Genome of Wild Olive and the Evolution of Oil Biosynthesis

Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at similar to 28 and similar to 59 Mya. These events contributed to the expansion and neo-functionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2,3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics

Assessment of temporal and spatial genetic diversity of wheat streak mosaic virus using mobile nurseries and physical mapping of genes controlling agronomic traits present on chromosome 3A of wheat (Triticum aestivum)

Grain yield loss due to wheat streak mosaic virus is very common in wheat especially in the Great Plains of the U.S.A. Variation among WSMV isolates is important for deployment of resistance wheat varieties. Using reverse transcriptase polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP) analyses genetic variation was detected among and within WSMV populations collected from mobile nurseries for two years, four sampling dates and three geographical regions in Nebraska. According to analysis of molecular variance (AMOVA) results, genetic total variation within populations of each group accounted for approximately 90% of the variation. Less variation was detected among groups and populations within groups. Physical localization of the genes of interest in a specific wheat chromosome also provides valuable information in terms of increasing the grain yield. The second experiment used 41 Chinese spring lines with terminal deletions on chromosome 3 and 13 RFLP markers, which are found to be linked to the trait loci (QTLs) in wheat. The results suggested that two chromosomal regions on group 3A chromosome contained those QTLs and appear to be highly recombinogenetic, hence, are amenable to further molecular characterizations. The objectives of this study are: (1) To address the levels of genetic diversity and genetic structure in coat protein sequence of WSMV isolates, (2) To compare distribution patterns of WSMV isolates with respect to differentiation by mite transmission and host/environmental conditions, (3) To physically localize genes linked to the agronomic traits or QTLs. This study will help breeders use suitable isolates to screen wheat for WSMV resistance and pathologists understand the range of factors in WSMV epidemiology. It will also be helpful in cloning genes including but not limited to yield genes and disease resistance genes

Nadir buğday (Triticum aestivum L.) transkript'lerinin etkin klonlanması

EST (expressed sequence tag) teknolojisi çeşitli organizmalarda genomun işlevsel kısımlarının klonlanmasmı hedeflemede büyük mesafe kat etmeyi sağlamıştır. Bol miktar traskriptlerden (redundant) oluşturulan cDNA kütüphaneleri genelde aralıksız (constitutive) ve yoğun (over-expressed) eksprese olan genleri içermektedir. Ancak, organ spesifik ve çok az eksprese olan genler kolaylıkla işaretlenip klonlanamamaktadır. Bu çalışma, ekmeklik buğdayda düşük seviyede ve nadir sıklıkla eksprese olan gen parçacıklarının klonlanmasmı amaçlamaktadır. Poliakrilamid jel ve motife (farklı baz dizilimli genlerin aynı veya benzer sekansları) dayalı PCR (Polymerase Chain Reaction) amplifikasyonunun birlikte kullanımıyla, 189 buğday gen parçacığı taşıyan 144 bant klonlanmıştır. Gen baz dizilimlerinin analizi yalnızca 22'si gen bankasında kayıtlı olan 74 farklı kontig (contig) ile sonuçlanmıştır. Diğer 52 ise özgün (unique) ve herhangi bir EST veya 'non-redundant' gen bankasında rastlanmamıştır. EST gen bankasının % 5'lik özgün gen klonlama oranına karşın çalışmamızda bu oran yaklaşık % 28 olmuştur. Tanımladığımız bu yaklaşım, buğday da ve belki de farklı genomlarda nadir bulunan ve çok düşük seviyede eksprese edilen genlerin hedeflenmesi ve klonlanması konusunda oldukça ümit vericidir.Expressed sequence tag (EST) technology has spurred targeting the functional portion of genomes for several organisms. Constructed redundant complementary DNA (cDNA) libraries have targeted a majority of constitutive and over-expressed genes. However, the majority of lowly expressed and un-induced genes have not been able to be easily tagged and cloned. The objective of this study was to clone low and rarely expressed transcripts in wheat. Using a combination of a polyacrylamide gel and a motif-based PCR amplification, we cloned 144 bands containing 189 wheat fragments. Sequence analysis revealed 74 contigs, of which only 22 being present in database. The remaining 52 were unique, and were not present in any public EST or non-redundant database. Compared to 5% efficiency in thejxiblic EST database, the efficiency of cloning of unique sequences was about 28%. Therefore, the approach we describe here is highly promising for targeting the rarely and lowly expressed genes in wheat and, probably, various other genomes

