Barley (Hordeum vulgare L.) Improvement Past, Present and Future

Barley has been cultivated for more than 10,000 years. Barley improvement studies always have the privilege of the breeders and scientists. This review is expected to provide a resource for researchers interested in barley improvement research in terms of mutation breeding, tissue culture, gene transfers, gene editing, molecular markers, transposons, epigenetic, genomic studies and system biology. We aimed to discuss some important and/or recent studies and improvements about barley for understanding the factors responsible for converting barley plants into the superior cereals, which occurred through gene transfers, gene editing and molecular breeding, which is important and could help us enhance the current pool of cultivated barley species to provide enough material for the future

Distinctive Sire1 Retrotransposon Patterns on Barley Chromosomes?

DergiPark: 773302trkjnatSIRE1, Tyl/Copia Uzun Uç Tekrarlı (Long Terminal Repeats- LTR) retrotranspozon üst ailesine ait olan aktif, nispeten yüksek kopyalı bir retroementtir. Arpa genomundaki ayırt edici SIRE1 elementlerinin (ENV ve GAG) dağılımları floresan in situ hibridizasyonu (FISH) kullanılarak gözlemlendi. Tetramethylrhodamine-dUTP (TRITC)-işaretli probların elde edilmesinde PCR gerçekleştirildi. SIRE1 ENV ve GAG domainlerinin yerleşimleri, Hordeum vulgare L. cv. Hasat kök preparatlarında konfokal mikroskobu altında gösterildi. Sonuçlarımız, arpa genomundaki SIRE1 elementlerinin ENV ve GAG dağılımlarını göstermektedir. Bu sonuçlar, SIRE1 elementlerinin arpa genomunun organizasyonunun ortaya çıkarılmasına katkı sağlayacaktır. SIRE1 is an active and relatively high copy-number retroelement belongs to the Tyl/Copia long terminal repeat (LTR) retrotransposon superfamily. Distinctive SIRE1 elements (ENV and GAG) distributions in barley genome were observed by using fluorescent in situ hybridization (FISH). We performed PCR to obtain tetramethylrhodamine-dUTP (TRITC)-labelled probes. Localizations of SIRE1 ENV and GAG domains were demonstrated under confocal microscope on Hordeum vulgare L. cv. Hasat root preparations. Our results revealed the distributions of SIRE1 elements ENV and GAG in barley genome. These results may provide to uncover the organization of SIRE retrotransposon pattern in barley genome

Abiotic Stress Alleviation with Brassinosteroids in Plant Roots

This chapter covers the advances in establishment and optimization of brassinosteroids (BRs) in the alleviation of abiotic stresses such as water, salinity, temperature, and heavy metals in plant system, especially roots. Plant roots regulate their developmental and physiological processes in response to various internal and external stimuli. Studies are in progress to improve plant root adaptations to stress factors. BRs are a group of steroidal hormones that play important roles in a wide range of developmental phenomena, and recently they became an alleviation agent for stress tolerance in plants. This review is expected to provide a resource for researchers interested in abiotic stress alleviation with BRs

Pioneering in Vitro Studies For Callus Formation of Colchicum Chalcedonicum Azn.

