2R, 4A.4R, 5A.5R, 5B.5R and 7A.7R among the examined BC₁F₉s. The reported translocation lines could serve as valuable sources of wheat chromatin suitable for further improvements of rye.     

Gene dosage effects in human diploid and tetraploid fibroblasts

The effects of cell ploidy on the biochemical characteristics of cultured cells were compared using human diploid vs tetraploid fibroblasts isolated with a non-selective method. Their DNA replication was compared by thymidine incorporation, and DNA content by Feulgen staining and quantitative analysis. Their RNA and protein content, cell sizes and the specific activities of glucose-6-phosphate dehydrogenase (G-6-PD) and 6-phosphogluconate dehydrogenase (6-PGD) were assayed quantitatively. With the exception of RNA content, all other parameters demonstrated a 2-fold increase reflecting the increase in cell ploidy. These direct gene dosage effects on the genetic material and functional expression of the human genome were in contrast to previous observations in other species and validate the use of human intraspecific euploid hybrids for biochemical and genetic studies.     

Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration

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Region specific knock-out reveals distinct roles of chromatin modifiers in adult neurogenic niches

Histone methyltransferases (HMTs) are present in heterogeneous cell populations within the adult brain including neurogenic niches. Yet the question remains whether loss of HMTs and the resulting changes in histone methylation alter cell fate in a region-specific manner. We utilized stereotaxic injection of Cre recombinant protein into the adult neurogenic niches, the subventricular zone (SVZ) adjacent to the lateral ventricle and the subgranular zone (SGZ) of the dentate gyrus. We confirmed that Cre protein was enzymatically active in vivo and recombination events were restricted to the vicinity of injection areas. In this study, we focus on using Cre mediated recombination in mice harboring floxed HMT: enhancer of zeste homolog 2 (EZH2) or suppressor of variegation homolog (Suv4-20h). Injectable Cre protein successfully knocked out either EZH2 or Suv4-20h, allowing assessment of long-term effects in a region-specific fashion. We performed meso-scale imaging and flow cytometry for phenotype analysis and unbiased quantification. We demonstrated that regional loss of EZH2 affects the differentiation paradigm of neural stem progenitor cells as well as the maintenance of stem cell population. We further demonstrated that regional loss of Suv4-20h influences the cell cycle but does not affect stem cell differentiation patterns. Therefore, Cre protein mediated knock-out a given HMT unravel their distinguishable and important roles in adult neurogenic niches. This Cre protein-based approach offers tightly-controlled knockouts in multiple cell types simultaneously for studying diverse regulatory mechanisms and is optimal for region-specific manipulation within complex, heterogeneous brain architectures.     

Meiotic prophase in diploid and tetraploid strains ofAllomyces macrogynus

Summary Three-dimensional serial section reconstructions of meiotic prophase nuclei ofAllomyces macrogynus (Chytridiomycetes, Blastocladiales) have been carried out. Serial section reconstructions of pachytene nuclei have revealed that the fungus when grown at 23 °C is an autotetraploid and is a diploid when grown at 35 °C for at least 6 months or on a substrate containing para-fluorophenylalanine for 1–2 weeks.Studies of the duplication and migration of the centrioles during the first stages of prophase revealed the existence of four centrioles in the 23 °C strain after centriole duplication and two centrioles in the 35 °C strain after duplication. It is observed that a bivalent attaches to the nuclear envelope at a site where a centriole is situated. It is proposed that the presence of the four centrioles in the 23 °C strain is due to the fact that each bivalent is represented twice in the strain.     

A comparison of mutation induction in diploid and tetraploid rice

Summary A comparative assessment of the frequency and spectrum of chlorophyll mutations in the M ₂ and M ₃ of three diploids and one tetraploid of rice after X-irradiation was made. As well as a linear relationship of the frequency of mutations with the dose of mutagen, a saturation effect was also evident. Among the three diploids, the maximum frequency of mutations was observed in T. N. 1, followed by G. E. B. 24 and A. S. D. 8. The diploid of G. E. B. 24 showed a higher frequency of mutations than the tetraploid when measured on the M₁ plant basis only. The diploids showed a higher rate of mutations in the M ₂ than in the M₃.There was no relationship between the frequency of different types of chlorophyll mutations and the dose of X-rays. Albina, occurred in greater proportion than the other types of mutations in the diploids as well as in the tetraploid. The diploid showed a wider spectrum in the M ₂, whereas the tetraploid recorded the maximum types of mutations in the M ₃. Striking differences in the spectrum and the relative frequency of each type were observed among the three diploids and also between the diploid G. E. B. 24 and its tetraploid.The frequency and spectrum of induced mutations in the diploid and autotetraploid provided an insight into the genetic behaviour of the diploid and autotetraploid of G. E. B. 24, indicating that the genetics of diploidisation of the existing diploid rice may give evidence on the nature of the evolutionary pathway.