Genomic Prediction and Genome Wide Association Mapping for Disease Resistance in Wheat

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ISBN 13 :
Total Pages : 400 pages
Book Rating : 4.:/5 (1 download)

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Book Synopsis Genomic Prediction and Genome Wide Association Mapping for Disease Resistance in Wheat by : Philomin Juliana

Download or read book Genomic Prediction and Genome Wide Association Mapping for Disease Resistance in Wheat written by Philomin Juliana and published by . This book was released on 2017 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat (Triticum aestivum L.) is one of the major food crops in the world that is grown on more land area than any other commercial crop. The demand for wheat is expected to increase by 60% by 2050 which cannot be met with the current yield gain of 1%. Hence, it is important to evaluate different strategies for increasing the genetic gain in wheat. With this focus, we evaluated two strategies, genomic prediction and genome-wide association studies (GWAS) for disease resistance in CIMMYT’s international bread wheat screening nurseries (IBWSN). Our objective was to compare different prediction models for resistance to leaf rust (LR), stem rust (SR), stripe rust (STR), Septoria tritici blotch (STB), Stagonospora nodorum blotch (SNB) and tan spot (TS) in the 45th and 46th IBWSN entries. The prediction models tested include: Least-squares (LS), genomic-BLUP (G-BLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes C (BC), Bayesian least absolute shrinkage and selection operator (BL), reproducing kernel Hilbert spaces (RKHS) markers (RKHS-M), RKHS pedigree (RKHS-P) and RKHS markers and pedigree (RKHS-MP). The 333 lines in the 45th IBWSN and the 313 lines in the 46th IBWSN were genotyped using genotyping-by-sequencing markers. For the rusts, the mean prediction accuracies were 0.74 for LR seedling, 0.56 for LR APR, 0.65 for SR APR, 0.78 for YR seedling and 0.71 for YR APR. For the leaf spotting diseases, the mean genomic prediction accuracies were 0.45 for STB APR, 0.55 for SNB seedling, 0.66 for TS seedling and 0.48 for TS APR. Using genome-wide marker based models resulted in an average of 42-48% increase in accuracy over LS. Overall, the RKHS-MP model gave the highest accuracies, while LS gave the lowest. GWAS was also performed on these traits and several significant markers and candidate genes were identified. We conclude that implementing GWAS and genomic selection in breeding for these diseases would help to achieve higher accuracies and rapid gains from selection. ...

Genome-wide Association Mapping and Genomic Prediction for Enhancing FHB Resistance in Hard Winter Wheat

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ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)

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Book Synopsis Genome-wide Association Mapping and Genomic Prediction for Enhancing FHB Resistance in Hard Winter Wheat by : Jinfeng Zhang

Download or read book Genome-wide Association Mapping and Genomic Prediction for Enhancing FHB Resistance in Hard Winter Wheat written by Jinfeng Zhang and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Stripe Rust

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Publisher : Springer
ISBN 13 : 9402411119
Total Pages : 723 pages
Book Rating : 4.4/5 (24 download)

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Book Synopsis Stripe Rust by : Xianming Chen

Download or read book Stripe Rust written by Xianming Chen and published by Springer. This book was released on 2017-07-11 with total page 723 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprehensively introduces stripe rust disease, its development and its integral control. Covering the biology, genetics, genome, and functional genomics of the pathogen, it also discusses host and non-host resistance, their interactions and the epidemiology of the disease. It is intended for scientists, postgraduates and undergraduate studying stripe rust, plant pathology, crop breeding, crop protection and agricultural science, but is also a valuable reference book for consultants and administrators in agricultural businesses and education.

