Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae)

BACKGROUND: Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. GENETIC RESOURCES: The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes.     

The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV

Background

Aerobic methanotrophs can grow in hostile volcanic environments and use methane as their sole source of energy. The discovery of three verrucomicrobial Methylacidiphilum strains has revealed diverse metabolic pathways used by these methanotrophs, including mechanisms through which methane is oxidized. The basis of a complete understanding of these processes and of how these bacteria evolved and are able to thrive in such extreme environments partially resides in the complete characterization of their genome and its architecture.

Results

In this study, we present the complete genome sequence of Methylacidiphilum fumariolicum SolV, obtained using Pacific Biosciences single-molecule real-time (SMRT) sequencing technology. The genome assembles to a single 2.5 Mbp chromosome with an average GC content of 41.5%. The genome contains 2,741 annotated genes and 314 functional subsystems including all key metabolic pathways that are associated with Methylacidiphilum strains, including the CBB pathway for CO₂ fixation. However, it does not encode the serine cycle and ribulose monophosphate pathways for carbon fixation. Phylogenetic analysis of the particulate methane mono-oxygenase operon separates the Methylacidiphilum strains from other verrucomicrobial methanotrophs. RNA-Seq analysis of cell cultures growing in three different conditions revealed the deregulation of two out of three pmoCAB operons. In addition, genes involved in nitrogen fixation were upregulated in cell cultures growing in nitrogen fixing conditions, indicating the presence of active nitrogenase. Characterization of the global methylation state of M. fumariolicum SolV revealed methylation of adenines and cytosines mainly in the coding regions of the genome. Methylation of adenines was predominantly associated with 5′-^m6ACN₄GT-3′ and 5′-CC^m6AN₅CTC-3′ methyltransferase recognition motifs whereas methylated cytosines were not associated with any specific motif.

Conclusions

Our findings provide novel insights into the global methylation state of verrucomicrobial methanotroph M. fumariolicum SolV. However, partial conservation of methyltransferases between M. fumariolicum SolV and M. infernorum V4 indicates potential differences in the global methylation state of Methylacidiphilum strains. Unravelling the M. fumariolicum SolV genome and its epigenetic regulation allow for robust characterization of biological processes that are involved in oxidizing methane. In turn, they offer a better understanding of the evolution, the underlying physiological and ecological properties of SolV and other Methylacidiphilum strains.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-914) contains supplementary material, which is available to authorized users.     

Agrobacterium tumefaciens-mediated genetic transformation of Digitalis purpurea L.

Genetic transformation is a tool of special interest for developing new biotechnological strategies for the production of bio-active compounds such as cardenolides, which are exclusively obtained from plants. To date, Digitalis plants are the main economically viable source of cardenolides for the pharmaceutical industry. This study describes the development of efficient plant regeneration and Agrobacterium-mediated genetic transformation protocols for Digitalis purpurea L. First, a plant regeneration procedure starting from leaf segments of in vitro-cultivated plants was established and the minimal inhibitory concentration of G-418 (geneticin) for callus induction was determined. Both leaf segments and callus tissue were sensitive to G-418 70 mg l^?1. Afterwards, two Agrobacterium strains were used to test their T-DNA transfer ability on D. purpurea leaf tissues, EHA105 and C58C1Rif^R (pMP90), both harboring the binary vector pTJK136. Strain C58C1Rif^R (pMP90) yielded a higher number of transformed plants than EHA105. Successful transformation was confirmed by histochemical β-glucuronidase (GUS) assays of the putative transgenic tissues and PCR analyses using β-glucuronidase (uidA)- and neomycin phosphotransferase II (nptII)-specific primers. Southern blot hybridization confirmed the stable integration of the nptII gene in the transgenic plants. In total, 518 independent transgenic lines were regenerated with an average of 6.91 transgenic lines per initial leaf segment infected with A. tumefaciens strain C58C1Rif^R (pMP90). To date, only a few studies have been published on the genetic transformation of Digitalis species. The protocols for plant regeneration and genetic transformation described in this paper will contribute to functional studies for a better understanding of cardenolide biosynthetic pathways and the metabolic engineering of cardenolides to develop high-yielding improved genotypes.     

