Interactions between the scs and Vi genes in alloplasmic durum wheat.

Two nuclear genes, vitality (Vi) on an A- or B-genome chromosome and species cytoplasm specific (scs) on a 1DL telosome from Triticum aestivum L. or a telosome from Aegilops uniaristata Vis. (un telosome), improved compatibility between the nucleus of Triticum turgidum L. var. durum and the cytoplasm of Ae. longissima S. &M. or Ae. uniaristata. To study interactions between Vi and scs and to determine the chromosomal location of Vi, 29-chromosome fertile plants were crossed with 13 D-genome disomic-substitution (d-sub) lines [except 5D(5A)] of 'Langdon' durum. F1 and backcross progenies were examined for meiotic chromosome number and pairing, fertility, and plant vigor. In 11 crosses, Vi restored seed viability but produced double-monosomics (d-monos) with greatly reduced growth and vigor. In contrast, crosses involving 1D(1A) and 1D(1B) d-sub lines produced d-monos with normal vigor and anthesis but nonfunctional pollen. A backcross of 1D + 1A d-mono F1 and 1D(1A) d-sub lines produced 11 male steriles; 3 had 13 II + 1 II 1D + 1 I 1A, 2 had 13 II + 2 I, 1 had 13 II + 1 II 1D(1A), and 5 were not examined. Crosses of 1D + 1A d-mono F1 with control durum, lo durum (with 1DL), and un durum (with un telosome) lines produced 16 male-sterile d-monos and 14 fertiles with 14 II + 1 I 1D, showing that 15-chromosome female gametes transmitted monosomes 1A and 1D. However, BC2F1's from 1D + 1B d-mono x fertile line with un telosome included 20 male-sterile d-monos, 6 fertile triple monosomics (13 II + 1 I 1D + 1 I 1B + t I un telosome), and 1 fertile plant with a 1B/1D translocation. Unlike d-mono 1A + 1D, d-mono 1B + 1D did not transmit 15-chromosome female gametes with monosomes 1D and 1B. Additional backcrosses also indicated that homozygous scs caused male sterility in 1D(1A) and 1D(1B) d-subs and that the procedure used was not suitable for the chromosomal location of Vi.     

Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat

Background

Wheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological properties than their parents. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic condition, three mitochondrial genomes of the Triticum-Aegilops species were sequenced: 1) durum alloplasmic line with the Ae. longissima cytoplasm that carries the T. turgidum nucleus designated as (lo) durum, 2) the cytoplasmic donor line, and 3) the nuclear donor line.

Results

The mitochondrial genome of the T. turgidum was 451,678 bp in length with high structural and nucleotide identity to the previously characterized T. aestivum genome. The assembled mitochondrial genome of the (lo) durum and the Ae. longissima were 431,959 bp and 399,005 bp in size, respectively. The high sequence coverage for all three genomes allowed analysis of heteroplasmy within each genome. The mitochondrial genome structure in the alloplasmic line was genetically distant from both maternal and paternal genomes. The alloplasmic durum and the Ae. longissima carry the same versions of atp6, nad6, rps19-p, cob and cox2 exon 2 which are different from the T. turgidum parent. Evidence of paternal leakage was also observed by analyzing nad9 and orf359 among all three lines. Nucleotide search identified a number of open reading frames, of which 27 were specific to the (lo) durum line.

Conclusions

Several heteroplasmic regions were observed within genes and intergenic regions of the mitochondrial genomes of all three lines. The number of rearrangements and nucleotide changes in the mitochondrial genome of the alloplasmic line that have occurred in less than half a century was significant considering the high sequence conservation between the T. turgidum and the T. aestivum that diverged from each other 10,000 years ago. We showed that the changes in genes were not limited to paternal leakage but were sufficiently significant to suggest that other mechanisms, such as recombination and mutation, were responsible. The newly formed ORFs, differences in gene sequences and copy numbers, heteroplasmy, and substoichiometric changes show the potential of the alloplasmic condition to accelerate evolution towards forming new mitochondrial genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-67) contains supplementary material, which is available to authorized users.     