Effects of seeding rates on competition indices of barley and vetch intercropping systems in the Eastern Mediterranean

Forage mixtures are common agricultural practices for the energy and protein needs of animals. In this study, common vetch (Vicia sativa L.), Hungarian vetch (Vicia pannonica L.), and barley ( Hordeum vulgare L.) mixtures in diferent seeding rates were investigated in terms of forage yield and quality. In order to evaluate the efect of vetch, cereal intercropping and the competition/ economic indices of 8 diferent legume–barley mixtures, along with their pure stands, were assessed during the 2008–2009 and 2009– 2010 growth seasons in the Eastern Mediterranean region of Turkey. Te feld experiment was arranged as a randomized complete block design with 3 replications for each year. Intercropping indices were calculated by means of land equivalent ratio (LER), aggressivity (A), crowding ratio (CR), and actual yield loss (AYL). Competition indices revealed that both the common vetch–barley and the Hungarian vetch–barley intercroppings at a seeding ratio of 80%:20%, respectively, were advantageous due to their high yield, land use efciency, and economic value compared to other mixtures or pure stands. All samples were analyzed for quality parameters such as dry matter (DM), crude protein (CP), neutral detergent fber (NDF), and acid detergent fber (ADF) content. While digestible dry matter (DDM) content did not difer among treatments, CP, NDF, ADF, TDN (total digestible nutrients), DDM, RFV (relative feed value), and NE1 (net energy for lactation) content signifcantly difered among the diferent vetches–barley mixtures (P < 0.01). Te results emphasize that both vetch species combined with barley and using the seeding ratio of 80% vetch:20% barley should be proftable for farmers in terms of implementation and maximum yield per unit area under Eastern Mediterranean conditions.Forage mixtures are common agricultural practices for the energy and protein needs of animals. In this study, common vetch (Vicia sativa L.), Hungarian vetch (Vicia pannonica L.), and barley ( Hordeum vulgare L.) mixtures in diferent seeding rates were investigated in terms of forage yield and quality. In order to evaluate the efect of vetch, cereal intercropping and the competition/ economic indices of 8 diferent legume–barley mixtures, along with their pure stands, were assessed during the 2008–2009 and 2009– 2010 growth seasons in the Eastern Mediterranean region of Turkey. Te feld experiment was arranged as a randomized complete block design with 3 replications for each year. Intercropping indices were calculated by means of land equivalent ratio (LER), aggressivity (A), crowding ratio (CR), and actual yield loss (AYL). Competition indices revealed that both the common vetch–barley and the Hungarian vetch–barley intercroppings at a seeding ratio of 80%:20%, respectively, were advantageous due to their high yield, land use efciency, and economic value compared to other mixtures or pure stands. All samples were analyzed for quality parameters such as dry matter (DM), crude protein (CP), neutral detergent fber (NDF), and acid detergent fber (ADF) content. While digestible dry matter (DDM) content did not difer among treatments, CP, NDF, ADF, TDN (total digestible nutrients), DDM, RFV (relative feed value), and NE1 (net energy for lactation) content signifcantly difered among the diferent vetches–barley mixtures (P < 0.01). Te results emphasize that both vetch species combined with barley and using the seeding ratio of 80% vetch:20% barley should be proftable for farmers in terms of implementation and maximum yield per unit area under Eastern Mediterranean conditions

Transferability of SSR markers from distantly related legumes to Glycyrrhiza species

