Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.

Summary: Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse‐transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S‐genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D‐genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass that has been used to assess population level genomic variation. We have previously established a collection of 55 Brachypodium accessions that were sampled to reflect five different climatic regions of Turkey; designated 1a, 1c, 2, 3 and 4. Genomic and methylomic variation differentiated the collection into two subpopulations designated as coastal and central (respectively from regions 1a, 1c and the other from 2, 3 and 4) which were linked to environmental variables such as relative precipitation. Here, we assessed how far genomic variation would be reflected in the metabolomes and if this could be linked to an adaptive trait. Metabolites were extracted from eight-week-old seedlings from each accession and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Principal Component Analysis (PCA) of the derived metabolomes differentiated between samples from coastal and central subpopulations. The major sources of variation between seedling from the coastal and central subpopulations were identified. The central subpopulation was typified by significant increases in alanine, aspartate and glutamate metabolism and the tricarboxylic acid (TCA) cycle. Coastal subpopulation exhibited elevated levels of the auxin, indolacetic acid and rhamnose. The metabolomes of the seedling were also determined following the imposition of drought stress for seven days. The central subpopulation exhibited a metabolomic shift in response to drought, but no significant changes were seen in the coastal one. The drought responses in the central subpopulation were typified by changes in amino acids, increasing the glutamine that could be functioning as a stress signal. There were also changes in sugars that were likely to be an osmotic counter to drought, and changes in bioenergetic metabolism. These data indicate that genomic variation in our Turkish Brachypodium collection is largely reflected as distinctive metabolomes (“metabolotypes”) through which drought tolerance might be mediated.

With an annual global production of approximately 25 million tons, the common bean (Phaseolus vulgaris L), a member of the genus Phaseolus, is one of the major protein sources used as food for humans. In this study, it was aimed to investigate the genome size of the common bean genetic resource collection (154 common bean accessions) in Turkey by flow cytometry (FCM) and determine whether geographical variables affected the genome size. In addition, the number and distribution of 5S and 45S ribosomal DNA loci were designated by performing a fluorescence in situ hybridization (FISH) analysis in some of the accessions. The FCM analyses revealed that the mean nuclear DNA content of the accessions varied from 1.28 pg2C-1 to 1.55 pg2C-1 (mean 1.35 pg2C-1), and the differences between these accessions were statistically significant (P < 0.01). Intraspecific variation in the genome size was determined, and a positive correlation was found between the altitude and genome size. However, latitude and longitude did not have any statistically significant effect on the genome size. In the principal coordinate analysis, the accessions were divided into 3groups. Based on the results of the FISH analysis performed on 5 different accessions with varying genome sizes, using 5S and 45S rDNA genes as probes, the number of 5S rDNA loci was 4 in the common bean and stable among the common bean accessions, while the number of 45S rDNA loci was highly polymorphic, varying between 6 and 16. Consequently, it was determined in the present study that the genetic resource collection of common bean had a wide variation in terms of genome size and genome organization.

Amaç: Gül ıslahında ebeveyn seçimi başarıyı etkileyen faktörler arasında yer alır. Ebeveyn seçimi ve kombinasyonların belirlenmesinde ıslahçının; ploidi seviyesi, ebeveynlerin verimliliği, polen canlılığı, meyve başına tohum sayısı ve tohumların çimlenme oranı gibi faktörleri dikkate alması başarı oranını etkilemektedir. Bu çalışma, tozlamada polen kaynağı olarak kullanılan kokulu ve kokusuz gül genotiplerinin meyve tutum oranı ve meyve başına tohum sayısı üzerine etkilerini belirlemek amacıyla yürütülmüştür. Materyal ve Metod: Çalışmada, baba ebeveyn olarak iki kokulu gül türü (Rosa damascena Mill., Rosa odarata cv. Louis XIV) ile melez çay gülleri olarak bilinen Rosa hybrida L. türüne ait iki ticari kesme gül çeşidi (Magnum ve First Red), anne ebeveyn olarak ise Rosa hybrida türüne ait ticareti yapılan iki farklı kesme gül çeşidi (Polar Star ve Black Magic) kullanılmıştır. Tozlama amacıyla 12 farklı kombinasyon oluşturulmuş ve 01 Mayıs-30 Aralık tarihleri arasında kombinasyon başına 20’şer adet melezleme yapılmıştır. Bulgular: Çalışmada kullanılan bütün ebeveynlerin ploidi seviyelerinin 2n=4x=28 yani tetraploid olduğu belirlenmiştir. Baba ebeveyn olarak kullanılan tür ve çeşitlerde polen canlılık oranlarının % 52.76-58.92, çimlenme güçlerinin ise % 24.61-45.24 arasında değiştiği saptanmıştır. Tozlamalarda meyve başına en yüksek tohum sayısı 25.67 adet ile Black Magic x R. damascena kombinasyonunda belirlenirken bunu 23.00 adet ile Polar Star x R. odorata cv. Louis XIV kombinasyonu izlemiştir. Meyve başına en düşük tohum sayısı ise 7.00 adet ile Black Magic x Magnum kombinasyonundan elde edilmiştir. Sonuç: Çalışmada baba ebeveyn olarak kullanılan kokulu gül türleri ile yapılan tozlamaların meyve başına tohum sayısını arttırdığı sonucuna varılmıştır.