Plant Chromosomes Research Articles

Heterosis as Investigated in Terms of Polyploidy and Genetic Diversity Using Designed Brassica juncea Amphiploid and Its Progenitor Diploid Species

Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB) as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA) and B. nigra (2n = 16; BB). Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11) and the corresponding progenitor genotypes of B. rapa (10×10) and B. nigra (9×9) were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47) of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis.

Distribution of 45S rDNA sites in chromosomes of plants: Structural and evolutionary implications

Background45S rDNA sites are the most widely documented chromosomal regions in eukaryotes. The analysis of the distribution of these sites along the chromosome in several genera has suggested some bias in their distribution. In order to evaluate if these loci are in fact non-randomly distributed and what is the influence of some chromosomal and karyotypic features on the distribution of these sites, a database was built with the position and number of 45S rDNA sites obtained by FISH together with other karyotypic data from 846 plant species.ResultsIn angiosperms the most frequent numbers of sites per diploid karyotype were two and four, suggesting that in spite of the wide dispersion capacity of these sequences the number of rDNA sites tends to be restricted. The sites showed a preferential distribution on the short arms, mainly in the terminal regions. Curiously, these sites were frequently found on the short arms of acrocentric chromosomes where they usually occupy the whole arm. The trend to occupy the terminal region is especially evident in holokinetic chromosomes, where all of them were terminally located. In polyploids there is a trend towards reduction in the number of sites per monoploid complement. In gymnosperms, however, the distribution of rDNA sites varied strongly among the sampled families.ConclusionsThe location of 45S rDNA sites do not vary randomly, occurring preferentially on the short arm and in the terminal region of chromosomes in angiosperms. The meaning of this preferential location is not known, but some hypotheses are considered and the observed trends are discussed.

Foreword: sex and sex chromosomes—new clues from nonmodel species

IntroductionTheinvitationfromtheeditorsDrConlyRiederandProfHerbert Macgregor to edit this issue gave us the oppor-tunity to highlight some biological situations in whichsex chromosomes and sex determination are nonstan-dard, as the result of mutation or capricious evolution.Althoughtheymay,indeed,seemweird,thesenonmodelspecies provide us with the genetic variation that candeliver unique, and sometimes surprising, information.The focus of this issue is, therefore, how much wecan learn from such accidents of nature, comple-mented by variants produced to order. This issuetherefore contains articles on sex chromosomes inplants and insects as well as nonmodel vertebrates.The articles contain new data as well as new ideas,hypotheses and opinions, which we hope will attractcomment and reaction from readers in other fields. Wehave gathered articles on sex chromosomes and thegenes directly involved in sex determination but alsoincludedarticlesonsexdifferentiation,includinggeneticpathways in the development of gonads.Our other focus is on the extraordinarily rapidprogress that can be made using the tools of moderngenomics, even in quite bizarre organisms. Each of thesystems highlighted in this issue have had their loyaladherents, often over a very long time: for instance,the Y chromosome-less mole vole was first describedby Karl Fredga (1970), karyotypes of reptiles were allthe rage in the 1970s and bird sex determination hasbeen studied avidly for more than 50 years. However,without access to the armory of molecular techniques,many of these systems have been accessible only atthe cytological level.Sex chromosome organization and evolutionSex chromosomes are defined by a sex determininggene or genes, which trigger the genetic pathways thatcause undifferentiated gonads to differentiate intoeither ovary or testes. Depending on whether the sex-determining gene is male- or female-determining, sexchromosome systems are defined as XX female:XYmale (in which the heterogametic XY male producesX- or Y-bearing sperm) or ZZ male:ZW female (inwhich the heterogametic ZW female produces Z- or

The sex-specific region of sex chromosomes in animals and plants

Our understanding of the evolution of sex chromosomes has increased greatly in recent years due to a number of molecular evolutionary investigations in divergent sex chromosome systems, and these findings are reshaping theories of sex chromosome evolution. In particular, the dynamics of the sex-determining region (SDR) have been demonstrated by recent findings in ancient and incipient sex chromosomes. Radical changes in genomic structure and gene content in the male specific region of the Y chromosome between human and chimpanzee indicated rapid evolution in the past 6 million years, defying the notion that the pace of evolution in the SDR was fast at early stages but slowed down overtime. The chicken Z and the human X chromosomes appeared to have acquired testis-expressed genes and expanded in intergenic regions. Transposable elements greatly contributed to SDR expansion and aided the trafficking of genes in the SDR and its X or Z counterpart through retrotransposition. Dosage compensation is not a destined consequence of sex chromosomes as once thought. Most X-linked microRNA genes escape silencing and are expressed in testis. Collectively, these findings are challenging many of our preconceived ideas of the evolutionary trajectory and fates of sex chromosomes.

