Genome size and Giemsa C-banded karyotype of tetraploid \u3ci\u3eBromus ciliatus\u3c/i\u3e L.

Tetraploid Bromus ciliatus L. is a North American bromegrass that has been placed in the Pnigma section of Bromus. The objective of this study was to characterize the genome of tetraploid B. ciliatus by cytogenetic methods and compare it to the genomes of other species included in the section Pnigma. All the plants of the accession (USDA PI 232214) selected for chromosome counting were tetraploids (2n = 28). The mean 2C nuclear DNA content for tetraploid B. ciliatus was 19.13 ± 0.07 pg as determined by flow cytometry which is significantly greater than the tetraploid DNA content of B. inermis Leyss. (11.74 ± 0.16 pg). C-banding procedures were used to identify individual mitotic chromosomes and to develop a karyotype for B. ciliatus. The genome of the tetraploid B. ciliatus consisted of 16 median chromosomes, eight submedian chromosomes, and four chromosomes with satellites which included one pair with a large satellite and one pair with a small satellite. The general pattern of the distribution of constitutive heterochromatin in B. ciliatus was quite different than the other bromegrasses that have been analyzed to date. Except for two pairs of chromosomes, all chromosomes in tetraploid B. ciliatus had telomeric bands on one or both arms. Some of the chromosomes with telomeric bands had centromeric bands that were located at one or both sides of the centromere and intercalary bands which were generally absent in the other bromegrass species. It was possible to identify all chromosomes of tetraploid B. ciliatus and to match the pairs of homologous chromosomes by using chromosome lengths, arm length ratios and C-banding patterns. The results of this study indicate that tetraploid B. ciliatus has different genomes than the European species evaluated to date in the section Pnigma

Cytogenetic and Nuclear DNA Content Characterization of Diploid \u3ci\u3eBromus erectus\u3c/i\u3e and \u3ci\u3eBromus variegatus\u3c/i\u3e

Bromus erectus Huds. (erect brome) and B. variegatus M. Bieb. are Eurasian Bromus species that have been tentatively identified as potential progenitors of smooth bromegrass (B. inermis Leyss) which is the principal cultivated bromegrass in North America. The objective of this study was to characterize the genome of diploid accessions of B. erectus (2n = 2x = 14) and B. variegatus (2n = 2x = 14) using nuclear DNA content and cytogenetic analysis using Giemsa C-banding. The nuclear DNA content for B. erectus (6.19 ± 0.08 pg 2C-1) was less than that of B. variegatus (6.76 ± 0.05 pg 2C-1). These two species can be distinguished cytogenetically with the karyotypes that were developed. Complete karyotypes were not developed for both species because within species, multiple chromosomes were similar in size and C-banding. Both species had two pairs of chromosomes with satellites but the size of the satellites and the number and position of C-bands on these chromosomes differed between species. Bromus variegatus had five pairs of chromosomes with telomeric C-bands on both arms, while B. erectus had four pairs of chromosomes with a single telomeric band on the long arm and a single pair with telomeric bands on both arms. Comparison with the previously reported karyotypes and nuclear DNA contents for tetraploid and octaploid B. inermis suggest that if the diploid species B. erectus and B. variegatus were the donor species for these polyploids, significant evolutionary changes have occurred since the initial formation of these species including chromosome loss and re-arrangement

Bazı Buğdaygil Yem Bitkisi Türlerine Ait Populasyonların Çekirdek Dna Içeriklerinin Flow Sitometri Yöntemiyle Belirlenmesi Ve Ploidy Analizi Ile Tür Teşhisinde Kullanımı

Buğdaygil yem bitkisi türlerinin taksonomisi oldukça karmaşık olup türlerin teşhisi ve sınıflandırılması ciddi bir uzmanlık gerektirmektedir. Aynı cins içerisinde yer alan buğdaygil türlerinin birbirlerine çok benzemeleri, aralarında kolayca melezlenerek hibrit türler oluşturabilmeleri ve doğal varyasyon sebebiyle bu türlerin teşhislerinde ciddi sorunlar yaşanmaktadır. Buna ilave olarak buğdaygil yem bitkilerinde polyploidi olayıda çok yaygındır ve aynı türün dahi farklı kromozom sayılarına sahip formları mevcuttur. Bundan dolayı buğdaygil bitkilerine ait genetik kaynakların bilimsel araştırma ve ıslah çalışmalarında kullanılmadan önce tür teşhislerinin doğru bir şekilde yapılarak ploidi düzeylerinin belirlenmesi zorunludur. Bu çalışmanın amacı ıslah programlarında kullanmak amacıyla ülkemizin Doğu Anadolu Bölgesinden yeni toplanmış olan 215 buğdaygil yem bitkisi populasyonunun (Festuca sp, Phleum sp, Koeleria sp ve Agropyron sp) çekirdek DNA içeriklerini flow sitometri yöntemi ile ilk defa belirlemek ve elde edilen bilgiyi koleksiyonuı oluşturan türlerin teşhisi ve ploidi düzeyilerinin belirlenmesinde kullanmaktır. Çalışmadan elde edilen sonuçlara göre çalışma kapsamında karakterize edilen Koeleria, Festuca ve Phleum genetik kaynak kolleksiyonlarının birden fazla tür ve ploidy düzeyini içerdiği belirlenmiştir. Elde edilen bu sonuçlarda buğdaygil yem bitkisi genetik kaynaklarının ıslah programlarına dahil edilmeden önce muhakkak karakterize edilmelerinin gerekli olduğunu bu tür çalışmalar içinde flow sitometrinin şu an mevcut olan en hassas, hızlı, ucuz ve güvenilir metot olduğunu ortaya koymaktadır.Grass species included in the same genus are very similar to each other morphologically. They hybridize with each other in the nature easily and create hybrids. They also show natural variation. All of these make identification of the forage grasses and their taxonomy quite complicated. In addition to this, ploidy is also a common phenomenon in grasses and chromosome number varies even within the same species due to polyploidy. Therefore, it is necessary to identify species included in the forage grass germplasm collections and determine their ploidy correctly prior using them in research and breeding programmes. The objective of this study was to determine nuclear DNA content of 215 grass populations (Festuca sp, Phleum sp, Koeleria sp ve Agropyron sp) collected from natural flora of Eastern Turkey and use the the information in identification of the species and ploidy analysis. Based on the results of the nulear DNA content analysis done by using flow cytometer, Koeleria, Festuca ve Phleum collections investigated in this study included more than one species and ploidy levels. The results of this study proved one more time that grass genetic material collected from nature can have a mixture of different species and ploidy levels. Therefore, they need to be characterized before include them in research and breeding programmes and flow cytometer is the most accurate, cheap, and fast method for this type of studies

Genetic characterization of banana clones grown in Turkey based on nuclear DNA content and SRAP markers

This study was conducted to investigate the genetic relationships among banana clones grown in Turkey based on their nuclear DNA contents and SRAP markers. Four banana clones including 'Dwarf Cavendish', 'Grand Nain', 'Azman' and local 'Erdemli' were used as plant material. Nuclear DNA content of the banana cultivars estimated by flow cytometer and varied between 1.766 pg ('Erdemli') and 2.028 pg ('Grand Nain'). 'Azman' and 'Dwarf Cavendish' was similar nuclear DNA content. Genetic similarities of 4 banana clones were between 0.63-0.91 based on SRAP molecular marker. The local  'Erdemli' banana clone was the most distinct from the others. In conclusion, there is a high level of genetic variation among the banana clones grown in Turkey and the local clone 'Erdemli' is the most distinct one. This study showed that nuclear DNA content analysis together with molecular markers can be useful to assess the relationships among banana clones

DNA Content and Ploidy Determination of Bromegrass Germplasm Accessions by Flow Cytometry

Species of the genus Bromus represent ploidy states from diploid to decaploid. Ploidy determination of Bromus germplasm is necessary before it can be effectively used in breeding or genetic studies. The objective of this study was to characterize the ploidy of 322 accessions of four Bromus species [Bromus inermis Leyss, B. riparius Rehm, B. biebersteinii Roem and Schult., and B. inermis ssp. pumpellianus (Scribn) Wagnon] that are in the USDA National Plant Germplasm System (NPGS). Flow cytometry was used to determine DNA content of 10 plants of each accession. Mean DNA contents were correlated to ploidy level with root tip chromosome counts on selected accessions whose DNA content indicated that they represented different ploidy levels. On the basis of DNA content (pg [2C.sup.-1] = DNA content of a diploid somatic nucleus) and chromosome counts, mean DNA content and chromosome number was 22.62 pg [2C.sup.-1] for octaploid B. biebersteinii (2n = 8x = 56), 26.07 pg [2C.sup.-1] for decaploid B. biebersteinii (2n = 10x = 70), 11.74 pg [2C.sup.-1] for tetraploid B. inermis (2n = 4x = 28), 22.28 pg [2C.sup.-1] for octaploid B. inermis (2n = 8x = 56), 22.72 pg [2C.sup.-1] for octaploid B. inermis ssp. pumpellianus (2n = 8x = 56), 26.5 pg [2C.sup.-1] for decaploid B. inermis ssp. pumpellianus (2n = 10x = 70), 6.14 pg [2C.sup.-1] for diploid B. riparius (2n = 2x = 14), 22.15 pg [2C.sup.-1] for octaploid B. riparius (2n = 8x = 56), and 26.64 pg [2C.sup.-1] for decaploid B. riparius (2n = 10x = 70). Standard deviations of the mean values were 0.88 pg [2C.sup.-1] or less. Most B. inermis and B. inermis ssp. pumpellianus accessions were octaploid (93.75%), while the majority of the B. riparius and B. biebersteinii were decaploid (92.30%). The B. inermis and related species in the USDA NPGS were collected primarily from areas in the former USSR. The NPGS bromegrass germplasm could be enhanced by collections from western and central Europe, the Middle East, and China

C-Banding Analyses of \u3ci\u3eBromus inermis\u3c/i\u3e Genomes

Smooth bromegrass (Bromus inermis Leyss.) has both tetraploid (2n = 28) and octaploid (2n = 56) ploidy levels that have been difficult to characterize cytogenetically because of similar chromosome morphology. Objectives of this study were to identify individual chromosomes of tetraploid and octaploid B. inermis with C-banding procedures along with chromosome length and arm length ratios, develop more detailed karyotypes than those previously available, and use the karyotypes to examine the genomic relationship of tetraploid and octaploid B. inermis. Root tips of the plants from four tetraploid and three octaploid accessions were used to produce chromosome squash preparations for cytogenetic analysis. The tetraploid B. inermis genome consisted of 12 chromosomes with a telomeric band on each arm and sixteen chromosomes with only one telomeric band on one arm. All of the chromosomes of the tetraploid form, except for four chromosomes, were identified by C-banding patterns, chromosome length, and arm length ratio. The octaploid B. inermis genome consisted of four chromosomes with no C-bands, ≈14 chromosomes with two telomeric bands, and ≈38 chromosomes with only one telomeric band on either the short or long arm. The combined use of C-banding, chromosome size, and arm length ratio only enabled groups of 2, 4, 6, or 8 similar chromosomes to be identified because of similarities in chromosome morphology of the octaploids. Results indicate that tetraploid B. inermis is an allotetraploid since all chromosomes except four could be separated into identifiable pairs. Because of differences between expected and actual numbers of satellite chromosomes and chromosomes with specific C-banding patterns, octaploid B. inermis is probably not a doubled form of the tetraploid B. inermis

Characterization of nuclear DNA content and chromosome numbers of Tulipa luanica Millaku, T. kosovarica Kit Tan, Shuka & Krasniqi and T. albanica Kit Tan & Shuka

The Balkan Peninsula is considered an important centre of native tulip species. Tulipa kosovarica and Tulipa luanica are new species recently discovered in Kosovo, and Tulipa albanica in Albania. The current study aims at the investigating the nuclear DNA content and chromosome number of these three tulipa species in order to provide for the first time data on their genome size and differences among these three Tulipa species. Analysis of nuclear DNA content was performed by flow cytometer (Partec CyFlow Space) in mature fresh leaves for each Tulipa species. Samples for chromosome analysis were taken from the root tip meristem of the bulbs. Results showed significantly higher amounts of nuclear DNA (2C) in T. luanica compared to T. kosovarica and T. albanica. The chromosome number for these three species was 2n = 2x = 24, while the chromosome sizes of T. luanica resulted larger, compared to that of T. kosovarica and T. albanica. A correlation between the nuclear DNA content and chromosome size was found among these tulipa species. Moreover, nuclear DNA content and chromosome sizes of T. luanica, T. kosovarica and T. albanica showed clear differences among these species

Metabolomic Variation Aligns with Two Geographically Distinct Subpopulations of Brachypodium Distachyon before and after Drought Stress

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). Princi-pal 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 sig-nificant 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 subpopu-lation 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

Determination of nuclear DNA content and ploidy levels of oat (Avena spp.) accessions belongs to different species

Genom büyüklüğü biyoloji, genetik, taksonomi ve evrim çalışmaları için son derece yararlı birölçüttür. Bu ölçüt türlere özel olduğundan, tür teşhisine ve gen bankalarında korunan genetikmateryalin etiket bilgilerinin hızlı bir şekilde teyit edilebilmesine imkân sağlamaktadır. Buçalışmada flow sitometri ile 13 farklı Avena türüne ait 64 aksesyonun ortalama genombüyüklüklerinin ve ploidi seviyelerinin belirlenmesi hedeflenmiştir. Analiz edilen A. brevis, A.hirtula, A. longiglumis, A. nuda, A. strigosa, A. ventricosa, A. abyssinica, A. barbata, A.murphyi, A. vaviloviana, A. fatua, A. sativa ve A. sterilis türlerine ait aksesyonların ortalamaçekirdek DNA içeriklerinin 8.58 ile 26.54 pg/2C arasında değiştiği belirlenmiştir. Avenaaksesyonlarının çekirdek DNA içerikleri arasındaki farklılık istatistiki olarak önemli bulunmuşve aksesyonların ploidi düzeylerinin diploid ile hekzaploid arasında değiştiği saptanmıştır.Analizlerden elde edilen sonuçlar USDA-NSGC gen bankasında saklanan bu aksesyonlardanbazılarının etiket bilgilerinin doğru olmadığını ortaya çıkarmıştır. Literatürde mevcutçalışmaların sonuçlarından farklı olarak, incelenen dokuz A. brevis aksesyonunun DNAiçeriklerinin 12.21–12.61 pg/2C aralığında olduğu tespit edilmiştir. Benzer şekilde, USDAGRIN sisteminde mevcut tek A. hirtula aksesyonunda daha önce yapılmış çalışmaların aksineçekirdek DNA miktarı 16.16 pg/2C olarak bulunmuştur.Genome size is a good metric used in taxonomy and breeding studies for characterization of the genome and determination of evolutionary distances. It is mostly invariable within species; therefore, genome size estimations could be used for species identification and determination of genetic material integrity in germplasm collections. The present study targets verification of genome sizes and ploidy levels of 64 accessions classified in 13 Avena species using flow cytometry. Estimated nuclear DNA content of A. brevis, A. hirtula, A. longiglumus, A. nuda, A. strigosa, A. ventricosa, A. abyssinica, A. barbata, A. murphyi, A. vaviloviana, A. fatua, A. sativa ve A. sterilis accessions in this study ranged between 8.58–26.45 pg/2C. It was found that nuclear DNA contents of the Avena accessions were statistically different, and ploidy levels of accessions are between diploid and hexaploid. Based on the data obtained from the flow cytometry analyses, it was concluded that some accessions were labelled wrongly in the USDA-NSGC collection. Contradicted from the studies in the literature, nuclear DNA content of nine A. brevis accessions were found between 12.21–12.61 pg/2C. Similarly, nuclear DNA content of the sole A. hirtula accession available in the USDA-GRIN system was found as 16.16 pg/2C, which was reported differently in the previous studies