Genetic dissection of grain architecture-related traits in a winter wheat population

Background: The future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated. Results: Genome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767–602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture. Conclusions: These results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.Fil: Schierenbeck, Matías. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Cátedra de Cerealicultura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Alqudah, Ahmad M.. University Aarhus; DinamarcaFil: Lohwasser, Ulrike. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Tarawneh, Rasha A.. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Simon, Maria Rosa. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Cátedra de Cerealicultura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Börner, Andreas. Leibniz Institute of Plant Genetics and Crop Plant Research; Alemani

Genomic Selection, Quantitative Trait Loci and Genome-Wide Association Mapping for Spring Bread Wheat (Triticum aestivum L.) Improvement

Molecular breeding involves the use of molecular markers to identify and characterize genes that control quantitative traits. Two of the most commonly used methods to dissect complex traits in plants are linkage analysis and association mapping. These methods are used to identify markers associated with quantitative trait loci (QTL) that underlie trait variation, which are used for marker assisted selection (MAS). Marker assisted selection has been successful to improve traits controlled by moderate to large effect QTL; however, it has limited application for traits controlled by many QTL with small effects. Genomic selection (GS) is suggested to overcome the limitation of MAS and improve genetic gain of quantitative traits. GS is a type of MAS that estimates the effects of genome-wide markers to calculate genomic estimated breeding values (GEBVs) for individuals without phenotypic records. In recent years, GS is gaining momentum in crop breeding programs but there is limited empirical evidence for practical application. The objectives of this study were to: i) evaluate the performance of various statistical approaches and models to predict agronomic and end-use quality traits using empirical data in spring bread wheat, ii) determine the effects of training population (TP) size, marker density, and population structure on genomic prediction accuracy, iii) examine GS prediction accuracy when modelling genotype-by-environment interaction (G × E) using different approaches, iv) detect marker-trait associations for agronomic and end-use quality traits in spring bread wheat, v) evaluate the effects of TP composition, cross-validation technique, and genetic relationship between the TP and SC on GS accuracy, and vi) compare genomic and phenotypic prediction accuracy. Six studies were conducted to meet these objectives using two populations of 231 and 304 spring bread wheat lines that were genotyped with the wheat 90K SNP array and phenotyped for nine agronomic and end-use quality traits. The main finding across these studies is that GS can accurately predict GEBVs for wheat traits and can be used to make predictions in different environments; thus, GS should be applied in wheat breeding programs. Each study provides specific insights into some of the advantages and limitations of different GS approaches, and gives recommendations for the application of GS in future breeding programs. Specific recommendations include using the GS model BayesB (especially for large effect QTL) for genomic prediction in a single environment, across-year genomic prediction using the reaction norm model, using a large TP size for making accurate genomic predictions, and not making across-population genomic predictions except for highly related population

Dissection of Soil Waterlogging Tolerance in Soft Red Winter Wheat using Genomic Approaches

Genomic methods including genome wide association analysis (GWAS), genomic selection (GS) and RNA-seq allow for faster selection of superior breeding lines and for identification and resolution of candidate genes. A panel of 240 soft red winter wheat (Triticum aestivum L.) cultivars and breeding lines were subjected to soil waterlogging stress over two seasons at Stuttgart, AR and St. Joseph, LA, US. Total concentrations of P, K, Ca, Mg, Mn, Fe, Al, B, Cu, Na, S and Zn were determined in wheat shoots post-waterlogging using inductively coupled plasma spectroscopy. Yield components kernel number per spike (KNPS), kernel weight per spike (KWS) and thousand kernel weight (TKW) were measured at plant maturity. Negative correlations between TKW and KWS with aluminum and iron concentrations indicated the impact of elemental toxicity on grain production. A ten-fold cross-validation (CV) analysis and ridge regression BLUP (RR-BLUP) model found GS prediction accuracies (rgs) of micro and macronutrient concentrations to range from rgs = 0.06 to 0.52 and improved as more site-years were included in the analysis. The ratio of genomic to phenotypic prediction accuracy (rgs /H1/2) was greater than 0.50 for eight of the twelve elements, indicating the potential for using GS to select for shoot micro and macronutrient concentrations in the absence of phenotypic data. GWAS identified forty-seven highly significant (p \u3c 0.00001), twenty-three very significant and consistent (p \u3c 0.0005) and eight significant and consistent (p \u3c 0.001) marker trait associations (MTA) for the twelve micro and macronutrients measured. Lastly, RNA-seq was used for transcriptome and gene expression analysis under waterlogged and non-waterlogged conditions in wheat cultivars ‘Pioneer Brand 26R61’ and ‘AGS 2000’. Around 300 million pair-end reads were developed, covering approximately 16 Gb of the wheat transcriptome. In total, 64,911 (AGS200) and 60,414 (26R61) were obtained and 58,753 expressed genes were observed across both cultivars and treatments. Overall, the results of this study have and will enable genomics assisted breeding for waterlogging tolerance within the University of Arkansas Wheat Breeding Program by allowing for selection of materials with reduced micro and macronutrient concentrations in new breeding lines in the absence of phenotypic dat

