| 1. |
- Abebe, Admas Alemu, et al.
(author)
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Genomic selection in plant breeding: key factors shaping two decades of progress
- 2024
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In: Molecular Plant. - 1674-2052 .- 1752-9867. ; 17, s. 552-578
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Research review (peer-reviewed)abstract
- Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
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| 2. |
- Abreha, Kibrom Berhe, et al.
(author)
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Understanding the Sorghum–Colletotrichum sublineola interactions for enhanced host resistance
- 2021
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
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Research review (peer-reviewed)abstract
- Improving sorghum resistance is a sustainable method to reduce yield losses due to anthracnose, a devastating disease caused by Colletotrichum sublineola. Elucidating the molecular mechanisms of sorghum–C. sublineola interactions would help identify biomarkers for rapid and efficient identification of novel sources for host-plant resistance improvement, understanding the pathogen virulence, and facilitating resistance breeding. Despite concerted efforts to identify resistance sources, the knowledge about sorghum–anthracnose interactions remains scanty. Hence, in this review, we presented an overview of the current knowledge on the mechanisms of sorghum-C. sublineola molecular interactions, sources of resistance for sorghum breeding, quantitative trait loci (QTL), and major (R-) resistance gene sequences as well as defense-related genes associated with anthracnose resistance. We summarized current knowledge about C. sublineola populations and its virulence. Illustration of the sorghum-C. sublineola interaction model based on the current understanding is also provided. We highlighted the importance of genomic resources of both organisms for integrated omics research to unravel the key molecular components underpinning compatible and incompatible sorghum–anthracnose interactions. Furthermore, sorghum-breeding strategy employing rapid sorghum germplasm screening, systems biology, and molecular tools is presented.
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| 3. |
- Chawade, Aakash, et al.
(author)
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A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region
- 2018
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In: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 164, s. 442-451
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Research review (peer-reviewed)abstract
- The Baltic Sea is one of the largest brackish water bodies in the world. Eutrophication is a major concern in the Baltic Sea due to the leakage of nutrients to the sea with agriculture being the primary source. Wheat (Triticum aestivum L.) is the most widely grown crop in the countries surrounding the Baltic Sea and thus promoting sustainable agriculture practices for wheat cultivation will have a major impact on reducing pollution in the Baltic Sea. This approach requires identifying and addressing key challenges for sustainable wheat production in the region. Implementing new technologies for climate-friendly breeding and digital farming across all surrounding countries should promote sustainable intensification of agriculture in the region. In this review, we highlight major challenges for wheat cultivation in the Baltic Sea region and discuss various solutions integrating transnational collaboration for pre-breeding and technology sharing to accelerate development of low input wheat cultivars with improved host plant resistance to pathogen and enhanced adaptability to the changing climate.
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| 4. |
- Chawade, Aakash, et al.
(author)
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High-Throughput Field-Phenotyping Tools for Plant Breeding and Precision Agriculture
- 2019
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In: Agronomy. - : MDPI AG. - 2073-4395. ; 9
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Research review (peer-reviewed)abstract
- High-throughput field phenotyping has garnered major attention in recent years leading to the development of several new protocols for recording various plant traits of interest. Phenotyping of plants for breeding and for precision agriculture have different requirements due to different sizes of the plots and fields, differing purposes and the urgency of the action required after phenotyping. While in plant breeding phenotyping is done on several thousand small plots mainly to evaluate them for various traits, in plant cultivation, phenotyping is done in large fields to detect the occurrence of plant stresses and weeds at an early stage. The aim of this review is to highlight how various high-throughput phenotyping methods are used for plant breeding and farming and the key differences in the applications of such methods. Thus, various techniques for plant phenotyping are presented together with applications of these techniques for breeding and cultivation. Several examples from the literature using these techniques are summarized and the key technical aspects are highlighted.
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| 5. |
- Chawade, Aakash, et al.
(author)
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RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture
- 2021
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In: Plants. - : MDPI AG. - 2223-7747. ; 10
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Research review (peer-reviewed)abstract
- With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA-based approaches i.e., RNAi-mediated gene regulation and the site-specific nuclease-based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting the downregulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops’ genome sequences to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture.
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| 6. |
- Desta, Zeratsion Abera, et al.
(author)
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Genomic selection: genome-wide prediction in plant improvement
- 2014
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In: Trends in Plant Science. - : Elsevier BV. - 1360-1385 .- 1878-4372. ; 19, s. 592–601-
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Research review (peer-reviewed)abstract
- Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genomewide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or markerassisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy.
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| 7. |
- Dida, Mulatu Geleta, et al.
(author)
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Molecular and Genomic Tools Provide Insights on Crop Domestication and Evolution
- 2016
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In: Advances in Agronomy. - : Elsevier. - 0065-2113 .- 2213-6789. ; 135, s. 181-223
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Research review (peer-reviewed)abstract
- Rapid progress in genomic research and the development of genome-wide molecular markers for various crops significantly improved our knowledge on plant domestication and evolution. Molecular markers and other genomic tools have been used to understand the evolutionary changes that converted wild plants into domesticated crops, and the identification of loci behind domestication syndrome traits will have significant importance in the fast-track domestication of new plants. The application of genomics- assisted selection in plant breeding programs has significantly contributed to efficient plant breeding for desirable traits. Genomic tools also facilitated the efficient identification of progenitors of crops as well as centers of domestication. Multiple genomic regions with signature of selection during plant domestication have been found in various crops. Extensive analyses of plant genomes revealed that genes underlying domestication syndrome traits show a significant loss of diversity, for example, up to 95% of genetic diversity in wild relatives has been lost during domestication process in extreme cases. Genomic research revealed repeated occurrence of polyploidization during plant evolution and various interesting events that occurred following polyploidization such as gene loss and silencing. The loss of most replicated genes through time and nonrandom retention of some duplicated genes that serve as signatures of polyploidy are among interesting changes in polyploid plant genomes. Further insights into the advances in our knowledge on plant domestication and evolution made through the use of DNA markers and genomic tools is provided in this paper.