Expression of ATP6V1C1 during oral carcinogenesis

We investigated the gene and protein expressions of V-type ATPase protein subunit C1 (ATP6V1C1) in cases of oral squamous cell carcinoma (OSCC) and contralateral normal mucosa in smokers, nonsmokers and former smokers. Subjects were separated into five groups of 15: group 1, smokers with OSCC; group 2, normal contralateral mucosa of OSCC patients; group 3, chronic smokers; group 4, former smokers who had stopped smoking 1 year earlier; group 5, individuals who had never smoked. Exfoliative cytology specimens from oral mucosa of smokers, former smokers and nonsmokers showed normal gene and protein expression. We found significantly greater gene expression in the OSCC group than in the nonsmoker groups. No difference in gene expression was observed between normal contralateral mucosa and nonsmoker groups, smoker and nonsmoker groups or former smoker and nonsmoker groups. We observed intense immunostaining for ATP6V1C1 protein in all cases of OSCC and weak or no staining in smoker, former smoker and nonsmoker groups. Significantly greater expression of ATP6V1C1 protein was observed in the OSCC group compared to the other groups, which supports the role of ATP6V1C1 in effecting changes associated with oral cancer. Analysis of the mucosae of chronic smokers, former smokers and the normal contralateral mucosa of patients with OSCC showed unaltered ATP6V1C1 gene and protein expression. Early stages of carcinogenesis, represented by altered epithelium of chronic smokers, had neither gene nor protein alterations as seen in OSCC. Therefore, we infer that the changes in ATP6V1C1 occur during later stages of carcinogenesis. Our preliminary study provides a basis for future studies of using ATP6V1C1 levels for detecting early stage OSCC.     