Genome-wide Association Mapping and Genomic Prediction for Resistance to Rusts (Puccinia Spp.) in Wheat Germplasm Collections

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ISBN 13 :
Total Pages : 208 pages
Book Rating : 4.:/5 (969 download)

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Book Synopsis Genome-wide Association Mapping and Genomic Prediction for Resistance to Rusts (Puccinia Spp.) in Wheat Germplasm Collections by : Kebede Tadesse Muleta

Download or read book Genome-wide Association Mapping and Genomic Prediction for Resistance to Rusts (Puccinia Spp.) in Wheat Germplasm Collections written by Kebede Tadesse Muleta and published by . This book was released on 2016 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic selection has the potential to enhance the utilization of germplasm collections through prediction of genomic estimated breeding values (GEBV) for as many traits as have been measured. We assessed the effect of different population genetic properties and marker density scenarios on GEBV accuracy in the context of applying GS for wheat germplasm utilization. The results of the cross-validation tests demonstrated that prediction accuracy increased with increase in population size and marker density. The results of the current GS suggests that larger germplasm collections may be more efficiently sampled based on lower-density genotyping methods, while genetic relationships between the training and validation populations remain critical when exploiting GS to select from germplasm collections.

Genome wide association studies and genomic selection for crop improvement in the era of big data

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Publisher : Frontiers Media SA
ISBN 13 : 2889763382
Total Pages : 192 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Genome wide association studies and genomic selection for crop improvement in the era of big data by : Nunzio D’Agostino

Download or read book Genome wide association studies and genomic selection for crop improvement in the era of big data written by Nunzio D’Agostino and published by Frontiers Media SA. This book was released on 2023-05-05 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Wheat Blast

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Publisher : CRC Press
ISBN 13 : 0429894074
Total Pages : 157 pages
Book Rating : 4.4/5 (298 download)

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Book Synopsis Wheat Blast by : Sudheer Kumar

Download or read book Wheat Blast written by Sudheer Kumar and published by CRC Press. This book was released on 2020-04-09 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat Blast provides systematic and practical information on wheat blast pathology, summarises research progress and discusses future perspectives based on current understanding of the existing issues. The book explores advance technologies that may help in deciding the path for future research and development for better strategies and techniques to manage the wheat blast disease. It equips readers with basic and applied understanding on the identification of disease, its distribution and chances of further spread in new areas, its potential to cause yield losses to wheat, the conditions that favour disease development, disease prediction modelling, resistance breeding methods and management strategies against wheat blast. Features: Provides comprehensive information on wheat blast pathogen and its management under a single umbrella Covers disease identification and diagnostics which will be helpful to check introduction in new areas Discusses methods and protocol to study the different aspects of the disease such as diagnostics, variability, resistance screening, epiphytotic creation etc. Gives deep insight on the past, present and future outlook of wheat blast research progress This book’s chapters are contributed by experts and pioneers in their respective fields and it provides comprehensive insight with updated findings on wheat blast research. It serves as a valuable reference for researchers, policy makers, students, teachers, farmers, seed growers, traders, and other stakeholders dealing with wheat.

Genomic Approaches for Mapping and Predicting Disease Resistance in Wheat (Triticum Aestivum L.)

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (12 download)

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Book Synopsis Genomic Approaches for Mapping and Predicting Disease Resistance in Wheat (Triticum Aestivum L.) by : Cristiano Lemes Da Silva

Download or read book Genomic Approaches for Mapping and Predicting Disease Resistance in Wheat (Triticum Aestivum L.) written by Cristiano Lemes Da Silva and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat diseases cause significant economic losses every year. To ensure global food security, newly released cultivars must possess increased levels of broadly-effective resistance against wheat pathogens, acceptable end-use quality, and high yield potential. Genetic host resistance stands out from other management strategies as the most viable option for controlling diseases. New genotyping platforms allow whole genome marker discovery at a relatively low cost, favoring the identification of novel loci underlying traits of interest. The work presented here describes genomic approaches for mapping and predicting the resistance to Fusarium head blight (FHB) and wheat rusts. The first study used biparental mapping to identify quantitative trait loci (QTL) associated with Fusarium head blight (FHB) resistance. A doubled haploid population (DH) was originated from a cross of Everest and WB-Cedar, which are widely grown wheat cultivars in Kansas with moderately resistant and moderately susceptible reactions to FHB, respectively. We confirmed that neither of the parents carry known large-effect QTLs, suggesting that FHB resistance is native. Eight small-effect QTLs were identified as associated with multiple mechanisms of FHB resistance. All QTLs had additive effects, providing significant improvements in levels of resistance when they were found in combinations within DH lines. In the second study, a genome-wide association mapping (GWAS) and genomic selection (GS) models were applied for FHB resistance in a panel of 962 elite lines from the K-State Wheat Breeding Program. Significant single nucleotide polymorphisms (SNPs) associated with the percentage of symptomatic spikelets were identified but not reproducible across breeding panels tested in each year. Accuracy of predictions ranged from 0.25 to 0.51 depending on GS model, indicating that it can be a useful tool to increase levels of FHB resistance. GWAS and GS approaches were also applied to a historical dataset to identify loci underlying resistance to leaf and stem rust at seedling stage in a panel of elite winter wheat lines. Infection types of multiple races of wheat rusts from the last sixteen years of the Southern Regional Performance Nursery (SRPN) were used in this study. A total of 533 elite lines originating from several breeding programs were tested in the SRPN during this period of time. GWAS identified significant SNP-trait associations for wheat rusts, confirming the effectiveness of already known genes and revealing potentially novel loci associated with resistance.

Crop Production and Global Environmental Issues

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Publisher : Springer
ISBN 13 : 3319231626
Total Pages : 604 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis Crop Production and Global Environmental Issues by : Khalid Rehman Hakeem

Download or read book Crop Production and Global Environmental Issues written by Khalid Rehman Hakeem and published by Springer. This book was released on 2015-12-08 with total page 604 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meeting the world’s food security challenge will require a multi-national, collaborative effort to integrate the best research from science, engineering and socioeconomics so that technological advances can bring benefits where they are most needed. The present book covers the effect of major environmental problems on crop production and how to cope with these issues for sustainable agriculture and improvements of crops. The world’s population is predicted to hit 9.6 Billion by 2050, up from today’s total of nearly 7.3 Billion, and with it food demand is predicted to increase substantially. The post-war ‘second agricultural revolution’ in developed countries, and the ‘green revolution’ in developing nations in the mid- 1960s converted agricultural practices and elevated crop yields spectacularly, but the outcome is levelling off and will not meet projected demand. Simultaneously, crop production is affected by many other factors, including industrial pollution, overuse of fertilizers and insecticides, heavy metal and radiation stresses etc. It has been noted that many pests are becoming resistant to insecticides. Estimates vary, but around 25% of crops can be lost to pests and diseases. Climate change associated with agriculture is also a global issue. Agriculture is a significant contributor to greenhouse gases and is estimated to account for 10-12% of total greenhouse gas (GHG) emissions. Many of the issues highlighted are global problems and are addressed thoroug hly in this work.

Association Mapping and Genomic Selection for Yield and Agronomic Traits in Soft Winter Wheat

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ISBN 13 :
Total Pages : 344 pages
Book Rating : 4.:/5 (11 download)

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Book Synopsis Association Mapping and Genomic Selection for Yield and Agronomic Traits in Soft Winter Wheat by : Dennis Nicuh Bulusan Lozada

