| 1. |
- Abebe, Admas Alemu, et al.
(författare)
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Genomic selection in plant breeding: key factors shaping two decades of progress
- 2024
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Ingår i: Molecular Plant. - 1674-2052 .- 1752-9867. ; 17, s. 552-578
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Forskningsöversikt (refereegranskat)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. |
- Chawade, Aakash, et al.
(författare)
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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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Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 164, s. 442-451
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Forskningsöversikt (refereegranskat)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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| 3. |
- Chawade, Aakash, et al.
(författare)
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High-Throughput Field-Phenotyping Tools for Plant Breeding and Precision Agriculture
- 2019
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Ingår i: Agronomy. - : MDPI AG. - 2073-4395. ; 9
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Forskningsöversikt (refereegranskat)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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| 4. |
- Chawade, Aakash, et al.
(författare)
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RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture
- 2021
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Ingår i: Plants. - : MDPI AG. - 2223-7747. ; 10
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Forskningsöversikt (refereegranskat)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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| 5. |
- Leiva, Fernanda, et al.
(författare)
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The Combination of Low-Cost, Red–Green–Blue (RGB) Image Analysis and Machine Learning to Screen for Barley Plant Resistance to Net Blotch
- 2024
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Ingår i: Plants. - 2223-7747. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Challenges of climate change and growth population are exacerbated by noticeable environmental changes, which can increase the range of plant diseases, for instance, net blotch (NB), a foliar disease which significantly decreases barley (Hordeum vulgare L.) grain yield and quality. A resistant germplasm is usually identified through visual observation and the scoring of disease symptoms; however, this is subjective and time-consuming. Thus, automated, non-destructive, and low-cost disease-scoring approaches are highly relevant to barley breeding. This study presents a novel screening method for evaluating NB severity in barley. The proposed method uses an automated RGB imaging system, together with machine learning, to evaluate different symptoms and the severity of NB. The study was performed on three barley cultivars with distinct levels of resistance to NB (resistant, moderately resistant, and susceptible). The tested approach showed mean precision of 99% for various categories of NB severity (chlorotic, necrotic, and fungal lesions, along with leaf tip necrosis). The results demonstrate that the proposed method could be effective in assessing NB from barley leaves and specifying the level of NB severity; this type of information could be pivotal to precise selection for NB resistance in barley breeding.
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| 6. |
- Odilbekov, Firuz, et al.
(författare)
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QTL Mapping for resistance to early blight in a tetraploid potato population
- 2020
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Ingår i: Agronomy. - : MDPI AG. - 2073-4395. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Early blight of potato, caused by Alternaria solani, is an economically important foliar disease in most potato-growing regions. Growing cultivars with higher levels of resistance to early blight can reduce tuber yield losses and the need for fungicide applications. In this research, a bi-parental tetraploid potato population, segregating for resistance to early blight in leaves and tubers, was characterized to identify novel quantitative trait loci (QTL) associated with foliar and tuber early blight resistance. Assessment of the disease resistance in the foliage was performed by field evaluation and in tuber under controlled conditions. Results from this study revealed significant differences (P < 0.001) in resistance to A. solani among potato clones both in the leaves and in tubers. There was no statistically significant correlation (r = 0.06, P = 0.35) between the resistance scores from leaves and tubers. Several clones exhibited; however, high levels of resistance both in leaves and tubers and are; thus, promising candidates for breeding for early blight resistance. Linkage mapping revealed several QTL for early blight affecting both foliage and tubers. QTL associated with disease resistance in the tuber were found on chromosomes 1, 2, 3, 4, 8, 11 and 12. QTL associated with disease resistance in foliage were also examined for independence from defoliation, and independent QTL were; thus, found on chromosomes 5 and 11.
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| 7. |
- Selga, Catja, et al.
(författare)
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A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding
- 2021
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Ingår i: Plants. - : MDPI AG. - 2223-7747. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.
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| 8. |
- Selga, Catja, et al.
(författare)
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Diversity and population structure of Nordic potato cultivars and breeding clones
- 2022
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 22
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Tidskriftsartikel (refereegranskat)abstract
- Background: The genetic diversity and population structure of breeding germplasm is central knowledge for crop improvement. To gain insight into the genetic potential of the germplasm used for potato breeding in a Nordic breeding program as well as all available accessions from the Nordic genebank (NordGen), 133 potato genotypes were genotyped using the Infinium Illumina 20 K SNP array. After SNP filtering, 11 610 polymorphic SNPs were included in the analysis. In addition, data from three important breeding traits – percent dry matter and uniformity of tuber shape and eye – were scored to measure the variation potato cultivars and breeding clones.Results: The genetic diversity among the genotypes was estimated using principal coordinate analysis based on the genetic distance between individuals, as well as by using the software STRUCTURE. Both methods suggest that the collected breeding material and the germplasm from the gene‑bank are closely related, with a low degree of population structure between the groups. The phenotypic distribution among the genotypes revealed significant differences, especially between farmer’s cultivars and released cultivars and breeding clones. The percent heterozygosity was similar between the groups, with a mean average of 58–60%. Overall, the breeding germplasm and the acces‑ sions from the Nordic genebank seems to be closely related with similar genetic background.Conclusion: The genetic potential of available Nordic potato breeding germplasm is low, and for genetic hybridiza‑ tion purposes, genotypes from outside the Nordic region should be employed.
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