Licorice (Glycyrrhiza spp.) is an important medicinal plant and its distribution of natural habitats has been shrinking day by day due to extensive collection. Genetic diversity identifcation will likely assist in conserving the diferent Glycyrrhiza species. A total of 127 simple sequence repeat (SSR) markers from Medicago truncatula Gaertn., Phaseolus vulgaris L., and Cicer arietinum L. were used and 26 of them were amplifed on Glycyrrhiza genomes. Te highest transferability rate (33%) was obtained from M. truncatula markers, while the highest genetic diversity values were obtained in P. vulgaris markers. Te markers BM153 and PV-ag004 from P. vulgaris had the largest polymorphism information content. Te amplifed primers were also used to identify genetic diversity among three Glycyrrhiza species. Te gene diversity values among Glycyrrhiza species appeared to be similar; however, donor species mostly had lower diversity values than those of Glycyrrhiza species. Additionally, the genetic analysis showed that G. favescens Boiss. subsp. favescens is more distantly related to species G. glabra L. var. glandulifera and G. echinata L. Te number of alleles was mostly higher than in the donor species, possibly proposing a multiallelic and/or polyploid structure in Glycyrrhiza species.Licorice (Glycyrrhiza spp.) is an important medicinal plant and its distribution of natural habitats has been shrinking day by day due to extensive collection. Genetic diversity identifcation will likely assist in conserving the diferent Glycyrrhiza species. A total of 127 simple sequence repeat (SSR) markers from Medicago truncatula Gaertn., Phaseolus vulgaris L., and Cicer arietinum L. were used and 26 of them were amplifed on Glycyrrhiza genomes. Te highest transferability rate (33%) was obtained from M. truncatula markers, while the highest genetic diversity values were obtained in P. vulgaris markers. Te markers BM153 and PV-ag004 from P. vulgaris had the largest polymorphism information content. Te amplifed primers were also used to identify genetic diversity among three Glycyrrhiza species. Te gene diversity values among Glycyrrhiza species appeared to be similar; however, donor species mostly had lower diversity values than those of Glycyrrhiza species. Additionally, the genetic analysis showed that G. favescens Boiss. subsp. favescens is more distantly related to species G. glabra L. var. glandulifera and G. echinata L. Te number of alleles was mostly higher than in the donor species, possibly proposing a multiallelic and/or polyploid structure in Glycyrrhiza species

Diversity analysis of genetic, agronomic, and quality characteristics of bread wheat (Triticum aestivum L.) cultivars grown in Turkey

Turkey is an important bread wheat producer. The objective of this study was to dissect the diversity of genetic, agronomic, and quality characteristics of bread wheat cultivars grown on 25% of the total wheat area in Turkey. A total of 24 wheat cultivars and 5 wild progenitors of wheat were examined using 24 simple sequence repeat (SSR) primers with a known physical locus on the A, B, and D genomes of hexaploid wheat. A total of 72 bands produced 939 alleles on the wheat cultivars and wild progenitors. Markers were efficient in discriminating the species and the highest genetic diversity information was obtained from the markers Xgwm312 and Xgwm372. Microsatellite markers clearly separated cv. Pandas from all other cultivars although it was closely related to most of them in terms of agronomic and quality traits. Four agronomic characteristics including yield component traits and eight bread quality analyses were used for the diversity analyses. A significant association between morphological and bread wheat quality traits was observed while the correlation was weak with the genetic data. Cultivars were also classified with respect to release year and origin. Molecular variance between old (released before the year 2000) and new cultivars accounted for 1% of the total variation and the variance was 3% between national and foreign cultivars. Results showed that the number of alleles was lower in national and new cultivars compared to foreign and old cultivars. Therefore, breeding sources do not appear to improve the genetic base of wheat cultivars in Turkey. Introducing new variation sources may be needed to broaden the narrowed gene pool of bread wheat.Turkey is an important bread wheat producer. The objective of this study was to dissect the diversity of genetic, agronomic, and quality characteristics of bread wheat cultivars grown on 25% of the total wheat area in Turkey. A total of 24 wheat cultivars and 5 wild progenitors of wheat were examined using 24 simple sequence repeat (SSR) primers with a known physical locus on the A, B, and D genomes of hexaploid wheat. A total of 72 bands produced 939 alleles on the wheat cultivars and wild progenitors. Markers were efficient in discriminating the species and the highest genetic diversity information was obtained from the markers Xgwm312 and Xgwm372. Microsatellite markers clearly separated cv. Pandas from all other cultivars although it was closely related to most of them in terms of agronomic and quality traits. Four agronomic characteristics including yield component traits and eight bread quality analyses were used for the diversity analyses. A significant association between morphological and bread wheat quality traits was observed while the correlation was weak with the genetic data. Cultivars were also classified with respect to release year and origin. Molecular variance between old (released before the year 2000) and new cultivars accounted for 1% of the total variation and the variance was 3% between national and foreign cultivars. Results showed that the number of alleles was lower in national and new cultivars compared to foreign and old cultivars. Therefore, breeding sources do not appear to improve the genetic base of wheat cultivars in Turkey. Introducing new variation sources may be needed to broaden the narrowed gene pool of bread wheat

