Intermediate complex morphophysiological dormancy in seeds of the cold desert sand dune geophyte Eremurus anisopterus (Xanthorrhoeaceae; Liliaceae s.l.)

Background and Aims

Little is known about morphological (MD) or morphophysiological (MPD) dormancy in cold desert species and in particular those in Liliaceae sensu lato, an important floristic element in the cold deserts of Central Asia with underdeveloped embyos. The primary aim of this study was to determine if seeds of the cold desert liliaceous perennial ephemeral Eremurus anisopterus has MD or MPD, and, if it is MPD, then at what level.

Methods

Embryo growth and germination was monitored in seeds subjected to natural and simulated natural temperature regimes and the effects of after-ripening and GA₃ on dormancy break were tested. In addition, the temperature requirements for embryo growth and dormancy break were investigated.

Key Results

At the time of seed dispersal in summer, the embryo length:seed length (E:S) ratio was 0·73, but it increased to 0·87 before germination. Fresh seeds did not germinate during 1 month of incubation in either light or darkness over a range of temperatures. Thus, seeds have MPD, and, after >12 weeks incubation at 5/2 °C, both embryo growth and germination occurred, showing that they have a complex level of MPD. Since both after-ripening and GA₃ increase the germination percentage, seeds have intermediate complex MPD.

Conclusions

Embryos in after-ripened seeds of E. anisopterus can grow at low temperatures in late autumn, but if the soil is dry in autumn then growth is delayed until snowmelt wets the soil in early spring. The ecological advantage of embryo growth phenology is that seeds can germinate at a time (spring) when sand moisture conditions in the desert are suitable for seedling establishment.     

Morphological description and DNA barcoding study of sand rice (<Emphasis Type="Italic">Agriophyllum squarrosum</Emphasis>, Chenopodiaceae) collected in Kazakhstan

Background

Sand rice (Agriophyllum squarrosum (L.) Moq.) is an annual shrub-like plant adapted to the mobile sand dunes in desert and semi-desert regions of Asia. It has a balanced nutrient composition with relatively high concentration of lipids and proteins, which results in its nutrition being similar to legumes. Sand rice’s proteins contain the full range of essential amino acids. However, calories content is more similar to wheat. These features together with desert stress resistance make sand rice a potential food crop resilient to ongoing climate change. It is also an important fodder crop (on young stages of growth) for cattle in arid regions of Kazakhstan. In our work, sand rice samples were collected from two distant regions of Kazakhstan as a part of the nation-wide project to determine genetic variation of the native flora.

Results

Samples were collected in western and southeastern parts of Kazakhstan separated by distances of up to 1300 km. Sequences of the nuclear ribosomal DNA ITS1-5.8S-ITS2 region and the chloroplast matK gene confirmed the identity of species defined by morphological traits. Comparison with GenBank sequences revealed polymorphic sequence positions among Kazakh populations and GenBank references, and suggested a distinction among local populations of sand rice. The phylogenetic analysis of nucleotide sequences showed a clear partition of A. squarrosum (L.) Moq. from Agriophyllum minus Fisch. & C.A. Mey, which grows in the same sand dunes environment.

Conclusions

DNA barcoding analyses of ITS and matK sequences showed a segregation of A. squarrosum from A. minus into separate clades in Maximum-Likelhood dendrograms. ITS analysis can be successfully used to characterize A. squarrosum populations growing quite distant from each other. The data obtained in this work provide the basis for further investigations on A. squarrosum population structure and may play a role in the screening of sand rice plants growing in desert and semi-desert environments of Central Asia and China.

     

Building the sugarcane genome for biotechnology and identifying evolutionary trends

Background

Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.

Results

Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.

Conclusion

This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.     

Aerial and soil seed banks enable populations of an annual species to cope with an unpredictable dune ecosystem

Background and Aims

Simultaneous formation of aerial and soil seed banks by a species provides a mechanism for population maintenance in unpredictable environments. Eolian activity greatly affects growth and regeneration of plants in a sand dune system, but we know little about the difference in the contributions of these two seed banks to population dynamics in sand dunes.

Methods

Seed release, germination, seedling emergence and survival of a desert annual, Agriophyllum squarrosum (Chenopodiaceae), inhabiting the Ordos Sandland in China, were determined in order to explore the different functions of the aerial and soil seed banks.

Key Results

The size of the aerial seed bank was higher than that of the soil seed bank throughout the growing season. Seed release was positively related to wind velocity. Compared with the soil seed bank, seed germination from the aerial seed bank was lower at low temperature (5/15 °C night/day) but higher in the light. Seedling emergence from the soil seed bank was earlier than that from the aerial seed bank. Early-emerged (15 April–15 May) seedlings died due to frost, but seedlings that emerged during the following months survived to reproduce successfully.

Conclusions

The timing of seed release and different germination behaviour resulted in a temporal heterogeneity of seedling emergence and establishment between the two seed banks. The study suggests that a bet-hedging strategy for the two seed banks enables A. squarrosum populations to cope successfully with the unpredictable desert environment.     

Genetic architecture of resistance to Septoria tritici blotch in European wheat

Background

Septoria tritici blotch is an important leaf disease of European winter wheat. In our survey, we analyzed Septoria tritici blotch resistance in field trials with a large population of 1,055 elite hybrids and their 87 parental lines. Entries were fingerprinted with the 9 k SNP array. The accuracy of prediction of Septoria tritici blotch resistance achieved with different genome-wide mapping approaches was evaluated based on robust cross validation scenarios.

Results

Septoria tritici blotch disease severities were normally distributed, with genotypic variation being significantly (P < 0.01) larger than zero. The cross validation study revealed an absence of large effect QTL for additive and dominance effects. Application of genomic selection approaches particularly designed to tackle complex agronomic traits allowed to double the accuracy of prediction of Septoria tritici blotch resistance compared to calculation methods suited to detect QTL with large effects.

Conclusions

Our study revealed that Septoria tritici blotch resistance in European winter wheat is controlled by multiple loci with small effect size. This suggests that the currently achieved level of resistance in this collection is likely to be durable, as involvement of a high number of genes in a resistance trait reduces the risk of the resistance to be overcome by specific pathogen isolates or races.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-858) contains supplementary material, which is available to authorized users.     

Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications

Background

The ~17 Gb hexaploid bread wheat genome is a high priority and a major technical challenge for genomic studies. In particular, the D sub-genome is relatively lacking in genetic diversity, making it both difficult to map genetically, and a target for introgression of agriculturally useful traits. Elucidating its sequence and structure will therefore facilitate wheat breeding and crop improvement.

Results

We generated shotgun sequences from each arm of flow-sorted Triticum aestivum chromosome 5D using 454 FLX Titanium technology, giving 1.34× and 1.61× coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. By a combination of sequence similarity and assembly-based methods, ~74% of the sequence reads were classified as repetitive elements, and coding sequence models of 1314 (5DS) and 2975 (5DL) genes were generated. The order of conserved genes in syntenic regions of previously sequenced grass genomes were integrated with physical and genetic map positions of 518 wheat markers to establish a virtual gene order for chromosome 5D.

Conclusions

The virtual gene order revealed a large-scale chromosomal rearrangement in the peri-centromeric region of 5DL, and a concentration of non-syntenic genes in the telomeric region of 5DS. Although our data support the large-scale conservation of Triticeae chromosome structure, they also suggest that some regions are evolving rapidly through frequent gene duplications and translocations.

Sequence accessions

EBI European Nucleotide Archive, Study no. ERP002330

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1080) contains supplementary material, which is available to authorized users.