Breeding technology of alloplasmic wheat

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Unusual inheritance of the mitochondrial genome organization in the progeny of reciprocal crosses between alloplasmic hexaploid wheat regenerants

The transmission of a structurally-hypervariable fraction of the mitochondrial genome has been studied in 42 F₁ progenies obtained from reciprocal crosses between self-pollinated alloplasmic wheat plants regenerated after long-term somatic embryogenesis. This fraction of the genome is maternally and stoichiometrically inherited. In contrast, some additional restriction fragments specific to regenerated plants display a more complex mode of sexual transmission: one of the additional fragments was stoichiometrically and systematically inherited whereas two others were detected only in certain F₁ hybrids. Assuming that the detection, by Southern analysis, of such a fragment in regenerated plants is due to the amplification of a pre-existing substoichiometric molecule generated by the activation of a rare recombination event, our results suggest that the probability of detecting a novel fragment in the F₁ hybrids could be determined by the length of the repeated sequence at which recombination occurs.     

Responses of alloplasmic (cytoplasm=Triticum timopheevii) and euplasmic wheats (Triticum aestivum) to photoperiod and vernalization

Summary Heritability estimated from sire family variance components, ignoring dams, pools conventional paternal and maternal half sib estimates, in a way which is biased upward, and sub-optimal for minimizing the sampling variance. Standard error of a sire family estimate will be smaller than that of the equivalent paternal half sib estimate, but not as small as that of an estimate obtained by optimal pooling of paternal and maternal half sib estimates. If only additive genetic variance components are significant, the bias may be removed by use of a computed average genetic relationship for sire families, in place of a nominal R = 0.25. Average genetic relationship may be computed from mean and variance of dam family size within sire families. If dominance, epistatic, or maternal components are significant, this simple correction is not appropriate. In situations likely to be encountered in large domestic species such as sheep and cattle (dam family size small and uniform) bias will be negligible. The method could be useful where cost of dam identification is a limiting factor.     

The adaptability of wheat alloplasmic lines during hybridization

The adaptability of alloplasmic wheat lines and their hybrids with a wheat-allogenic amphiploid and wheat was studied. The influence of the nuclear genome and the interaction of nuclear and cytoplasm genomes on the adaptability of wheat and its hybrids has been established. For an assessment of adaptability, it is necessary to use a complex of attributes (morphological, cytogenetic, and resistance to abiotic and biotic factors of the environment).     

Heteroplasmy of mitochondrial DNA in the ophiuroid Astrobrachion constrictum

We demonstrate the presence of mitochondrial heteroplasmy for the cytochrome oxidase I (COI) gene of the brittle star (Astrobrachion constrictum). One of the 117 individuals analyzed contained two distinct single-strand conformation polymorphism (SSCP) haplotypes differing by two substitutions; another showed sequence evidence for heteroplasmy. We used polymerase chain reaction (PCR) cloning, SSCP, and sequencing of a 480 bp region of the 5' end of COI to isolate and characterize these haplotypes. This is the first properly substantiated case of heteroplasmy in an echinoderm species and may have arisen from paternal leakage.     

Plasmon analysis in wheat alloplasmic lines using morphological and chloroplast microsatellite markers