DergiPark: 776974trkjnatColchicum calcedonicum Azn, pek çok endemik bitki türünün görüldüğü Türkiye'de yayılış gösteren endemik türlerden biridir. Toprak altında uzun-oval şekilli soğanı ile genellikle 3-4 yapraklıdır. Kallus kültürü kullanarak endemik türlerin in vitro üretimi, bu türlerin korunmasında umut verici bir çalışma haline gelmiştir. Bu çalışmanın amacı, in vitro C. chalcedonicum üretimi için verimli kallus protokolünün oluşturulabilmesidir. Explantların sterilizasyonunda, 20 dk %0.25 (w/v) cıva klorür (HgCl2) kullanılmıştır. Cıva klorüre ilaveten, yüzey sterilizasyonunda 30 dk boyunca Tween 80, %6,5 NaCl ile birlikte kullanılmıştır. Bu çalışmada, 19 farklı besiyeri kullanılmış olup primer kallus oluşumu 2,4-D (2 mg L-1), 2IP (0,5 mg L-1), %3 sükroz ve %0,05 aktif karbon içeren Murashige amp; Skoog bazal besiyerinde elde edilmiştir. Çalışmamız, aktif karbon kullanımının primer kallus oluşumunda etkili olduğunu göstermiştir. Bu çalışma, C. chalcedonicum’un primer kallus oluşumu için ilk rapordur. Bununla birlikte, çalışmamız endemik tür olan C. chalcedonicum'un in vitro korunması ve kallus oluşum protokolünün geliştirilmesinde öncü bir çalışmadır. Colchicum calcedonicum Azn is one of the endemic species distributed in Turkey, where many endemic plant species occur. It has long-oval shaped corm under the soil, and usually 3-4 leaves on it. In vitro production of endemic species using callus culture has become promising study for conservation. The aim of this study is to generate an efficient callus protocol for in vitro production of C. chalcedonicum. To sterilize the explants, 0.25% (w/v) mercuric chloride (HgCl2) was used for 20 min. In addition to mercuric chloride, surface sterilization was conducted by using 6.5% NaCl with Tween 80 for 30 min. We used 19 different mediums and the primary callus formation was obtained in Murashige amp; Skoog’s basal medium (MS) supplemented with 2,4-D (2 mg L-1), 2IP (0.5 mg L-1), 3% sucrose and 0.05% active carbon. Our study demonstrated the active carbon usage was effective for the primary callus formation. This study is the first report for primary callus formation of C. chalcedonicum. However, our work is a pioneering study to improve callus formation protocol system for in vitro conservation of endemic species C. chalcedonicum

Origin and distribution of different retrotransposons in different taxa

Novel genome analysis technologies enable genomic studies of transposable elements (TEs) in different organisms. Population studies of human genome show thousands of individual TE insertions. These insertions are important source of natural human genetic variation. Researchers are beginning to develop population genomic data sets for evaluating the phenotypic impact of human TE polymorphisms. Because of the evidences of horizontal transfer of retrotransposons between different species genome, in this study we aimed to detect barley retrotransposons (Nikita and BAGY2) in the human genome. Inter retrotransposon amplified polymorphism polymerase chain reaction (IRAP PCR) were used to measure the distribution of Nikita and BAGY2 retroelements in the human genome. Analyses reveals that Nikita and BAGY2 are present in the human genome and show different distribution in the genome. The polymorphism ratios of retroelements suggest that Nikita and BAGY2 have been active retrotransposons in the human genome

EFFECTS OF HYPERBARIC OXYGENATION ON CULTURED BARLEY EMBRYOS

Changes in relative water content (RWC), lipid peroxidation, proline and antioxidant system in relation to the tolerance to oxidative stress enzymes mediated high pressure were investigated in Hordeum vulgare L. cv. Tokak. For this purpose, mature embryos cultured on MS media were treated in a hyperbaric oxygenation chamber (approx. 59.06 feets, 2 kp/cm(2)) with pure oxygen for 60 minutes/day for a growth period of ten days in a plant growth chamber. Constitutive activities of SOD, APOX, GR and POX were higher in hyperbaric oxygenated (HBO) explants, being 96.07%, 28.57%, 77.77% and 54.14% for the 5th days; 95.78%, 40%, 37.5%, and 94.98% for the 10th days of culture, respectively, than in the control plants. Increase in SOD activity was also shown on polyacrilamide gel electrophoresis on the 10th day of application. Proline accumulation was increased in HBO-treated explants both on the 5th days (85.71%) and 10th days (37.14%) of treatment. MDA content was found to be higher in HBO treated explants both on the 5th (53.84%) and 10th (59.83%) days of culture