Virus induced gene silencing in cold season cereals : The use of Bsmv vector

Bitkiler doğada canlılıklarını sürdürebilmek için çeşitli savunma mekanizmaları geliştirmişlerdir. RNA ortamlı antiviral savunma mekanizması olarak bilinen Virüs Kaynaklı Gen Susturma (VIGS) bu mekanizmalardan biridir. Virüsle enfekte olmuş bitkilerde, virüs genomuna karşı savunma mekanizması çalışmaktadır. Aynı zamanda hedef geni taşıyan virüs vektörleri homolog içgen mRNA’larını da bozabilmektedir. Bununla birlikte VIGS genin fonksiyonunu anlamada ve fonksiyonel genomik analizleri için kullanılmaktadır. Birçok bitki için virüs vektörleri geliştirilmiştir. Son zamanlarda tahıllar için Arpa Çizgili Mozaik Virüsü (Barley Stripe Mosaic Virus = BSMV) kullanılmaya başlanmıştır. BSMV geniş bir konukçu aralığına sahip pozitif polariteli bir RNA virüsü olup, Hordeivirüs genusunun bir üyesidir. Üç farklı genom RNA (?, ? ve ?)’ dan oluşmaktadır. Bu çalışmada BSMV vektörünün çalışma prensibi ve bazı tahıllarda BSMV – VIGS’in uygulamaları hakkında bilgi verilmiştir.Plants developed various defense mechanisms in order to maintain their lives in nature. Virus induced gene silencing (VIGS) which is known as RNA mediated antiviral defense mechanism is one of these mechanisms. In plants with infected unmodified viruses, the mechanism is target against the viral genome. The virus vectors carrying the target genes can be also targeted homogeneous mRNAs. However, VIGS has been widely used for analysis of gene function and functional genomics. These virus vectors were developed for a lot of plants. Recently, Barley Stripe Mosaic Virus (BSMV) has been started utilizing for cereals. BSMV is a positive-sense RNA virus with a broad experimental host range and is the type member of the Hordeivirus genus. The tripartite genome consists of RNAs α, β and γ. In this study, the experimental principles of BSMV vector and the knowledge about BSMV – VIGS studies applied in some cereals were given

Toksik Multinodüler Guatrda Çok Uzun Süreli Propiltiourasil Kullanımına Bağlı Nötropeni

