Allele expression biases in mixed-ploid sugarcane accessions.

Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, genes showing ASE (ASEGs) were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.

Limited allele-specific gene expression in highly polyploid sugarcane.

Polyploidy is widespread in plants, allowing the different copies of genes to be expressed differently in a tissue-specific or developmentally specific way. This allele-specific expression (ASE) has been widely reported, but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole-genome level in the highly polyploid sugarcane genome. Very high depth whole-genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single-copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning.

BACKGROUND: The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucrose accumulation, fiber content and stalk number. To expand the understanding of the biological pathways related to these traits, we evaluated gene expression of two groups of genotypes contrasting in biomass composition. RESULTS: First visible dewlap leaves were collected from 12 genotypes, six per group, to perform RNA-Seq. We found a high number of differentially expressed genes, showing how hybridization in a complex polyploid system caused extensive modifications in genome functioning. We found evidence that differences in transposition and defense related genes may arise due to the complex nature of the polyploid Saccharum genomes. Genotypes within both biomass groups showed substantial variability in genes involved in photosynthesis. However, most genes coding for photosystem components or those coding for phosphoenolpyruvate carboxylases (PEPCs) were upregulated in the high biomass group. Sucrose synthase (SuSy) coding genes were upregulated in the low biomass group, showing that this enzyme class can be involved with sucrose synthesis in leaves, similarly to sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP). Genes in pathways related to biosynthesis of cell wall components and expansins coding genes showed low average expression levels and were mostly upregulated in the high biomass group. CONCLUSIONS: Together, these results show differences in carbohydrate synthesis and carbon partitioning in the source tissue of distinct phenotypic groups. Our data from sugarcane leaves revealed how hybridization in a complex polyploid system resulted in noticeably different transcriptomic profiles between contrasting genotypes.

Chloroplast Genome of Novel Rice Germplasm Identified in Northern Australia.

Rice (Oryza sativa L.) was probably domesticated from O. rufipogon in Asia in the last 10,000 years. Relatives of cultivated rice (A genome species of Oryza) are found in South America, Africa, Australia and Asia. These A genome species are the close relatives of cultivated rice and represent the effective gene pool for rice improvement. Members of this group in Northern Australia include, an annual species, O. meridionalis, and two recently distinguished perennial taxa, to one of which the name O. rufipogon has been applied and the other a perennial form of O. meridionalis. Comparison of whole chloroplast genome sequences of these taxa has now been used to determine the relationships between the wild taxa and cultivated rice. The chloroplast genomes of the perennials were both found to be distinguished from O. rufipogon from Asia by 124 or 125 variations and were distinguished from each other by 53 variations. These populations have remained isolated from the overwhelming genetic impact of the large domesticated rice populations in Asia and may be unique descendants of the gene pool from which domesticated rice arose. The conservation of this wild genetic resource may be critical for global food security.

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

Exploring natural selection to guide breeding for agriculture.

Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate-resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.

The wheat Em promoter drives reporter gene expression in embryo and aleurone tissue of transgenic barley and rice.

The early methionine (Em) proteins are members of the late embryogenesis abundant (LEA) group of proteins that have been considered to be embryo specific. The ability of a 646-bp wheat Em promoter to control green fluorescent protein (gfp) expression was investigated in transgenic barley and rice. Seeds of transgenic plants expressed gfp in the developing embryo but also in the aleurone layer. The 646-bp Em promoter also directed strong gfp expression in cells comprising the junction between the endosperm transfer cells and cells of the aleurone layer. Em-gfp expression in transgenic barley showed differences in spatial and temporal control when compared with that observed in transgenic rice. Em-gfp expression was also detected in mature aleurone cells of transgenic barley and rice with and without abscisic acid (ABA) treatment. Reverse transcriptase-polymerase chain reaction (RT-PCR) results indicated the presence of Em and Em-homologous transcript in embryo, aleurone and endosperm tissues of wheat and of barley and rice, respectively. These results suggest that Em proteins may be expressed in both the embryo and aleurone during seed development, possibly providing protection against desiccation in these two tissues that survive seed drying. They may also have a similar role in these tissues during germination. The Em promoter from wheat may be useful in the expression of novel genes in cereal grains, as an embryo- and aleurone-specific promoter complementing other available endosperm- and pericarp-specific promoters to collectively increase the expression of transgenes in seeds.