Download or read book Association Mapping and Genomic Selection for Yield and Agronomic Traits in Soft Winter Wheat written by Dennis Nicuh Bulusan Lozada and published by . This book was released on 2018 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tools such as genome-wide association study (GWAS) and genomic selection (GS) have expedited the development of crops with improved genetic potential. While GWAS aims to identify significant markers associated with a trait of interest, the goal of GS is to utilize all marker effects to predict the performance of new breeding lines prior to testing. A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft winter wheat (SWW) lines evaluated in eight site-years in Arkansas and Oklahoma. Broad sense heritability of GY (H2=0.48) was moderate compared to other traits including plant height (H2=0.81) and kernel weight (H2=0.77). Markers associated with multiple traits on chromosomes 1A, 2D, 3B, and 4B serve as potential targets for marker assisted breeding to select for GY improvement. Validation of GY-related loci using spring wheat from the International Maize and Wheat Improvement Center (CIMMYT) in Mexico confirmed the effects of three loci in chromosomes 3A, 4B, and 6B. Lines possessing the favorable allele at all three loci (A-C-G allele combination) had the highest mean GY of possible haplotypes. The same population of 239 lines was used in a GS study as a training population (TP) to determine factors that affect the predictability of GY. The TP size had the greatest effect on predictive ability across the measured traits. Adding covariates in the GS model was more advantageous in increasing prediction accuracies under single population cross validations than in forward predictions. Forward validation of the prediction models on two new populations resulted in a maximum accuracy of 0.43 for GY. Genomic selection was "superior" to marker-assisted selection in terms of response to selection and combining phenotypic selection with GS resulted in the highest response. Results from this study can be used to accelerate the process of GY improvement and increase genetic gains in wheat breeding programs.

From Agriculture Genome to Phenome: Genome-Wide Association, Prediction and Selection

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Publisher : Frontiers Media SA
ISBN 13 : 2832540619
Total Pages : 147 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis From Agriculture Genome to Phenome: Genome-Wide Association, Prediction and Selection by : Kefei Chen

Download or read book From Agriculture Genome to Phenome: Genome-Wide Association, Prediction and Selection written by Kefei Chen and published by Frontiers Media SA. This book was released on 2023-12-11 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advances in “omics” technologies have enabled unprecedented progress in agricultural and biological sciences. The synergy of high-performance computing, high throughput omics approaches, and high dimensional phenotyping data with high spatial and temporal resolution have demonstrated the capacity to enhance our understanding of biological mechanisms but also to provide powerful insights into dissecting the genetic basis of complex traits with agricultural and economical importance. Genome-wide association study (GWAS) has become a useful approach to identify mutations that underlie diseases and complex traits and has provided important insights in exploring genetic profiles. However, it is less suitable for quantitative traits influenced by a large number of genes with small effects. In addition, false discoveries are a major concern and can be partially attributed to population structure. Genomic selection holds the promise to overcome the limitations by using whole-genome information to predict the genetic merits of phenotypes. It has been a powerful tool for predicting the breeding values of candidates for selection in breeding populations. One of the challenges of genomic prediction of breeding values with large-p-with-small-n regressions is to develop robust and efficient approaches that accurately predict phenotypic traits as functions of genotypic and environmental inputs. In addition, the integration of multi-omics data in phenotypic prediction would offer the opportunity to understand the flow of information that underlies the phenotypic traits.

Genome-Wide Association Studies Combined with Genomic Selection as a Tool to Increase Fusarium Head Blight Resistance in Wheat and Its Wild Relatives

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (133 download)

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Book Synopsis Genome-Wide Association Studies Combined with Genomic Selection as a Tool to Increase Fusarium Head Blight Resistance in Wheat and Its Wild Relatives by : Sampurna Bartaula

Download or read book Genome-Wide Association Studies Combined with Genomic Selection as a Tool to Increase Fusarium Head Blight Resistance in Wheat and Its Wild Relatives written by Sampurna Bartaula and published by . This book was released on 2022 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Fusarium head blight (FHB) is a devastating wheat (Triticum aestivum L.) disease worldwide. Presently, there is insufficient FHB resistance in the Canadian wheat germplasm. Genome-wide association study (GWAS) and genomic selection (GS) can be utilized to identify sources of resistance that could benefit wheat breeding. To define the genetic architecture of FHB resistance, association panels from a spring and a winter collection were evaluated using the Wheat Illumina Infinium 90K array. A total of 206 accessions from the spring panel and 73 from the winter panel were evaluated in field trials for 3-4 years at two locations, namely Morden (Manitoba) and Ottawa (Ontario). These accessions were phenotyped for FHB incidence (INC), severity (SEV), visual rating index (VRI), and deoxynivalenol (DON) content. Significant (p