Identification and mapping of QTL for resistance against Zymoseptoria tritici in the winter wheat accession HTRI1410 (Triticum aestivum L. subsp. spelta)

Zymoseptoria tritici, der Erreger der Septoria-Blattdürre (STB), verursacht weltweit Ertragsver-luste von bis zu 50 % und hat an Bedeutung durch Veränderungen im Weizenanbau gewonnen. Der Anbau resistenter Sorten ist der kostengünstigste und umweltfreundlichste Weg, diese Ver-luste zu reduzieren. Typische Symptome dieses Schaderregers sind nekrotische Blattflecken. Häufig genutzte Fungizide, wie Strobilurine und Azole verlieren ihre Wirksamkeit bei der Be-kämpfung von STB. Folglich besteht die Notwendigkeit, Genbank-Akzessionen auf Resistenzen zu untersuchen, Informationen über die Genetik der Resistenz zu gewinnen und molekulare Marker für den effizienten Einsatz neuer Resistenzen in der Weizenzüchtung zu entwickeln. Die Spelzweizen Genbankakzession HTRI1410 erwies sich in Feldversuchen als resistent und da-mit wertvolle Quelle für die Verbesserung der Resistenz gegen Z. tritici in Brotweizen. Um die Genetik der STB-Resistenz in HTRI1410 zu untersuchen, wurde eine DH-Population, beste-hend aus 135 Linien, die aus Kreuzungen von HTRI1410 mit den drei anfälligen Sorten ‘Alcedo’, ‘Jenga’ und ‘Solitär’ stammen, erzeugt. Basierend auf zweijährigen und dreiortigen Feldver-suchsergebnissen ergab sich eine Heritabilität h²= 0,55 für die STB-Resistenz. Zusätzlich zu diesen umfangreichen Versuchen wurde eine künstliche Inokulation in einem Blattsegementtest mit drei ausgewählten Isolaten (IPO323, IPO98022, IPO98050) durchgeführt und die mittlere, nekrotisierte Blattfläche bestimmt. Eine quantitative Variation für die Reaktion hinsichtlich einer Zymoseptoria-Infektion wurde beobachtet und ein signifikanter genotypischer Effekt festgestellt. Parallel dazu wurde die Population mit dem 90k iSelect SNP Chip genotypisiert. Die genotypi-schen Daten wurden für die Erstellung einer genetischen Karte verwendet. Etwa 6.000 SNPs erwiesen sich als polymorph zwischen der resistenten Akzession und den drei anfälligen Eltern. Von diesen wurden 1.118 SNPs auf dem A-Genom kartiert, 1.326 SNPs auf dem B-Genom und 267 SNPs auf dem D-Genom. In QTL-Analysen basierend auf den Feldversuchsergebnissen, wurden QTL auf den Chromosomen 5A, 4B und 7B lokalisiert. Basierend auf dem Blattseg-menttest wurden 17 QTL auf den Chromosomen 1A, 2A, 3A, 4A, 6A und 1B, 2B, 5B nachge-wiesen. Weiterhin wurden KASP-Marker für entsprechende QTL entwickelt, die eine markerge-stützte Selektion auf STB-Resistenz erlauben.Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), causes yield losses of up to 50 % in wheat, globally. Growing of resistant cultivars is the most cost effective and envi-ronmental friendly way to avoid these losses. Zymoseptoria tritici is present worldwide and has gained evident importance due to changes in wheat growing practices. Fungicides such as strobilurins and azoles lost their efficiency in controlling STB. Therefore, there is a need to conducted screening of gene bank accessions for resistance, get information on the genetics of resistance and develop molecular markers for the efficient deployment of new resistances in wheat breeding. In extensive screening programs for resistance, the spelt wheat gene bank accession HTRI1410 turned out to be resistant in field trials and to be a valuable source for improvement of resistance to Zymoseptoria tritici in wheat, therefore. In order to get information on the genetics of the STB resistance in HTRI1410, a DH population consisting of 135 lines derived from crosses of HTRI1410 to three susceptible cultivars, i.e. ‘Alcedo’, ‘Jenga’ and ‘Sol-itär’, was generated. Based on two years and three locations, the heritability for STB resistance was calculated at h²= 0.55. In addition to the extensive field trials, artificial inoculation in de-tached leaf assays was conducted using three isolates (IPO323, IPO98022, IPO98050) and the necrotic mean leaf area was determined. A quantitative variation for the reaction to a Zy-moseptoria infection was observed and a significant genotypic effect detected. In parallel the DH population was genotyped by the wheat 90k iSelect SNP chip. The genotypic data were used for map construction. About 6,000 SNPs turned out to be polymorphic between HTRI1410 and the three susceptible cultivars. Out of these, 1,118 SNPs were mapped to the A genome, 1,326 SNPs mapped to the B genome and 267 SNPs to the D genome. QTL anal-yses based on field trials revealed QTL on chromosomes 5A, 4B and 7B. In addition, based on the detached leaf assay, 17 QTL were detected on chromosomes 1A, 2A, 3A, 4A, 6A and 1B, 2B, 5B. Furthermore, KASP markers for respective QTL were developed facilitating effi-cient marker based selection for resistance to STB