Overview of cDNA microarray analysis

cDNA microarray technology has become one of the most widely used functional genomics tool for gene expression analysis. With the use of this new and powerful technology, gene expression patterns of a tens of thousands of genes can be analyzed in a single experiment. This paper reviews array manufacturing, hybridization, scanning and data handling by focusing on critical factors affecting results of a cDNA microarray analysis

Salinity-induced Physiological and Molecular Changes in Barley and Wheat

In this study, it was aimed to compare salinity-induced changes in barley (Hordeum vulgare L. cv. Bornova-92) and bread wheat (Triticum aestivum L. cv. Gerek-79). Seeds were germinated under saline conditions (0, 50, 100, 250 and 500 mM NaCl) for 2 days and recovered under non-saline conditions for 2 days. At the end of the salt-treatment, germination, water content (WC), total soluble protein content, catalase (CAT, EC 1.11.1.6) activity were affected in both species while superoxide dismutase (SOD, EC 1.15.1.1) activity was affected in barley. Salinity affected WC, protein content and CAT activity in both species while affected germination in barley and affected fresh weight and SOD activity in wheat after recovery. Physiological responses of both species were correlated. Expression of a-tubulin, Atls1 and Lls1 genes were down-regulated in barley after 250 mM NaCl treatment. HVA1 gene was highly (more than 50-fold) stimulated by salinity in barley. However, a-tubulin, Atls1 genes were down-; Lls1 gene was up-regulated in wheat after recovery from 250 mM NaCl treatment. Increase in HVA1 expression was not significant in wheat. Expression profiles of barley and wheat under salinity are different and barley tended to regulate gene expression faster than wheat. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND licens

ANALYSIS OF RETROTRANSPOSITION AND DNA METHYLATION IN BARLEY CALLUS CULTURE

Mature barley (Hordeum vulgare cv. Zafer-160) embryos were cultured on callus induction medium (MS + 4 mg l(-1) Dicamba) for 30 days and embryogenic calli were transferred onto regeneration medium (MS + 0.5 mg l(-1) trans-zeatin riboside). Callus induction percentage was 67.2%; embryogenic callus induction percentage was 42.3% and their regeneration percentage was 63.8%. Retrotransposon movements and methylation alterations in 15-day-old, 30-day-old calli and 4-day-old barley seedling (control) were investigated with Inter-Retrotransposon Amplified Polymorphism (IRAP) and Methylation-Sensitive Restriction Fingerprinting (MSRF), respectively. IRAP patterns were quite monomorphic however MSRF indicated increase in cytosine methylation during callus formation. Changes in retroelement movements and methylation alterations were evaluated and discussed in the light of literature

Physiological and Molecular Changes in Barley and Wheat Under Salinity

In this study, it was aimed to compare salinity-induced changes in barley (Hordeum vulgare L. cv. Bornova-92) and bread wheat (Triticum aestivum L. cv. Gerek-79). Seeds were germinated under saline conditions (0, 50, 100, 250, and 500 mM NaCl) for 2 days and recovered under non-saline conditions for 2 days. At the end of the salt treatment, germination, water content (WC), total soluble protein content, and catalase (CAT, EC 1.11.1.6) activity were affected in both species, while superoxide dismutase (SOD, EC 1.15.1.1) activity was affected in barley. Salinity affected WC, protein content, and CAT activity in both species, while it affected germination in barley and affected fresh weight and SOD activity in wheat after recovery. Physiological responses of both species were correlated. Expression of alpha-tubulin, Atls1, and Lls1 genes was down-regulated in barley after 250 mM NaCl treatment. HVA1 gene was highly (more than 50-fold) stimulated by salinity in barley. However, alpha-tubulin and Atls1 genes were down-regulated, and Lls1 gene was up-regulated in wheat after recovery from 250-mM NaCl treatment. Increase in HVA1 expression was not significant in wheat. The expression profiles of barley and wheat under salinity are different, and barley tended to regulate gene expression faster than wheat