140 research outputs found
Geleneksel ve organik yetiştirme koşullarında dönem selekesiyon uygulanarak geliştirilen arpa (Hordeum vulgare L.) birkisinde derin kök fenotipinin ve haplotip alel frekanslarının analizi
No full textThe challenge of producing cultivars that will be productive given lesser amount of inputs, withstand changing climate condition and have higher ability for a more efficient extraction of soil resources led to the renewed interest in improving plant root system as a key strategy for plant stability under climate instability. To date, root architectural and anatomical variations of an evolving plant population particularly under conventional and organic cropping system still remains unexplored. For this study, BC2F23 barley population previously derived from a common founder population but evolved from long-term selection trial under 2 different agro-ecological systems: organic and conventional management system were considered for shoot and root phenotyping and molecular evaluations. Three-hundred barley genotypes were selected from this population and were grown under field and hydroponics conditions. The study aims to evaluate the shoot and root phenotypic variations and subsequently to identify the degree of variability on allele frequency based on the identified causative QTL's/gene that explained variation for root morphology in two groups of barley population. Results obtained shows that after more than 20 years of judicious selection in 2 differing management systems, the two barley population were able to produce variable root architectural and anatomical response when grown under uniform growing condition. Barley lines evolved under organic management system are characterized to have longer but narrower root system, higher root surface area, and root mass density, has thinner root size but possess high number of metaxylem vessels. Comparatively, those evolved under conventional cropping system tend to have shorter and broader roots system, bigger root volume and had thicker root size as result of bigger root tissues but has lesser number of metaxylem vessels. Furthermore, multivariate analysis and the subsequent haplotype allele frequency of ISR 42-8 (wild-type parent) analysis on the 14 identified QTLs/genes also confirms the variations existed between the two groups. Lines selected under organic management systems shows substantial increase of the favorable allele from the first generation (BC2F23) to the currently studied population (BC2F23) as compared to those under conventionally managed lines. The consistent increase of favorable alleles from the superior wild-type parent observed among lines in the organic group could provide greater possibilities for adaptation and better equip these plants to grow and survive more successfully under stressful growing condition. Finally, determining the effect of several years of selection under these two different cropping systems on adaptive changes in plant root systems offers great potential in breeding specifically for organic and low-input cropping system that has not been achieved in breeding so far.Daha az miktarda girdi ile verimli olacak çeşitler üretmenin zorluğu, değişen iklim koşullarına dayanabilir ve toprak kaynaklarının daha verimli bir şekilde çıkarılması için daha yüksek kabiliyete sahip olacak, iklim altında bitki stabilitesi için temel bir strateji olarak bitki kök sisteminin iyileştirilmesine olan ilginin yenilenmesine yol açmıştır. Bugüne kadar, özellikle geleneksel ve organik ürün yetiştirme sistemi koşullarına gelişen bitki popülasyonunun kök yapısı ve anatomik varyasyonları hala keşfedilmemiş durumda. Bu çalışma için, BC2F23 arpa popülasyonu daha önce ortak bir kurucu popülasyondan türetilmiş, ancak 2 farklı agro-ekolojik sistem altında uzun vadeli seçim denemesinden gelişmiştir: sürgün ve kök fenotipleme ve moleküler değerlendirmeler için organik ve geleneksel yönetim sistemi dikkate alınmıştır. Bu popülasyondan üç yüz arpa genotipi seçilmiş ve tarla ve hidroponik koşullar altında yetiştirilmiştir. Çalışma, sürgün ve kök fenotipik varyasyonlarını değerlendirmeyi ve ardından, iki grup arpa popülasyonunda kök morfolojisi için varyasyonu açıklayan tanımlanmış nedensel QTL / genine dayalı olarak alel frekansı üzerindeki değişkenlik derecesini belirlemeyi amaçlamaktadır. Elde edilen sonuçlar, 2 farklı yönetim sisteminde 20 yıldan fazla akıllı seçimden sonra, iki arpa popülasyonunun, tek tip büyüme koşulu altında büyüdüğünde değişken kök mimari ve anatomik yanıt üretebildiğini göstermektedir. Organik yönetim sistemi altında gelişen arpa hatları, daha uzun fakat daha dar kök sistemine, daha yüksek kök yüzey alanına ve kök kütle yoğunluğuna sahip, daha ince kök boyutuna sahip, ancak çok sayıda metaksilem damarına sahip olma özelliğine sahiptir. Nispeten, geleneksel kırpma sistemi altında evrimleşenler, daha kısa ve daha geniş kök sistemine, daha büyük kök hacmine ve daha büyük kök dokularının bir sonucu olarak daha kalın kök boyutuna sahip olma eğilimindedir, ancak daha az sayıda metaksem damarına sahiptir. Ayrıca, çok değişkenli analiz ve izleyen haplotip alel frekansı ISR 42-8 (vahşi tip ebeveyn) analizi, 14 tanımlanan QTL / gen üzerinde ayrıca iki grup arasında var olan varyasyonları doğrular. Organik yönetim sistemleri altında seçilen hatlar, geleneksel olarak yönetilen hatlar altındakilere kıyasla, birinci nesilden (BC2F23) halihazırda çalışılan popülasyona (BC2F23) uygun alelde önemli bir artış göstermektedir. Organik gruptaki soylar arasında gözlemlenen üstün yabani tip ebeveynden olumlu alellerin tutarlı artışı, adaptasyon için daha büyük olanaklar sağlayabilir ve bu bitkileri büyümek ve stresli büyüme koşulu altında daha başarılı bir şekilde hayatta kalmaları için daha iyi donatabilir. Son olarak, bu iki farklı kırpma sistemi altında birkaç yıllık seçimin bitki kök sistemlerindeki adaptif değişiklikler üzerindeki etkisinin belirlenmesi, ıslahta, şu ana kadar ıslahta elde edilemeyen, özellikle organik ve düşük girdili mahsul sistemi için büyük bir potansiyel sunmaktadır