ABC50 Promotes Translation Initiation in Mammalian Cells

ABC50 is an ATP-binding cassette (ABC) protein, which, unlike most ABC proteins, does not possess membrane-spanning domains. ABC50 interacts with eukaryotic initiation factor 2 (eIF2), which plays a key role in translation initiation and its control. ABC50 binds to ribosomes, and this interaction requires both the N-terminal domain and at least one ABC domain. Knockdown of ABC50 by RNA interference impaired translation of both cap-dependent and -independent reporters, consistent with a positive role for ABC50 in the function of eIF2, which is required for both types of translation initiation. Mutation of the Walker box A or B motifs in both ABC regions of ABC50 yielded a mutant protein that exerted a dominant-interfering phenotype with respect to protein synthesis and translation initiation. Importantly, although dominant-interfering mutants of ABC50 impaired cap-dependent translation, translation driven by certain internal ribosome entry segments was not inhibited. ABC50 is located in the cytoplasm and nucleoplasm but not in the nucleolus. Thus, ABC50 is not likely to be directly involved in early ribosomal biogenesis, unlike some other ABC proteins. Taken together, the present data show that ABC50 plays a key role in translation initiation and has functions that are distinct from those of other non-membrane ABC proteins.ABC50 was first reported as a protein whose expression is increased following treatment of synoviocytes with tumor necrosis factor α (1). ABC50 was subsequently identified independently as a protein that co-purified extensively with eukaryotic initiation factor 2 (eIF2)² (2). In common with other members of the ATP-binding cassette (ABC) family of proteins, ABC50 contains two ATP-binding cassettes (also termed nucleotide-binding domains (NBDs)) (1). Unlike most other members of the group, however, it lacks recognizable trans-membrane domains.Sequence analysis revealed that ABC50 is a close relative of the yeast protein Gcn20p, which is required for the control by amino acids of the yeast eIF2 kinase, Gcn2p, which is activated by binding to uncharged tRNA molecules (3). Gcn20p is thought to cooperate with Gcn1p to bring uncharged tRNAs to Gcn2p during the elongation process; this couples the availability of amino acids for tRNA charging to the control of Gcn2p (4). However, Gcn20p and ABC50 differ in important respects. For example, whereas Gcn20p associates with ribosomes that are engaged in elongation, ABC50 apparently binds ribosomes involved in initiation as well as elongation (2). Its association with ribosomes is stimulated by ATP. In addition, although Gcn20p and ABC50 are similar in their ABC domains, they differ markedly in their N termini. Since it is only the N terminus of Gcn20p that is required to support the function of Gcn2p in yeast (4), it seems likely that ABC50 and Gcn20p play distinct roles.Tyzack et al. (2) have provided initial data indicating that ABC50 stimulates the formation of complexes between eIF2, GTP, and the initiator methionyl-tRNA in vitro. It did so without affecting the binding of guanine nucleotides to eIF2, indicating that the effect is likely to be on the association of initiator methionyl-tRNA with eIF2. The available data thus suggested that ABC50 might play a positive role in the initiation of protein synthesis. However, no data for this have previously been presented. Similarly, the manner in which ABC50 binds to ribosomes, the significance of its ABC domains, and other features remained unclear.The two NBDs of ABC proteins are involved in nucleotide binding/hydrolysis and contain a number of conserved features, including the Walker box A and B motifs and the “ABC signature motif” (usually LSGGQ) (5, 6). The NBDs of eukaryotic ABC proteins “dimerize” such that the two ATP-binding/hydrolytic sites involve Walker box A of one NBD and the ABC signature motif of the other.Certain other non-membrane ABC proteins are known to be involved in translation or its control (7). Indeed, three of the eukaryotic ABCF classes contain proteins involved in the control of protein translation. Class I proteins are exemplified by ABC50 (also termed ABCF1). Class III proteins (exemplified by yeast Gcn20p) can interact with the ribosome in an ATP-dependent manner (4). The proteins of Class IVA (elongation factor 3) mediate translation elongation in certain fungi. eEF3 stimulates binding of the eEF1·GTP·aminoacyl-tRNA ternary complex to the ribosomal A site by facilitating the release of the deacylated tRNA from the E site, thus stimulating protein synthesis (8, 9). On the other hand, Class IVB contains proteins thought to be important for the export of mRNAs from the nucleus in yeast (10).The ABCE1 gene product was originally identified for its inhibition of ribonuclease L (11) and is hence also termed RLI1. Yeast Rli1p associates with 40 S ribosomal subunits in vivo and can interact with eIF3 and eIF5 independently of ribosomes (12). The available data indicate that ABCE1 is involved in both ribosome biogenesis and mRNA translation and shuttles between cytoplasm and nucleus, possibly as a nucleocytoplasmic transporter (13–17).Here, we report the first detailed investigation into the function and interactions of ABC50. The data described here identify features of ABC50 that are required for its interaction with ribosomes. Most importantly, we provide the first evidence that ABC50 is required for efficient translation initiation in living cells and show that the requirement for ABC50 differs between cap-dependent and internal ribosome entry segment (IRES)-dependent translation. These and other data indicate that the function of ABC50 is distinct from those of other ABC proteins.     

The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases

Background

Molecular genetic approaches have much to offer population biology. Despite recent advances, convenient techniques to develop and screen highly-resolving markers can be limiting for some applications and taxa. We describe an improved PCR-based, cloning-free, nuclear marker development procedure, in which single-stranded conformation polymorphism (SSCP) plays a central role. Sequence-variable alleles at putative nuclear loci are simultaneously identified and isolated from diploid tissues. Based on a multiple allele alignment, locus-specific primers are designed in conserved regions, minimizing 'null' alleles. Using two undescribed endemic Australian Collembola as exemplars, we outline a comprehensive approach to generating and validating suites of codominant, sequence-yielding nuclear loci for previously unstudied invertebrates.

Results

Six markers per species were developed without any baseline genetic information. After evaluating the characteristics of each new locus via SSCP pre-screening, population samples were genotyped on the basis of either DNA sequence, restriction site, or insertion/deletion variation, depending on which assay was deemed most appropriate. Polymorphism was generally high (mean of nine alleles per locus), and the markers were capable of resolving population structuring over very fine spatial scales (<100 km). SSCP coupled with targeted DNA sequencing was used to obtain genotypic, genic and genealogical information from six loci (three per species). Phylogeographic analysis identified introns as being most informative.

Conclusion

The comprehensive approach presented here feasibly overcomes technical hurdles of (i) developing suitably polymorphic nuclear loci for non-model organisms, (ii) physically isolating nuclear allele haplotypes from diploid tissues without cloning, and (iii) genotyping population samples on the basis of nuclear DNA sequence variation.     

Biologically relevant effects of mRNA amplification on gene expression profiles

Background  

Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results.