Inheritance of plant traits mainly depends upon nuclear genes, cytoplasmic factors and their interactions. In the present study, 32 alloplasmic lines accompanied by a euplasmic parental line (control) were evaluated using molecular (chloroplast microsatellite) and morpho-physiological traits during 2010–2011 and 2011–2012. The results of combined analysis of variance showed the significant effect of growing seasons on most of the studied traits as well as the significant effect of cytoplasm on plant height, leaf net CO₂ assimilation rate and grain yield per plant. Results of cluster analysis divided the six plasmons based on their phenotypic effects into three groups: (1) R and S^v type, D (Aegilops typica and Ae. ventricosa) and D² type, as well as B-type plasmon (euplasmic line); (2) a single plasmon of M type and three plasmons of B type; (3) all other B-type and a single D-type plasmon (Aegilops cylindrica). Molecular analysis showed that 20 primer pairs out of 26 chloroplastic microsatellite markers (cpSSR) produced polymorphic bands in the alloplasmic lines. A total of 50 alleles were identified with an average of 2.5 alleles per locus. In this study, polymorphism information content (PIC) ranged from 0.05 (WCt17 primer) to 0.49 (WCt9 primer). Cluster analysis of molecular data revealed that the alloplasmic lines belong to two major clusters, in which differentiation of cytoplasmic types belonging to the genus Triticum and Aegilops has been evident. Likewise, analysis of molecular variance showed significant differences between two studied groups (F _ST = 0.67, P < 0.001). Overall, our findings indicated that the cpSSR markers can be valuable resources of polymorphic markers for the analysis of cytoplasm of Triticeae species, with the potential for clear differentiation in close species and genera of this tribe.     

Inheritance of chloroplast and mitochondrial DNA in alloplasmic forms of the genus Daucus

The inheritance of mitochondrial (mt) and chloroplast (ct) DNA in the progeny from interspecific crosses between the cultivated carrot (Daucus carota sativus) and wild forms of the genus Daucus was investigated by analysis of mt and ct RFLPs in single plants of the parental and filial generations. We observed a strict maternal inheritance of the organellar DNAs in all interspecific crosses examined. Previous studies on putative F₂ plants from a cross between Daucus muricatus x D. carota sativus suggested paternal inheritance of ctDNA. Our reinvestigation of this material revealed that the mtDNA of the putative F₂ plants differed from the mtDNA of both putative parents. Therefore, our data suggest that the investigated material originated from other, not yet identified, parents. Consequently, the analysis of this material cannot provide evidence for a paternal inheritance of ctDNA.     

三个小麦春化基因的时空表达特性分析(英文)

为明确小麦春化基因的时空表达特性,以中国春和洛旱2号小麦品种为试验材料,利用半定量RT-PCR技术,分析了3个春化基因VERNALIZATION1(VRN1)、VRN2和VRN3的时空表达特性。结果表明,VRN1在中国春的三叶期叶片和根、灌浆期的茎秆和旗叶、花药、胚珠和发育的种子中均有不同程度的表达。在开花前,表达水平呈上升趋势,而花后呈降低的趋势,在干种子和萌发种子的胚芽中没有检测到表达;在洛旱2号中,除了在三叶期的叶片和根中没有检测到表达外,VRN1的表达特性与中国春有相同的趋势。VRN2只在三叶期的叶片和萌发种子的胚芽中表达,在其他检测的组织中没有表达;VRN3的表达与VRN1的时空表达特性相似,但在根中未检测到表达。这一结果为进一步分析普通小麦品种春化发育的分子调控机理提供了重要信息。     

Heteroplasmy in mice with deletion of a large coding region of mitochondrial DNA

Polymorphism of animal mitochondrial DNA (mtDNA) has been shown to involve point mutations and limited length variations affecting essentially noncoding regions. In two wild mice of the European subspecies Mus mus musculus we found a mitochondrial mutant with a very large deletion in a coding region. The deletion is 5 kbp long (31% of the mitochondrial chromosome) and encompasses six tRNA genes and seven protein genes. The two mice were heteroplasmic: they contained a mixture of normal mtDNA and the deletion mutant. Although the latter is functionally defective, it represents 78%-79% of the mtDNA molecules in our preparations from each animal.      

Heteroplasmy of mitochondrial genomes in clonal cultures from patients with Kearns-Sayre syndrome

We have analyzed heteroplasmy of mitochondrial DNA in clonal cultures from two patients with Kearns-Sayre syndrome, and have found that individual muscle or fibroblast clones contained either a mixed (i.e. heteroplasmic) population of normal and deleted mitochondrial DNAs, or only normal mitochondrial DNAs (i.e. homoplasmic at a level of detection of less than 1% deleted genomes). The heteroplasmic clones grew significantly more slowly than did "homoplasmic" clones, probably due to defects of respiratory chain enzymes containing mtDNA-encoded polypeptides.     

Differential rRNA genes expression in bread wheat and its inheritance

The expression of the ribosomal RNA (rRNA) genes from rye, located within the nucleolus organizer regions (NORs), is repressed by cytosine methylation in wheat x rye hybrids and in triticale, as consequence of nucleolar dominance. Our previous study revealed that bread wheat cultivars with a maximum number of four Ag-NORs presented high level of rDNA cytosine methylation when compared to others with a maximum of six Ag-NORs. In order to evaluate the inheritance of the Ag-NORs number and NOR methylation patterns, we produced F₁ hybrids between bread wheat cultivars with four Ag-NORs and bread wheat cultivars with six Ag-NORs (in the direct and reciprocal senses). The F₂ progenies of these F₁ hybrids were also evaluated for the NOR number and methylation patterns. Parent bread wheat cultivars with a maximum of four Ag-NORs after treated with 5-azacytidine evidenced a maximum of six Ag-NORs per metaphase cell and a maximum of six nucleoli per interphase nucleus, confirming that the expression of the rRNA genes in bread wheat is related to cytosine methylation. Most of the F₁ hybrids showed a maximum number of four or six Ag-NORs, similarly to that of the female parent suggesting a non-mendelian inheritance, while other hybrids presented four or six Ag-NORs in both senses of the cross. The F₁ NOR methylation patterns showed some fragments common to their parents but also novel fragments suggesting genomic and/or chromosome rearrangements after hybridization. Despite the different NOR patterns among the parents, an invariable NOR pattern was found among the F₁ plants suggesting a tendency to stability, which was also transmitted to the F₂. The F₂ progenies showed plants with a maximum of four, five and/or six Ag-NORs. The ratio of plants with four, five and/or six Ag-NORs per F₂ progeny was variable and did not follow any specific mendelian proportion. These results allowed us to suggest that the inheritance of the number of Ag-NORs by the F₁ and F₂ plants did not follow any mendelian inheritance and were not correlated to NOR methylation patterns in contrast to what was verified for their parents.     

Differential expression of wheat genes during cold acclimation

Overwintering crops such as winter wheat display a significant increase in freezing tolerance during periods of cold acclimation (CA). To gain a better understanding of the molecular mechanisms of CA, it is important to unravel the functions and regulations of CA-associated genes. Differential screening of a cDNA library constructed from cold acclimated crown tissue of winter wheat identified three novel CA-associated cDNA clones. Nucleotide sequence analysis showed that the clones encode a high mobility globular protein (HMGB1), a glycine-rich RNA-binding protein (TaGRP2), and a LEAD-11 dehydrin (DHN14). Accumulation of the three mRNAs during 14 days of CA was differentially regulated. In response to drought, and ABA, DHN14 mRNA rapidly accumulated while HMGB1 and TaGRP2 mRNA levels remained unchanged. The possible functions of each of these genes in cold acclimation are discussed. The text was submitted by the authors in English.     

Physiological mechanisms of adaptation of alloplasmic wheat hybrids to soil drought

We studied physiological mechanisms of plant adaptation to drought for two alloplasmic wheat (Triticum aestivum L.) hybrids (APHs) on the cytoplasm of rye (Secale cereale L.) or ovate goatgrass (Aegilops ovata L.) and two standard regionalized spring wheat cultivars, Kometa and Priokskaya. In response to plant tissue dehydration, APHs rapidly reduced the transpiration rate and lost much less water than standard cultivars. During drought, peroxidase activity was significantly increased only in APH on the rye cytoplasm, whereas it declined substantially in cv. Kometa. Peroxidation of lipids (POL) was activated in cv. Kometa stronger than in hybrids, which also indicates that, in this cultivar, there was no complete detoxification of hydrogen peroxide under stress conditions. After watering resumption, APHs displayed a better capacity for reparation than standard cultivars, which was manifested in peroxidase activation and POL suppression, i.e., in more complete reduction of the oxidative stress consequences. We concluded that a higher APH drought resistance, as compared with standard cultivars, was determined by their more efficient antioxidant defense and a better capacity for recovery.     

Differential expression of wheat genes during cold acclimation

Overwintering crops such as winter wheat display significant increase in freezing tolerance during a period of cold acclimation (CA). To gain better understanding of molecular mechanisms of CA, it is important to unravel functions and regulations of CA-associated genes. Differential screening of a cDNA library constructed from cold acclimated crown tissue of winter wheat identified three novel CA-associated cDNA clones. Nucleotide sequence analysis showed that the clones encode a high mobility globular protein (HMGB1), a glycine-rich RNA-binding protein (TaGRP2), and a LEA D-11 dehydrin (DHN14). Accumulation of the three mRNAs during 14 days of CA was differentially regulated. In response to drought, and ABA, DHN14 mRNA rapidly accumulated while HMGB1 and TaGRP2 mRNA levels remained unchanged. The possible functions of each of these genes in cold acclimation are discussed.     

Isolation and comparative expression analysis of six MBD genes in wheat

The 5-methylcytosines (m5C) play critical roles in epigenetic control, often being recognized by proteins containing an MBD. In this study, we isolated six wheat cDNAs with open reading frame encoding putative methyl-binding domain proteins, which were designated as TaMBD1-TaMBD6, respectively. BLASTX searches and phylogenetic analysis suggested that the six TaMBD genes belonged to four (I, II, III and VIII) of the eight subclasses of MBD family. Genomic analysis showed that a 1386 bp intron was included in TaMBD1 and a 12-bp intron was found in TaMBD4. The expression profiles of the six TaMBDs were studied via Q-RT-PCR and the results indicated that the TaMBDs were differentially expressed in detected wheat tissues. It was interesting to note that 3 TaMBDs were highly expressed in dry seeds and endosperms. Moreover, the differential expression patterns of TaMBDs were observed in leaves and roots under water-stress. We concluded that multiple wheat MBD genes were present and they might play important roles in wheat growth and development, as well as in the water-stress response.     

Segregation distortion of marker nuclear genes in alloplasmic and isoplasmic lines of barley

Inheritance of barley nuclear genes responsible for various morphological marker traits was studied in hybrid populations F2 and Fa. Nine marker genes showed deviation from Mendelian monogenic inheritance depending on the cross direction and maternal cytoplasm. Segregation biases to both recessive mutant and dominant normal phenotypes were observed. Mechanisms of the segregation bias related to cytoplasm substitution in iso- and alloplasmic lines are discussed.     

Limitations of allotopic expression of mitochondrial genes in mammalian cells

The possibility of expressing mitochondrial DNA-coded genes in the nuclear-cytoplasmic compartment provides an attractive system for genetic treatment of mitochondrial disorders associated with mitochondrial DNA mutations. In theory, by recoding mitochondrial genes to adapt them to the universal genetic code and by adding a DNA sequence coding for a mitochondrial-targeting sequence, one could achieve correct localization of the gene product. Such transfer has occurred in nature, and certain species of algae and plants express a number of polypeptides that are commonly coded by mtDNA in the nuclear-cytoplasmic compartment. In the present study, allotopic expression of three different mtDNA-coded polypeptides (ATPase8, apocytochrome b, and ND4) into COS-7 and HeLa cells was analyzed. Among these, only ATPase8 was correctly expressed and localized to mitochondria. The full-length, as well as truncated forms, of apocytochrome b and ND4 decorated the periphery of mitochondria, but also aggregated in fiber-like structures containing tubulin and in some cases also vimentin. The addition of a hydrophilic tail (EGFP) to the C terminus of these polypeptides did not change their localization. Overexpression of molecular chaperones also did not have a significant effect in preventing aggregations. Allotopic expression of apocytochrome b and ND4 induced a loss of mitochondrial membrane potential in transfected cells, which can lead to cell death. Our observations suggest that only a subset of mitochondrial genes can be replaced allotopically. Analyses of the hydrophobic patterns of different polypeptides suggest that hydrophobicity of the N-terminal segment is the main determinant for the importability of peptides into mammalian mitochondria.