Advances in Breeding Techniques for Cereal Crops

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Publisher :
ISBN 13 : 9781786762474
Total Pages : pages
Book Rating : 4.7/5 (624 download)

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Book Synopsis Advances in Breeding Techniques for Cereal Crops by : Frank Ordon

Download or read book Advances in Breeding Techniques for Cereal Crops written by Frank Ordon and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Wheat Landraces

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Publisher : Springer Nature
ISBN 13 : 3030773884
Total Pages : 268 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis Wheat Landraces by : Nusret Zencirci

Download or read book Wheat Landraces written by Nusret Zencirci and published by Springer Nature. This book was released on 2021-09-15 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Landraces possess a very large genetic base in population structure and are dynamic populations of cultivated plants with historical origin, distinct identity, and without any formal crop improvement. They are often genetically diverse, locally adapted, and associated with traditional farming systems. Resistance genes to biotic and abiotic stress factors, which are especially diversified in landraces, are of great interest to plant breeders, faced with global climate challenge. In addition, gene pools made of different landraces grown in different ecological conditions can be used for wheat breeding to enhance quality; yield and other desirable agricultural parameters. An estimated 75% of the genetic diversity of crop plants was lost in the last century due to the replacement of high yielding modern varieties. There is, thus, an urgent need to preserve existing species, not only for posterity but also as a means to secure food supply for a rising world population. In this book, we provide an overview of wheat landraces with special attention to genetic diversities, conservation, and utilization.

Genetic and Genomic Studies on Wheat Pre-harvest Sprouting Resistance

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (983 download)

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Book Synopsis Genetic and Genomic Studies on Wheat Pre-harvest Sprouting Resistance by : Meng Lin

Download or read book Genetic and Genomic Studies on Wheat Pre-harvest Sprouting Resistance written by Meng Lin and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain yield and end-use quality. Many quantitative trait loci (QTL) for PHS resistance have been reported in different sources. To determine the genetic architecture of PHS resistance and its relationship with grain color (GC) in US hard winter wheat, a genome-wide association study (GWAS) on both PHS resistance and GC was conducted using in a panel of 185 U.S. elite breeding lines and cultivars and 90K wheat SNP arrrays. PHS resistance was assessed by evaluating sprouting rates in wheat spikes harvested from both greenhouse and field experiments. Thirteen QTLs for PHS resistance were identified on 11 chromosomes in at least two experiments, and the effects of these QTLs varied among different environments. The common QTLs for PHS resistance and GC were identified on the long arms of the chromosome 3A and 3D, indicating pleiotropic effect of the two QTLs. Significant QTLs were also detected on chromosome arms 3AS and 4AL, which were not related to GC, suggesting that it is possible to improve PHS resistance in white wheat. To identify markers closely linked to the 4AL QTL, genotyping-by-sequencing (GBS) technology was used to analyze a population of recombinant inbred lines (RILs) developed from a cross between two parents, "Tutoumai A" and "Siyang 936", contrasting in 4AL QTL. Several closely linked GBS SNP markers to the 4AL QTL were identified and some of them were coverted to KASP for marker-assisted breeding. To investigate effects of the two non-GC related QTLs on 3AS and 4AL, both QTLs were transferered from "Tutoumai A" and "AUS1408" into a susceptible US hard winter wheat breeding line, NW97S186, through marker-assisted backcrossing using the gene marker TaPHS1 for 3AS QTL and a tightly linked KASP marker we developed for 4AL QTL. The 3AS QTL (TaPHS1) significantly interacted with environments and genetic backgrounds, whereas 4AL QTL (TaMKK3-A) interacted with environments only. The two QTLs showed additive effects on PHS resistance, indicating pyramiding these two QTLs can increase PHS resistance. To improve breeding selection efficiency, genomic prediction using genome-wide markers and marker-based prediction (MBP) using selected trait-linked markers were conducted in the association panel. Among the four genomic prediction methods evaluated, the ridge regression best linear unbiased prediction (rrBLUP) provides the best prediction among the tested methods (rrBLUP, BayesB, BayesC and BayesC0). However, MBP using 11 significant SNPs identified in the association study provides a better prediction than genomic prediction. Therefore, for traits that are controlled by a few major QTLs, MBP may be more effective than genomic selection.