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| 8. |
- Eriksson, Dennis, et al.
(author)
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Measuring the impact of plant breeding on sub-Saharan African staple crops
- 2018
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In: Outlook On Agriculture. - : SAGE Publications. - 0030-7270 .- 2043-6866. ; 47, s. 163-180
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Research review (peer-reviewed)abstract
- Many countries in sub-Saharan Africa (SSA) are facing huge challenges regarding food insecurity, low agricultural output, and agriculturally incurred environmental degradation. A sustainable and increased crop productivity and diversity is essential to achieve food security in a socially, economically, and environmentally sustainable way. Plant breeding is an important factor contributing to the increased crop productivity and diversity, giving farmers access to genetically improved cultivars that yield more, have better resistance to biotic and abiotic stresses, and meet consumer expectations. To motivate and encourage further investments, it is important to measure the actual impact of breeding. This review considers available research on the impact of breeding through yield gain and of food security, focusing on 10 important staple crops in SSA. The overall impression is that breeding produces a very high return on investment. Such investments remain centerpieces for meeting the challenges in this region. The discussion focuses on the most important future breeding priorities for each crop, the actors involved, and the importance of mechanisms for dissemination and farmer adoption, and concludes with some policy recommendations.
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| 9. |
- Goldman, Irwin, et al.
(author)
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Pursuing the Potential of Heirloom Cultivars to Improve Adaptation, Nutritional, and Culinary Features of Food Crops
- 2019
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In: Agronomy. - : MDPI AG. - 2073-4395. ; 9
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Research review (peer-reviewed)abstract
- The burdens of malnutrition, protein and micronutrient deficiency, and obesity cause enormous costs to society. Crop nutritional quality has been compromised by the emphasis on edible yield and through the loss of biodiversity due to the introduction of high-yielding, uniform cultivars. Heirloom crop cultivars are traditional cultivars that have been grown for a long time (>50 years), and that have a heritage that has been preserved by regional, ethnic, or family groups. Heirlooms are recognized for their unique appearance, names, uses, and historical significance. They are gaining in popularity because of their unique flavors and cultural significance to local cuisine, and their role in sustainable food production for small-scale farmers. As a contrast to modern cultivars, heirlooms may offer a welcome alternative in certain markets. Recently, market channels have emerged for heirloom cultivars in the form of farmer-breeder-chef collaborations and seed-saver organizations. There is therefore an urgent need to know more about the traits available in heirloom cultivars, particularly for productivity, stress tolerance, proximate composition, sensory quality, and flavor. This information is scattered, and the intention of this review is to document some of the unique characteristics of heirloom cultivars that may be channeled into breeding programs for developing locally adapted, high-value cultivars.
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| 10. |
- Ortiz Rios, Rodomiro Octavio
(author)
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Advanced analytics phenomics and biotechnology approaches to enhance genetic gains in plant breeding
- 2020
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In: Advances in Agronomy. - : Elsevier. - 0065-2113 .- 2213-6789. ; 162, s. 89-142
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Research review (peer-reviewed)abstract
- Agriculture production is a major driver of destabilization of the earth's planetary boundaries within which humanity can safely operate. Producing enough food that is safe and nutritious is the biggest challenge in 21st century agriculture. Yield gains through genetic enhancement have either slowed down or not rising to the level needed to meet the ever-growing demand for nutritious food. A continuous supply of high-quality crop germplasm is the key to developing climate-resilient, resource-use efficient, nutritious and productive cultivars. Global efforts are underway to develop pre-breeding populations, by exploiting exotic germplasm including wild and weedy relatives with required characteristics to support breeding programs. Comprehensive profiling of germplasm/breeding lines (relative to uncharacterized lines) and adopting a strategy based on physiological characterization of parental lines have the potential to facilitate the accumulation of favorable alleles to enhance genetic gain in plant breeding. Advances in genomics, phenomics and bioinformatic resources have led to the deployment of several knowledge-intensive approaches to accelerate genetic gains in diverse food crops. Enhanced capability in data storage, retrieval and analysis has greatly facilitated the development of genotype-phenotype models to predict phenotypes, thus enhancing selection efficiency. Genomic-aided breeding has been successful in enhancing genetic gain relative to pedigree-based phenotypic selection. Genes controlling "recombination hotspots" and targeted recombination may provide breeders opportunity to significantly increase genetic gains. Combining genomic selection with doubled haploid technology, speed breeding and high-throughput phenomics with genotype-by-sequencing profiling allows the fast transfer of increased genetic gains per unit time. An open source software system has the potential to increase breeding efficiency through data and code sharing, while open source seed systems should allow for continued seed saving, breeding, and seed exchange without restriction. Taken together, these approaches should provide breeders with the opportunity to make genetic gains through new technologies and through the infusion of useful genetic variation in crop breeding.
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