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Genome-wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces
No full textStripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a
major threat to bread wheat production worldwide. The breakdown in resistance
of certain major genes and newly emerging aggressive races of stripe rusts
pose serious concerns in all main wheat growing areas of the world. To identify
new sources of resistance and associated QTL for effective utilization in
future breeding programs an association mapping (AM) panel comprising of
600 bread wheat landraces collected from eight different countries conserved
at ICARDA gene bank were evaluated for seedling and adult plant resistance
against the PstS2 and Warrior races of stripe rust at the Regional Cereal Rust
Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of
25,169 informative SNP markers covering the whole genome were used to examine
the population structure, linkage disequilibrium and marker-trait associations
in the AM panel. The genome-wide association study (GWAS) was carried
out using a Mixed LinearModel (MLM).We identified 47 SNP markers across 19
chromosomes with significant SNP-trait associations for both seedling stage and adult plant resistance. The threshold of significance for all SNP-trait associations
was determined by the false discovery rate (q)≤0.05. Three genomic regions
(QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study do
not correspond to previously reported Yr genes or QTL, suggesting new genomic
regions for stripe rust resistance
Buğdayda sarı pasa dayanıklılık için ilişkilendirme haritalaması
No full textStripe rust, caused by Puccinia striiformis Westend. f. sp. tritici is an important threat to global wheat production. The breakdown in resistance of resistance genes and new virulent and more aggressive pathotypes of stripe rusts are causing serious problems in all main bread and durum wheat cultivating areas of the world. To look and identify new sources of resistance genes and associated QTL for utilization in breeding programs an association mapping panel comprising of 600 bread wheat landraces was assembled from eight countries preserved in ICARDA gene bank. The association mapping panel was evaluated for seedling and adult plant resistance against multiple yellow rust pathotypes in Izmir, Turkey during 2016, 2018 and 2019. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). 47 SNPs were postulated at 19 genomic regions with significant SNP-trait associations for both seedling and adult plant stage resistance, the threshold of significance for marker-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study are far away from any previously reported Yr gene or QTL thus, tagging novel genomic regions. The analysis for the candidate genes in the novel QTL regions identified several candidate resistance genes encoding proteins related to plants disease resistance and defense mechanism.Puccinia striiformis f. sp. tritici Westend'in neden olduğu sarı pas, küresel buğday üretimi için önemli bir tehdittir. Dayanıklılık genlerinin dayanıklılığındaki kırılma ve sarı pasın yeni virülans ve daha agresif patotipleri, dünyanın tüm büyük ekmeklik ve makarnalık buğday yetiştirme alanlarında ciddi sorunlara neden olmaktadır. Islah programlarında kullanılmak üzere yeni dayanıklılık genleri ve ilişkili QTL'lerin yeni kaynaklarını araştırmak ve belirlemek için, ICARDA gen bankasında muhafaza edilen sekiz ülkeden 600 ekmeklik buğday yerel çeşidinden oluşan bir ilişkilendirme haritalaması paneli oluşturulmuştur. İlişkilendirme haritalama paneli 2016, 2018 ve 2019 yıllarında İzmir, Türkiyede çok sayıda sarı pas patotipine karşı fide ve ergin bitki dayanıklılığı açısından değerlendirilmiştir. Genom çapında ilişki çalışması (GWAS), Karışık Doğrusal Model (MLM) kullanılarak gerçekleştirildi. 47 SNP, 19 genomik bölgede, hem fide hem de ergin bitki aşaması dayanıklılığı için önemli SNP-özelliği ilişkilerine sahip olarak varsayılmış ve markör-özellik ilişkileri için önem eşiği, hatalı keşif oranı (q) ≤ 0.05 ile belirlenmiştir. Bu çalışmada tanımlanan üç genomik bölge (QYr.1D_APR, QYr.3A_ve QYr.7D_fide dönemi), daha önce rapor edilen herhangi bir Yr geni veya QTL'den çok uzakta yer almaktadır, böylece etiketlenen yeni genomik bölgelerdir. Yeni QTL bölgelerindeki aday genlerin analizi sonucunda, bitkilerin hastalığa dayanıklılığı ve savunma mekanizması ile ilgili proteinleri kodlayan birkaç aday dayanıklılık geni belirlenmiştir
Comparison of Genomic Prediction Methods for Yellow, Stem, and Leaf Rust Resistance in Wheat Landraces from Afghanistan
No full textWheat rust diseases, including yellow rust (Yr; also known as stripe rust) caused by Puccinia striiformis Westend. f. sp. tritici, leaf rust (Lr) caused by Puccinia triticina Eriks. and stem rust (Sr) caused by Puccinia graminis Pres f. sp. tritici are major threats to wheat production all around the globe. Durable resistance to wheat rust diseases can be achieved through genomic-assisted prediction of resistant accessions to increase genetic gain per unit time. Genomic prediction (GP) is a promising technology that uses genomic markers to estimate genomic-assisted breeding values (GBEVs) for selecting resistant plant genotypes and accumulating favorable alleles for adult plant resistance (APR) to wheat rust diseases. To evaluate GP we compared the predictive ability of nine different parametric, semi-parametric and Bayesian models including Genomic Unbiased Linear Prediction (GBLUP), Ridge Regression (RR), Least Absolute Shrinkage and Selection Operator (LASSO), Elastic Net (EN), Bayesian Ridge Regression (BRR), Bayesian A (BA), Bayesian B (BB), Bayesian C (BC) and Reproducing Kernel Hilbert Spacing model (RKHS) to estimate GEBV's for APR to yellow, leaf and stem rust of wheat in a panel of 363 bread wheat landraces of Afghanistan origin. Based on five-fold cross validation the mean predictive abilities were 0.33, 0.30, 0.38, and 0.33 for Yr (2016), Yr (2017), Lr, and Sr, respectively. No single model outperformed the rest of the models for all traits. LASSO and EN showed the lowest predictive ability in four of the five traits. GBLUP and RR gave similar predictive abilities, whereas Bayesian models were not significantly different from each other as well. We also investigated the effect of the number of genotypes and the markers used in the analysis on the predictive ability of the GP model. The predictive ability was highest with 1000 markers and there was a linear trend in the predictive ability and the size of the training population. The results of the study are encouraging, confirming the feasibility of GP to be effectively applied in breeding programs for resistance to all three wheat rust diseases
Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan
No full textLandraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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