Applications of Genetic and Genomic Research in Cereals

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Publisher : Woodhead Publishing
ISBN 13 : 0081022131
Total Pages : 382 pages
Book Rating : 4.0/5 (81 download)

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Book Synopsis Applications of Genetic and Genomic Research in Cereals by : Thomas Miedaner

Download or read book Applications of Genetic and Genomic Research in Cereals written by Thomas Miedaner and published by Woodhead Publishing. This book was released on 2018-11-19 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applications of Genetic and Genomic Research in Cereals covers new techniques for practical breeding, also discussing genetic and genomic approaches for improving special traits. Additional sections cover drought tolerance, biotic stress, biomass production, the impact of modern techniques on practical breeding, hybrid breeding, genetic diversity, and genomic selection. Written by an international team of top academics and edited by an expert in the field, this book will be of value to academics working in the agricultural sciences and essential reading for professionals working in plant breeding. Provides in-depth and comprehensive coverage of a rapidly developing field Presents techniques used in genetic and genomics research, with coverage of genotyping, gene cloning, genome editing and engineering and phenotyping in various cereals Includes the latest genetic and genomic approaches for improving special traits - drought tolerance, biotic stress and biomass production Covers breeding practices, with chapters on the genetic diversity of wheat, hybrid breeding and the potential of rye and barley crops

Salinity: Environment — Plants — Molecules

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Publisher : Springer Science & Business Media
ISBN 13 : 0306481553
Total Pages : 551 pages
Book Rating : 4.3/5 (64 download)

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Book Synopsis Salinity: Environment — Plants — Molecules by : André Läuchli

Download or read book Salinity: Environment — Plants — Molecules written by André Läuchli and published by Springer Science & Business Media. This book was released on 2007-05-08 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: In biology, the very big global and thevery small molecular issues currently appear to be in the limelight ofpublic interest and research funding policies. They are in danger of drifting apart from each other. They apply very coarse and very fine scaling, respectively, but coherence is lost when the various intermediate levels of different scales are neglected. Regarding SALINITY we are clearly dealing with a global problem, which due to progressing salinization of arable land is of vital interest for society. Explanations and basic understanding as well as solutions and remedies may finally lie at the molecular level. It is a general approach in science to look for understanding of any system under study at the next finer (or "lower") level of scaling. This in itself shows that we need a whole ladder of levels with increasingly finer steps from the global impact to the molecular bases of SALINITY relations. It is in this vein that the 22 chapters of this book aim at providing an integrated view of SALINITY.

Field assessment of resistance in potato to Phytophthora infestans

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Publisher : International Potato Center
ISBN 13 : 9290604409
Total Pages : 40 pages
Book Rating : 4.2/5 (96 download)

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Book Synopsis Field assessment of resistance in potato to Phytophthora infestans by : Forbes, G

Download or read book Field assessment of resistance in potato to Phytophthora infestans written by Forbes, G and published by International Potato Center. This book was released on 2014-06-27 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: The present guide is designed to assist professionals and technicians in charge of evaluation trials designed to screen selected potato genotypes for resistance to this disease. The evaluation of breeding families, which is carried out under greenhouse or field conditions, can use the same methodology. The guide can help to organize trials, improve data collection and analysis and introduces new criteria for resistance measurement based on epidemiological principles.