Correction: UAV-based multispectral image analysis revealed stay-green haplotypes in wheat specific for different soil nitrogen levels
No full textUAV-based multispectral image analysis revealed stay-green haplotypes in wheat specific for different soil nitrogen levels
No full textAbstract Background The so-called stay-green trait, a delay in onset and progression of leaf senescence, is associated with slower chlorophyll degradation and higher photosynthesis rates during maturation resulting in higher crop yields. Understanding the genetic and physiological basis of the stay-green trait and breeding cultivars with stable stay-green behaviour across a range of different nitrogen (N) conditions and specifically under low N availability can contribute to ensuring wheat yields and reducing N fertilizer application. The goal of this study was therefore to identify haplotypes associated with high stay-green capacity under different N availability conditions in wheat. A diverse set of 221 wheat cultivars was grown under three different N levels and phenotyped by uncrewed aerial vehicle (UAV)-based multispectral imaging to characterise genetic and environmental variation in stay-green. Haplotypes associated with stay-green were identified across N levels and specifically under low N availability. Results The plant senescence reflectance index (PSRI) calculated from multispectral images was identified as the most specific stay-green indicator allowing for differentiation of genotypic effects due to its greater sensitivity to senescence-related changes in pigment composition and its higher reliability. We found genetic variance for stay-green and a consistent genetic correlation between stay-green and grain yield at all imaging dates and N levels within the utilised diversity panel confirming its potential as a future breeding target. Haplotype analyses revealed two favourable major allele haplotypes present in 95% of the stay-green cultivars, i.e. the top 25% of the diversity set based on PSRI values, which significantly enhance stay-green performance and grain yield. In addition, we identified a favourable minor allele haplotype specifically associated with stay-green under low N availability and capable of further increasing stay-green and grain yield when stacked onto the two favourable major allele haplotypes. Conclusions The newly identified stay-green haplotypes can be further used for fine-mapping and identifying the underlying genes as well as for selecting for higher stay-green and grain yield. Thereby our results can contribute to improving our understanding of the complex genetic regulation underlying stay-green in different environments and to breeding new cultivars with stable performance across N levels or specifically under low N availability
Neue Rapssorten für den Biolandbau
No full textObwohl Raps ein ernährungsphysiologisch sehr wertvolles Speiseöl bei gleichzeitig hohem Proteingehalt liefert, ist seine Bedeutung in der biologischen Landwirtschaft unterdurchschnittlich gering. Mit der Erneuerung des Verbots von Hybridsorten im Biorapsanbau in der Schweiz sind Produzent*innen auf leistungsfähige Liniensorten angewiesen. Zwei Projekte verfolgen das Ziel, den Biorapsanbau aus der Nische zu holen – indem angepasste Sorten entwickelt werden
THE CHARACTER OR THE AUTHOR? THE BATTLE OF DON QUIXOTE, SCHWEIK AND…, SHAKESPEARE TO THE READER
No full textThe character or the author is a debate that sometimes leans on the power of the reader and sometimes on the power of the author to describe the power of a work. But what distinguishes a work represented by the character, and what can distinguish another work represented by the author? When we say that the work is represented by the character, it is not about the idea thrown by Roland Barthes in his essay ‘the death of the author’, nor from Foucault’s question ‘who cares who speaks’, but about the case when the character manages to ‘walk on its own’, thus transforming him into an explanatory dictionary for phenomena. And, in the case of Don Quixote and Schweik, it all has to do with their ‘ability’ to be judged by the reader without the ‘presence’ of the author. Meanwhile Shakespeare’s characters, often extremely significant to some of the most disturbing phenomena in human life, such as betrayal, the desire for power or the desire for wealth, cannot be separated from the author by the reader. Why? According to the author of this work, this difference between Don Quixote, Schweik and Shakespeare is not due to the small number of characters of Cervantes and Hashek and the large number of those of Shakespeare. But Don Quixote and Schweik’s naive portrayal causes readers to dare to judge these characters by themselves. That is why the biggest misunderstandings happen with Schweik and Don Quixote, whereas Shakespeare is the painter of ‘betrayal’, ‘power’ and ‘wealth’ - three things we owe to the ability of thinking. Therefore, Shakespeare's ‘wisdom of the characters’ needs someone to introduce them. And the reader needs the author in order to believe this ‘character wisdom’.Keywords: Don Quixote, Schweik, Shakespeare, Cervantes, Hashek, characters, readers, the author, etc
The Character or The Author? The battle of Don Quixote, Schweik and…. Shakespeare to the reader