Genomic and phenomic tools to aid in the utilization of eastern European and central Asian wheat germplasm in U.S. hard winter wheat breeding

2017 Summer.Includes bibliographical references.To view the abstract, please see the full text of the document

Genetic dissection of grain architecture-related traits in a winter wheat population

Background: The future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated. Results: Genome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767-602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture. Conclusions: These results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.Este artículo tiene una corrección que puede verse haciendo clic en "Documentos relacionados".Facultad de Ciencias Agrarias y Forestale

Characterization of resistance to Fusarium head blight in bread and durum wheat

Fusarium head blight (FHB) caused primarily by Fusarium graminearum (Fg) Schwabe (telomorph: Gibberella zeae Schw. [Petch]) in North America, is one of the most devstating diseases of wheat in Canada. An integrated approach to manage this disease is recommended that combines the adoption of cultural practices (tillage and crop rotation), cultivar resistance, and fungicide application at recommended timings. Resistance to FHB in wheat is a quantitatively inherited trait and highly influenced by environmental conditions. Sources of resistance are available in common wheat but not for durum wheat. There are no commercially available durum cultivars which are moderately resistant in North America which in part, can be explained by a lack of resistance in the primary gene pool. The current study was designed to study the effects (on disease suppression and linkage-drag associated with introgressions) of Sumai 3 derived Fhb1, Fhb2, and Fhb5 genes in hard red spring wheat cultivars [near-isogenic lines (NILs) developed in CDC Go and CDC Alsask backgrounds] from western Canada, the interaction of Fhb1 and Fhb5 with metconazole fungicide, and the mapping of quantitative trait loci (QTL) from emmer and durum wheat lines. The last part of the study utilized X-ray computed tomography as a tool to image selected NILs in the CDC Alsask background and focused on identification of key tissues conferring Type-II resistance to Fg. The phenotypic response of NILs carrying combinations of Sumai 3-derived genes suggested non-additive responses and Fhb5 was as effective as Fhb1 in conferring field resistance in both populations. Four to five resistance improving alleles, other than Fhb1, Fhb2, and Fhb5, in both populations were identified and three of five in the CDC Go population were contributed by the susceptible parent. The regions carrying these resistance improving alleles encoded disease resistance proteins, protein kinases, nucleotide-binding and leucine rich repeats’ domains. Complex epistatic gene-gene interactions among marker loci (including Fhb1, Fhb2, Fhb5) explained >20% of the phenotypic variation in FHB infection measurements. For the linkage drag experiment, introgressions resulted in lower thousand kernel weight and increased plant height with Fhb5. Among end-use quality traits, SDS-sedimentation volume and grain protein content were affected. In addition to Fhb1, Fhb2, Fhb5, we identified 10 loci in CDC Alsask NILs and nine in CDC Go NILs that affected the traits measured and none of these additional loci were common in both populations indicating the presence of multiple alleles in