Tirotoksikoz çeşitli yollarla hemtopoezi etkiler ve tionamidlerle birlikte miyelosupresyona neden olabilir. Toksik multinodüer guatra bağlı 20 yıl gibi uzun bir süre propiltiourasil kullanan ve febril nötropeni nedeniyle hastaneye yatışı yapılan hipertirodili bir hasta sunduk. Total tiroidektomi olduktan sonra hasta ötiroid iken nötropenisi düzeldi. Postoperatif patoloji ise mikropapiller tiroid karsinomu olarak değerlendirildi.Thyrotoxicosis affects hematopoiesis in several ways and thioamides may cause myelosuppression. We report a case of febrile neutropenia in a patient with hyperthyroidism who was using propylthiouracil for nearly 20 years for the treatment of toxic multinodular goitre. After surgery, the patient was euthyroid and neutropenia resolved. Postoperative pathology was evaluated as micropapillary thyroid carcinoma

Prospective analysis of antibiotic susceptibility patterns of MRSA in a Turkish university hospital

Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen. The prevalence of MRSA in many countries is increasing and, in some hospitals, more than half of all S. aureus disease isolates are MRSA. MRSA strains are becoming increasingly multiresistant, and have recently developed resistance to vancomycin, which has been used successfully to treat MRSA for more than 30 years. In-vitro determination of resistance patterns of S. aureus is critical in terms of administering suitable antimicrobial treatments. The objective of this study was to identify the frequency of MRSA from various clinical samples and resistance patterns against various antibiotics used broadly for treatments. All isolated S. aureus strains were identified using standard procedures and tested for oxacillin resistance according to methods of the National Committee for Clinical Laboratory Standards. A total of 345 coagulase-positive Staphylococci and 187 MRSA were isolated. We found that the incidence of MRSA in intensive care units (ICUs) and burn center was 23.4% (145/620) and 29.6% (32/108), respectively. This rate was 7% (10/143) in the other units. Resistance rates of MRSA were 29.9% for trimethoprim-sulfamethoxazole, 60.8% for clindamycin, 71.8% for erythromycin, 7.7% for teikoplanin, 90.1% for gentamycin, 88.8% for ofloxacin, 88.1% for norfloxacin and 100% for penicillin. All isolates were found to be sensitive against vancomycin. In our region, although methicillin resistance increased in S. aureus strains, teicoplanin resistance remained low in MRSA, suggesting an effective alternative treatment for Staphylococcus aureus infections. These results indicated that vancomycin seemed to be the only antimicrobial agent effective against MRSA and it could be the choice of medicine in treating multidrug resistant MRSA infection.Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen. The prevalence of MRSA in many countries is increasing and, in some hospitals, more than half of all S. aureus disease isolates are MRSA. MRSA strains are becoming increasingly multiresistant, and have recently developed resistance to vancomycin, which has been used successfully to treat MRSA for more than 30 years. In-vitro determination of resistance patterns of S. aureus is critical in terms of administering suitable antimicrobial treatments. The objective of this study was to identify the frequency of MRSA from various clinical samples and resistance patterns against various antibiotics used broadly for treatments. All isolated S. aureus strains were identified using standard procedures and tested for oxacillin resistance according to methods of the National Committee for Clinical Laboratory Standards. A total of 345 coagulase-positive Staphylococci and 187 MRSA were isolated. We found that the incidence of MRSA in intensive care units (ICUs) and burn center was 23.4% (145/620) and 29.6% (32/108), respectively. This rate was 7% (10/143) in the other units. Resistance rates of MRSA were 29.9% for trimethoprim-sulfamethoxazole, 60.8% for clindamycin, 71.8% for erythromycin, 7.7% for teikoplanin, 90.1% for gentamycin, 88.8% for ofloxacin, 88.1% for norfloxacin and 100% for penicillin. All isolates were found to be sensitive against vancomycin. In our region, although methicillin resistance increased in S. aureus strains, teicoplanin resistance remained low in MRSA, suggesting an effective alternative treatment for Staphylococcus aureus infections. These results indicated that vancomycin seemed to be the only antimicrobial agent effective against MRSA and it could be the choice of medicine in treating multidrug resistant MRSA infection