Transformation of trehalose synthase gene (TPS Gene) into corn inbred line and identification of drought tolerance

Trehalose synthase gene (TPS gene) was transferred into maize inbred line Zheng58 with the improved pollen tube path method. At the three to five leaf stage, selection with spray Basta (0.7%) solution was conducted, and was then followed by polymerase chain reaction (PCR) and PCR-southern detection. The results showed that the new gene was transferred into the plants and integrated into the plant chromosomes. The initial drought-tolerance test in farmland confirmed that the drought resistance of transgenic plants was higher than that of non-transgenic plants. The results show that the new maize drought resistance germplasm can be gained by means of pollen tube path which is a feasible, effective and new way for maize drought resistance breeding. Key words: Maize, trehalose synthase gene (TPS Gene), drought resistance.

Transposon Ac/Ds -induced chromosomal rearrangements at the rice OsRLG5 locus

Previous studies have shown that pairs of closely-linked Ac/Ds transposable elements can induce various chromosomal rearrangements in plant genomes. To study chromosomal rearrangements in rice, we isolated a line (OsRLG5-161) that contains two inversely-oriented Ds insertions in OsRLG5 (Oryza sativa Receptor like kinase Gene 5). Among approximately 300 plants regenerated from OsRLG5-161 heterozygous seeds, 107 contained rearrangements including deletions, duplications and inversions of various sizes. Most rearrangements were induced by previously identified alternative transposition mechanism. Furthermore, we also detected a new class of rearrangements that contain juxtaposed inversions and deletions on the same chromosome. We propose that these novel alleles were generated by a previously unreported type of alternative transposition reactions involving the 5′ and 3′ termini of two inversely-oriented Ds elements located on the same chromatid. Finally, 11% of rearrangements contained inversions resulting from homologous recombination between the two inverted Ds elements in OsRLG5-161. The high frequency inheritance and great variety of rearrangements obtained suggests that the rice regeneration system results in a burst of transposition activity and a relaxation of the controls which normally limit the transposition competence of individual Ds termini. Together, these results demonstrate a greatly enlarged potential of the Ac/Ds system for plant chromosome engineering.

Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous FungusNeurospora tetrasperma

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (<5 MYA), combined with a long history of genetic and cytological research, make this fungus an ideal model for studying the evolutionary consequences of suppressed recombination. Here we compare genome sequences from two N. tetrasperma strains of opposite mating type to determine whether structural rearrangements are associated with the nonrecombining region and to examine the effect of suppressed recombination for the evolution of the genes within it. We find a series of three inversions encompassing the majority of the region of suppressed recombination and provide evidence for two different types of rearrangement mechanisms: the recently proposed mechanism of inversion via staggered single-strand breaks as well as ectopic recombination between transposable elements. In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration.

In vitro induction of tetraploid plants from callus cultures of diploid bananas (Musa acuminata, AA group) ‘Kluai Leb Mu Nang’ and ‘Kluai Sa’

Tetraploid plants were induced successfully from diploid bananas Musa acuminata (AA genome) ‘Kluai Leb Mu Nang’ and ‘Kluai Sa’ (2n = 2x = 22) with in vitro oryzalin treatment. Calluses from in vitro-grown shoot tips of both cultivars were treated with oryzalin at concentrations of 1.5 or 3 mg l−1 for 24, 48 and 72 h, respectively. The oryzalin treatments produced tetraploids at a frequency of 15.6% in ‘Kluai Leb Mu Nang’ and 16.7% in ‘Kluai Sa’ as detected by flow cytometry. Chromosome counting showed that the tetraploid plant chromosome number was (2n = 4x = 44). The selected tetraploid plants were transplanted in the field and variations in the morphological characteristic of leaf shape and fruit bunch compared to normal diploid plants were found under the same growing condition even after 3 years of cultivation.

TheIndex to Plant Chromosome Numbers(Ipcn): Three Decades of Publication by the Missouri Botanical Garden Come to An End

The<i>Index to Plant Chromosome Numbers</i>(Ipcn): Three Decades of Publication by the Missouri Botanical Garden Come to An End

Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes.

Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant- and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single- and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species.

Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences

The compactness of plant chromosomes and the structure of the plant cell wall and cytoplasm provide a great obstacle to fluorescence in situ hybridization (FISH) for single-copy or low-copy DNA sequences. Consequently, many new methods for improving spatial resolution via chromosomal stretching have been employed to overcome this technical challenge. In this article, a technique for extracting cell-wall free nuclei at mitotic interphase, then using these nuclei to prepare extended DNA fibers (EDFs) by the method of a receding interface, whereby slide-mounted chromatin produces EDFs in concert with gravity-assisted buffer flow, was adopted as a result of the low frequency of EDF damage produced by this procedure. To examine the quality of these EDFs, we used single-copy gene encoding S-locus receptor kinase and multi-copy 5S rDNA (ribosomal DNA) as probes. The resulting EDFs proved suitable for high-resolution FISH mapping for repetitive DNA sequences, and the localization of a single-copy locus.

Sex Chromosomes in Land Plants

Sex chromosomes in land plants can evolve as a consequence of close linkage between the two sex determination genes with complementary dominance required to establish stable dioecious populations, and they are found in at least 48 species across 20 families. The sex chromosomes in hepatics, mosses, and gymnosperms are morphologically heteromorphic. In angiosperms, heteromorphic sex chromosomes are found in at least 19 species from 4 families, while homomorphic sex chromosomes occur in 20 species from 13 families. The prevalence of the XY system found in 44 out of 48 species may reflect the predominance of the evolutionary pathway from gynodioecy towards dioecy. All dioecious species have the potential to evolve sex chromosomes, and reversions back from dioecy to various forms of monoecy, gynodioecy, or androdioecy have also occurred. Such reversals may occur especially during the early stages of sex chromosome evolution before the lethality of the YY (or WW) genotype is established.

Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties

BackgroundDue to its overarching role in genome function, sequence-dependent DNA curvature continues to attract great attention. The DNA double helix is not a rigid cylinder, but presents both curvature and flexibility in different regions, depending on the sequence. More in depth knowledge of the various orders of complexity of genomic DNA structure has allowed the design of sophisticated bioinformatics tools for its analysis and manipulation, which, in turn, have yielded a better understanding of the genome itself. Curved DNA is involved in many biologically important processes, such as transcription initiation and termination, recombination, DNA replication, and nucleosome positioning. CpG islands and tandem repeats also play significant roles in the dynamics and evolution of genomes.ResultsIn this study, we analyzed the relationship between these three structural features within rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genomes. A genome-scale prediction of curvature distribution in rice and Arabidopsis indicated that most of the chromosomes of both genomes have maximal chromosomal DNA curvature adjacent to the centromeric region. By analyzing tandem repeats across the genome, we found that frequencies of repeats are higher in regions adjacent to those with high curvature value. Further analysis of CpG islands shows a clear interdependence between curvature value, repeat frequencies and CpG islands. Each CpG island appears in a local minimal curvature region, and CpG islands usually do not appear in the centromere or regions with high repeat frequency. A statistical evaluation demonstrates the significance and non-randomness of these features.ConclusionsThis study represents the first systematic genome-scale analysis of DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant genomes, and finds that not all of the chromosomes in plants follow the same rules common to other eukaryote organisms, suggesting that some of these genomic properties might be considered as specific to plants.

IP6K gene identification in plant genomes by tag searching

BackgroundPlants have played a special role in inositol polyphosphate (IP) research since in plant seeds was discovered the first IP, the fully phosphorylated inositol ring of phytic acid (IP6). It is now known that phytic acid is further metabolized by the IP6 Kinases (IP6Ks) to generate IP containing pyro-phosphate moiety. The IP6K are evolutionary conserved enzymes identified in several mammalian, fungi and amoebae species. Although IP6K has not yet been identified in plant chromosomes, there are many clues suggesting its presences in vegetal cells.ResultsIn this paper we propose a new approach to search for the plant IP6K gene, that lead to the identification in plant genome of a nucleotide sequence corresponding to a specific tag of the IP6K family. Such a tag has been found in all IP6K genes identified up to now, as well as in all genes belonging to the Inositol Polyphosphate Kinases superfamily (IPK). The tag sequence corresponds to the inositol-binding site of the enzyme, and it can be considered as characterizing all IPK genes. To this aim we applied a technique based on motif discovery. We exploited DLSME, a software recently proposed, which allows for the motif structure to be only partially specified by the user. First we applied the new method on mitochondrial DNA (mtDNA) of plants, where such a gene could have been nested, possibly encrypted and hidden by virtue of the editing and/or trans-splicing processes. Then we looked for the gene in nuclear genome of two model plants, Arabidopsis thaliana and Oryza sativa.ConclusionsThe analysis we conducted in plant mitochondria provided the negative, though we argue relevant, result that IP6K does not actually occur in vegetable mtDNA. Very interestingly, the tag search in nuclear genomes lead us to identify a promising sequence in chromosome 5 of Oryza sativa. Further analyses are in course to confirm that this sequence actually corresponds to IP6K mammalian gene.