No full textThe character or the author is a debate that sometimes leans on the power of the reader and sometimes on the power of the author to describe the power of a work. But what distinguishes a work represented by the character, and what can distinguish another work represented by the author? When we say that the work is represented by the character, it is not about the idea thrown by Roland Barthes in his essay ‘the death of the author’, nor from Foucault’s question ‘who cares who speaks’, but about the case when the character manages to ‘walk on its own’, thus transforming him into an explanatory dictionary for phenomena. And, in the case of Don Quixote and Schweik, it all has to do with their ‘ability’ to be judged by the reader without the ‘presence’ of the author. Meanwhile Shakespeare’s characters, often extremely significant to some of the most disturbing phenomena in human life, such as betrayal, the desire for power or the desire for wealth, cannot be separated from the author by the reader. Why? According to the author of this work, this difference between Don Quixote, Schweik and Shakespeare is not due to the small number of characters of Cervantes and Hashek and the large number of those of Shakespeare. But Don Quixote and Schweik’s naive portrayal causes readers to dare to judge these characters by themselves. That is why the biggest misunderstandings happen with Schweik and Don Quixote, whereas Shakespeare is the painter of ‘betrayal’, ‘power’ and ‘wealth’ - three things we owe to the ability of thinking. Therefore, Shakespeare's ‘wisdom of the characters’ needs someone to introduce them. And the reader needs the author in order to believe this ‘character wisdom’
Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments
No full textBallvora A, Joecker A, Viehöver P, et al. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments. BMC Genomics. 2007;8(1): 112.Background: Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental
and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of
the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a
prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by
DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late
blight caused by the oomycete Phytophthora infestans and to root cyst nematodes.
Results: To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial
chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes
of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were
assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements,
stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by
inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs
from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the
sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one
ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable
elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five
micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5.
Conclusion: Comparative sequence analysis revealed highly conserved collinear regions that flank regions showing high
variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of
multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural
conservation between these distantly related plant specie
Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)
No full textRoot architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley
Local and Bayesian Survival FDR Estimations to Identify Reliable Associations in Whole Genome of Bread Wheat
No full textEstimating the FDR significance threshold in genome-wide association studies remains a major challenge in distinguishing true positive hypotheses from false positive and negative errors. Several comparative methods for multiple testing comparison have been developed to determine the significance threshold; however, these methods may be overly conservative and lead to an increase in false negative results. The local FDR approach is suitable for testing many associations simultaneously based on the empirical Bayes perspective. In the local FDR, the maximum likelihood estimator is sensitive to bias when the GWAS model contains two or more explanatory variables as genetic parameters simultaneously. The main criticism of local FDR is that it focuses only locally on the effects of single nucleotide polymorphism (SNP) in tails of distribution, whereas the signal associations are distributed across the whole genome. The advantage of the Bayesian perspective is that knowledge of prior distribution comes from other genetic parameters included in the GWAS model, such as linkage disequilibrium (LD) analysis, minor allele frequency (MAF) and call rate of significant associations. We also proposed Bayesian survival FDR to solve the multi-collinearity and large-scale problems, respectively, in grain yield (GY) vector in bread wheat with large-scale SNP information. The objective of this study was to obtain a short list of SNPs that are reliably associated with GY under low and high levels of nitrogen (N) in the population. The five top significant SNPs were compared with different Bayesian models. Based on the time to events in the Bayesian survival analysis, the differentiation between minor and major alleles within the association panel can be identified
Genetic and transcriptional variations in NRAMP‑2 and OPAQUE1 genes are associated with salt stress response in wheat.
No full textThe dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R2 = 0.12–63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na+ and K+ ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R2 ≥ 14.7%) and 68.45 cM (R2 ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na+-uptake, shoot K+/Na+ ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na+-uptake, shoot Na+/K+ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat
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