exotic sources that can result in linkage drag. Linkage drag is largely dependent on genetic background and the proportion of donor resistance alleles, thus, we observed more adverse effects among CDC Alsask NILs than among CDC Go NILs. Improvements in FHB resistance can still be made by introgressing the major genes examined in this study by using marker-assisted selection and selecting rare segregants with improved agronomy and end-use quality. There was an additive effect of Sumai 3-derived genes with metconazole in suppressing FHB and deoxynivalenol (DON) accumulation in the grain. Despite higher fungicide efficacy on moderately susceptible (MS) genotypes, FHB severity was greater on MS as compared to moderately resistant (MR) genotypes. Application of fungicides is warranted even on MR cultivars under moderate and high FHB disease pressure to reduce the amount of Fusarium damaged kernels (FDKs) and DON accumulation. In the QTL mapping study of tetraploid wheat, fifteen QTL (derived from both parents) for FHB resistance were identified on 11 of the 14 chromosomes using saturated linkage maps and a majority of the QTL were consistently detected in multiple environments. The combination of four relative large-effect and promising QTL reduced field FHB index, severity, incidence and visual rating index by 59%, 48%, 30%, and 29%, respectively. The majority of the QTL reported in the current study are novel and represent narrow intervals between the flanking markers; therefore, marker-assisted selection shoulb be of value in breeding FHB resistant durum wheat cultivars. In the final study of this thesis, as a proof-of-concept, we showcased the successful use of synchrotron-based X-ray imaging techniques to study the wheat-Fg interaction. This work indicated/re-confirmed the structural role of rachilla and rachis nodes in Type-II resistance to Fg in wheat. The results from all these studies will help wheat breeders to make decisions on introgressing exotic FHB resistance genes into common wheat. Additionally, novel QTL identified in tetraploid wheat can be used to enhance resistance in elite durum wheat lines by marker-assisted selection

Advances in Wheat Genetics: From Genome to Field: Proceedings of the 12th International Wheat Genetics Symposium

plant genetics; plant genomics; agricultur

QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations

The two recombinant inbred line (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). The quantitative trait loci (QTLs) were detected through multi-year phenotypic evaluations (2018–2020) and using high-throughput DArTseq genotyping technology. RILs exhibited significant genetic variation with p < 0.001, and the coefficient of variation ranged from 9.79% to 47.99% for both LR and YR in all Environments and stages of evaluations. The heritability is quite high and ranged between 0.47 and 0.98. We identified nine stable QTLs for YR APR on chromosomes 1B, 2A, 2B, 3D, and 4D and four stable QTLs for LR APR on chromosomes 2B, 3B, 4A, and 5A. Furthermore, in silico analysis revealed that the key putative candidate genes such as cytochrome P450, protein kinase-like domain superfamily, zinc-binding ribosomal protein, SANT/Myb domain, WRKY transcription factor, nucleotide sugar transporter, and NAC domain superfamily were in the QTL regions and probably involved in the regulation of host response toward pathogen infection. The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS)