Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands

Salt stress is a complex trait that poses a grand challenge in developing new crops better adapted to saline environments. Some plants, called recretohalophytes, that have naturally evolved to secrete excess salts through salt glands, offer an underexplored genetic resource for examining how plant development, anatomy, and physiology integrate to prevent excess salt from building up to toxic levels in plant tissue. In this review we examine the structure and evolution of salt glands, salt gland-specific gene expression, and the possibility that all salt glands have originated via evolutionary modifications of trichomes. Salt secretion via salt glands is found in more than 50 species in 14 angiosperm families distributed in caryophyllales, asterids, rosids, and grasses. The salt glands of these distantly related clades can be grouped into four structural classes. Although salt glands appear to have originated independently at least 12 times, they share convergently evolved features that facilitate salt compartmentalization and excretion. We review the structural diversity and evolution of salt glands, major transporters and proteins associated with salt transport and secretion in halophytes, salt gland relevant gene expression regulation, and the prospect for using new genomic and transcriptomic tools in combination with information from model organisms to better understand how salt glands contribute to salt tolerance. Finally, we consider the prospects for using this knowledge to engineer salt glands to increase salt tolerance in model species, and ultimately in crops.

Phylogeny and differentiation of the St genome in Elymus L. sensu lato (Triticeae; Poaceae) based on one nuclear DNA and two chloroplast genes

BACKGROUND

Hybridization and polyploidization can be major mechanisms for plant evolution and speciation. Thus, the process of polyploidization and evolutionary history of polyploids is of widespread interest. The species in Elymus L. sensu lato are allopolyploids that share a common St genome from Pseudoroegneria in different combinations with H, Y, P, and W genomes. But how the St genome evolved in the Elymus s. l. during the hybridization and polyploidization events remains unclear. We used nuclear and chloroplast DNA-based phylogenetic analyses to shed some light on this process.

RESULTS

The Maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) data showed that the Pseudoroegneria, Hordeum and Agropyron species served as the St, H and P genome diploid ancestors, respectively, for the Elymus s. l. polyploids. The ML tree for the chloroplast genes (matK and the intergenic region of trnH-psbA) suggests that the Pseudoroegneria served as the maternal donor of the St genome for Elymus s. l. Furthermore, it suggested that Pseudoroegneria species from Central Asia and Europe were more ancient than those from North America. The molecular evolution in the St genome appeared to be non-random following the polyploidy event with a departure from the equilibrium neutral model due to a genetic bottleneck caused by recent polyploidization.

CONCLUSION

Our results suggest the ancient common maternal ancestral genome in Elymus s. l. is the St genome from Pseudoroegneria. The evolutionary differentiation of the St genome in Elymus s. l. after rise of this group may have multiple causes, including hybridization and polyploidization. They also suggest that E. tangutorum should be treated as C. dahurica var. tangutorum, and E. breviaristatus should be transferred into Campeiostachys. We hypothesized that the Elymus s. l. species origined in Central Asia and Europe, then spread to North America. Further study of intraspecific variation may help us evaluate our phylogenetic results in greater detail and with more certainty.

Transcriptome analysis of two buffalograss cultivars

BACKGROUND

Buffalograss [Buchloë dactyloides (Nutt.) Engel. syn. Bouteloua dactyloides (Nutt.) Columbus] is a United States native turfgrass species that requires less irrigation, fungicides and pesticides compared to more commonly used turfgrass species. In areas where water is limited, interest in this grass species for lawns is increasing. While several buffalograss cultivars have been developed through buffalograss breeding, the timeframe for new cultivar development is long and is limited by a lack of useful genetic resources. Two high throughput next-generation sequencing techniques were used to increase the genomic resources available for buffalograss.

RESULTS

Total RNA was extracted and purified from leaf samples of two buffalograss cultivars. '378' and 'Prestige' cDNA libraries were subjected to high throughput sequencing on the Illumina GA and Roche 454 Titanium FLX sequencing platforms. The 454 platform (3 samples) produced 1,300,885 reads and the Illumina platform (12 samples) generated approximately 332 million reads. The multiple k-mer technique for de novo assembly using Velvet and Oases was applied. A total of 121,288 contigs were assembled that were similar to previously reported Ensembl commelinid sequences. Original Illumina reads were also mapped to the high quality assembly to estimate expression levels of buffalograss transcripts. There were a total of 325 differentially expressed genes between the two buffalograss cultivars. A glycosyl transferase, serine threonine kinase, and nb-arc domain containing transcripts were among those differentially expressed between the two cultivars. These genes have been previously implicated in defense response pathways and may in part explain some of the performance differences between 'Prestige' and '378'.

CONCLUSIONS

To date, this is the first high throughput sequencing experiment conducted on buffalograss. In total, 121,288 high quality transcripts were assembled, significantly expanding the limited genetic resources available for buffalograss genetic studies. Additionally, 325 differentially expressed sequences were identified which may contribute to performance or morphological differences between 'Prestige' and '378' buffalograss cultivars.

Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines

Brachypodium distachyon (brachypodium) is a small grass with the biological and genomic attributes necessary to serve as a model system for all grasses including small grains and grasses being developed as energy crops (e.g., switchgrass and Miscanthus ). To add natural variation to the toolkit available to plant biologists using brachypodium as a model system, it is imperative to establish extensive, well-characterized germplasm collections. The objectives of this study were to collect brachypodium accessions from throughout Turkey and then characterize the molecular (nuclear and organelle genome), morphological, and cytological variation within the collection. We collected 164 lines from 45 diverse geographic regions of Turkey and created 146 inbred lines. The majority of this material (116 of 146 inbred lines) was diploid. The similarity matrix for the diploid lines based on AFLP analysis indicated extensive diversity, with genetic distances ranging from 0.05 to 0.78. Organelle genome diversity, on the other hand, was low both among and within the lines used in this study. The geographic distribution of genotypes was not significantly correlated with either nuclear or organelle genome variation for the genotypes studied. Phenotypic characterization of the lines showed extensive variation in flowering time (7–22 weeks), seed production (4–193 seeds/plant), and biomass (15–77 g). Chromosome morphology of the collected brachypodium accessions varied from submetacentric to metacentric, except for chromosome 5, which was acrocentric. The diverse brachypodium lines developed in this study will allow experimental approaches dependent upon natural variation to be applied to this new model grass. These results will also help efforts to have a better understanding of complex large genomes (i.e., wheat, barley, and switchgrass).

Analysis of expressed sequence tags (ESTs) from Agrostis species obtained using sequence related amplified polymorphism

Bentgrass (Agrostis spp.), a genus of the Poaceae family, consists of more than 200 species and is mainly used in athletic fields and golf courses. Creeping bentgrass (A. stolonifera L.) is the most commonly used species in maintaining golf courses, followed by colonial bentgrass (A. capillaris L.) and velvet bentgrass (A. canina L.). The presence and nature of sequence related amplified polymorphism (SRAP) at the cDNA level were investigated. We isolated 80 unique cDNA fragment bands from these species using 56 SRAP primer combinations. Sequence analysis of cDNA clones and analysis of putative translation products revealed that some encoded amino acid sequences were similar to proteins involved in DNA synthesis, transcription, and signal transduction. The cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene (GenBank accession no. EB812822) was also identified from velvet bentgrass, and the corresponding protein sequence is further analyzed due to its critical role in many cellular processes. The partial peptide sequence obtained was 112 amino acids long, presenting a high degree of homology to parts of the N-terminal and C-terminal regions of cytosolic phosphorylating GAPDH (GapC). The existence of common expressed sequence tags (ESTs) revealed by a minimum evolutionary dendrogram among the Agrostis ESTs indicated the usefulness of SRAP for comparative genome analysis of transcribed genes in the grass species.

Organellar genome analysis of rye (Secale cereale) representing diverse geographic regions

Rye (Secale cereale) is an important diploid (2n = 14, RR) crop species of the Triticeae and a better understanding of its organellar genome variation can aid in its improvement. Previous genetic analyses of rye focused on the nuclear genome. In the present study, the objective was to investigate the organellar genome diversity and relationships of 96 accessions representing diverse geographic regions using chloroplast (cp) and mitochondrial (mt) DNA PCR-RFLPs. Seven cpDNA and 4 mtDNA coding and noncoding regions were amplified using universal cpDNA and mtDNA primer pairs. Each amplified fragment was digested with 13 different restriction enzymes. mtDNA analysis indicated that the number of polymorphic loci (20) was low and genetic differentiation (GST) was 0.60, excluding the outgroups (hexaploid wheat, Triticum aestivum, 2n = 6x = 42, AABBDD; triticale, xTriticosecale Wittmack, 2n = 6x = 42, AABBRR). cpDNA analysis revealed a low level of polymorphism (40%) among the accessions, and GST was 0.39. Of the 96 genotypes studied, 70 could not be differentiated using cpDNA PCR-RFLPs even though they are from different geographic regions. This is most likely due to germplasm exchange, indicating that genotypes might have a common genetic background. Two cpDNA and 3 mtDNA fragments were significantly correlated to the site of germplasm collection. However, there was no clear trend. These results indicate that the level of organellar polymorphism is low among the cultivated rye genotypes. The cpDNA and mtDNA PCR-RFLP markers used in the present study could be used as molecular markers in rye genetics and breeding programs.

Understanding ploidy complex and geographic origin of the Buchloe dactyloides genome using cytoplasmic and nuclear marker systems

Characterizing and inferring the buffalograss [Buchloe dactyloides (Nutt.) Engelm.] genome organization and its relationship to geographic distribution are among the purposes of the buffalograss breeding and genetics program. This buffalograss study was initiated to: (1) better understand the buffalograss ploidy complex using various marker systems representing nuclear and organelle genomes; (2) determine whether the geographic distribution was related to nuclear and organelle genome variation; and (3) compare the genetic structure of accessions with different ploidy levels. The 20 buffalograss genotypes (15 individuals from each genotype) that were studied included diploid, tetraploid, pentaploid, and hexaploid using nuclear (intersimple sequence repeat (ISSRs), simple sequence repeat (SSRs), sequence related amplified polymorphism (SRAPs), and random amplified polymorphic DNA (RAPDs)) and cytoplasmic markers (mtDNA and cpDNA). There was a significant correlation between the ploidy levels and number of alleles detected using nuclear DNA (ISSR, SSR, and SRAP, r = 0.39, 0.39, and 0.41, P<0.05, respectively), but no significant correlation was detected when mitochondrial (r = 0.17, P<0.05) and chloroplast (r = 0.11, P < 0.05) DNA data sets were used. The geographic distribution of buffalograss was not correlated with nuclear and organelle genome variation for the genotypes studied. Among the total populations sampled, regression analysis indicated that geographic distance could not explain genetic differences between accessions. However, genetic distances of those populations from the southern portion of buffalograss adaptation were significantly correlated with geographic distance (r= 0.48, P<0.05). This result supports the hypothesis that genetic relationship among buffalograss populations cannot be estimated based only on geographic proximity.