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

Polymorphism and pedigree analysis of β-amylase isozymes in Australian wheat

β-Amylase encoded by multiple loci on chromosomes of triticeae crop plants is a starch metabolic enzyme with a significant physiological role in flour functionality. In this study, wheat grain β-amylase isozymes were characterized using an extensive Australian wheat population and genetic breeding/mapping lines. β-amylase isozymes were fractionated by high-resolution native polyacrylamide gel electrophoresis (PAGE) and validated by zymogram and peptide sequencing using electrospray ionization tandem mass spectrometry (ESI-MS/MS). Specific antibodies were generated against the β-amylase purified through protein chromatography and used for β-amylase identification. Further characterization of wheat β-amylases was carried out with immunoblotting and 2-dimensional electrophoresis (2-DE). The enzyme was found to be polymorphic among the Australian and foreign wheat cultivars, with a total of six isozymes: two common and four varying isozymes, the latter group including one novel β-amylase isozyme of fast-mobility in native PAGE, According to pedigree analysis, the origin of this particular isozyme was from the ancestral genotype, Ciano F 67.

Development and characterization of wheat-Psathyrostachys huashanica partial amphiploids for resistance to stripe rust

Two partial amphiploid lines, B113 (32 plants) and B21 (13 plants), derived from a wheat-Psathyrostachys huashanica intergeneric cross were characterized by Giemsa C-banding and SDS-PAGE and evaluated for stripe rust resistance. All 15 partial amphiploid plants were aneuploids with either 50 (8 plants), 51 (6 plants) or 54 (1 plant) chromosomes. Some showed regular meiosis and all the P. huashanica chromosomes were included, although not in a single plant. Of 45 plants 34 showed specific bands on SDS-PAGE representing high molecular weight glutenin subunit (HMW-GS) and 41 had bands representing P. huashanica low molecular weight glutenin subunit (LMW-GS), including two new subunits. All 45 plants were highly resistant (10) or immune (35) to stripe rust mixed races CYR-30, CYR-31, Shuiyuan 7 and Shuiyuan 14. These amphiploid plants could be useful germplasm for enhancing stripe rust resistance and might improve wheat grain quality.

Towards the development of better crops by genetic transformation using engineered plant chromosomes

Plant Biotechnology involves manipulation of genetic material to develop better crops. Keeping in view the challenges being faced by humanity in terms of shortage of food and other resources, we need to continuously upgrade the genomic technologies and fine tune the existing methods. For efficient genetic transformation, Agrobacterium-mediated as well as direct delivery methods have been used successfully. However, these methods suffer from many disadvantages especially in terms of transfer of large genes, gene complexes and gene silencing. To overcome these problems, recently, some efforts have been made to develop genetic transformation systems based on engineered plant chromosomes called minichromosomes or plant artificial chromosomes. Two approaches namely, "top-down" or "bottom-up" have been used for minichromosomes. The former involves engineering of the existing chromosomes within a cell and the latter de novo assembling of chromosomes from the basic constituents. While some success has been achieved using these chromosomes as vectors for genetic transformation in maize, however, more studies are needed to extend this technology to crop plants. The present review attempts to trace the genesis of minichromosomes and discusses their potential of development into plant artificial chromosome vectors. The use of these vectors in genetic transformation will greatly ameliorate the food problem and help to achieve the UN Millennium development goals.

Transformation of trehalose synthase gene (TPS Gene) into corn inbred line and identification of drought tolerance

Trehalose synthase gene (TPS gene) was transferred into maize inbred line Zheng58 with the improved pollen tube path method. At the three to five leaf stage, selection with spray Basta (0.7%) solution was conducted, and was then followed by polymerase chain reaction (PCR) and PCR-southern detection. The results showed that the new gene was transferred into the plants and integrated into the plant chromosomes. The initial drought-tolerance test in farmland confirmed that the drought resistance of transgenic plants was higher than that of non-transgenic plants. The results show that the new maize drought resistance germplasm can be gained by means of pollen tube path which is a feasible, effective and new way for maize drought resistance breeding. Key words: Maize, trehalose synthase gene (TPS Gene), drought resistance.

Plant centromeric retrotransposons: a structural and cytogenetic perspective

BackgroundThe centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity.ResultsWe have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD). A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active.ConclusionsComprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A). These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their transcriptional activity is consistent with the notion that the transcription of centromeric retrotransposons has a role in normal centromere function.