| 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. |
- Abreha, Kibrom Berhe, et al.
(författare)
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Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress
- 2022
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Ingår i: Planta. - : Springer Science and Business Media LLC. - 0032-0935 .- 1432-2048. ; 255
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Forskningsöversikt (refereegranskat)abstract
- Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still signifcantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the efects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized fndings on the efects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn afect seed flling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.
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| 3. |
- Alsanius, Beatrix, et al.
(författare)
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The power of light from a non-phototrophic perspective: a phyllosphere dilemma
- 2024
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Ingår i: Frontiers in Photobiology. - 2813-8228. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Plants and crop stands are considered holobionts, colonized by both autotrophic and by non-phototrophic heterotrophic microbiota. The dilemma in the exisiting body of studies is that the focus is primarily directed towards environmental specificties relevant for phototrophic organisms (predominantly plants), but does not take into account non-phototrophs. By definition, non-phototrophic heterotrophic bacteria do not use light as an energy source. Light energy and wavelength are rather used as a signal that can provoke shifts in both their metabolism and microbial lifestyle. Reaction and recovery time can vary between organisms and is dependent on the organism’s physiological stage. The length of the lighting event affects the energy an organism is exposed to. We argue that to obtain a deeper and more distinct understanding of light exposure (irradiance, exposure length), quantity (light intensity), and quality (wavelength/spectral distribution, bandwidth at full-width half-maximum) related mechanisms on non-phototrophic bacteria in the phyllosphere, the light environment needs to be further strictly characterized. This includes information on the actual energy hitting planktonic or sessile non-phototrophic bacteria resident on and inside plants aboveground. Mapping the light environment in ecosystems aids in unraveling light-phyllosphere interactions and strengthens their transdisciplinary character. This issue is fundamental in order to revisit and repeat others’ experimental approaches and findings but also to be able to translate findings into further action.
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| 4. |
- Barin, Mohsen, et al.
(författare)
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Optimization of Biofertilizer Formulation for Phosphorus Solubilizing by Pseudomonas fluorescens Ur21 via Response Surface Methodology
- 2022
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Ingår i: Processes. - : MDPI AG. - 2227-9717. ; 10:4
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to analyze and quantify the effect of different ratios of vermicompost, phosphate rock, and sulfur on P solubilization and release by Pseudomonas fluorescens Ur21, and to identify optimal levels of those variables for an efficient biofertilizer. Twenty experiments were defined by surface response methodology based on a central composite design (CCD), and the effects of various quantities of vermicompost, phosphate rock, and sulfur (encoded by −1, 0, or +1) on P solubilization was explored. The results show that the CCD model had high efficiency for predicting P solubilization (R2 = 0.9035). The strongest effects of the included variables on the observed P solubilization were linear effects of sulfur and organic matter (vermicompost), a quadratic effect of phosphate rock, and an interactive effect of organic matter × phosphate rock. Statistical analysis of the coefficients in the CCD model revealed that vermicompost, vermicompost × phosphate rock, and phosphate rock × phosphate rock treatments increased P solubilization. The optimal predicted composition for maximal P solubilization by P. fluorescens Ur21 (at 1684.39 mg·kg−1, with more than 90% of the added phosphate dissolved) was 58.8% vermicompost, 35.3% phosphate rock, and 5.8% sulfur. ANOVA analysis confirmed the model’s accuracy and validity in terms of F value (10.41), p value (<0.001), and non-significant lack of fit.
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| 5. |
- Brhanie Mesfin, Haftom, et al.
(författare)
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Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Alsusceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
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| 6. |
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| 7. |
- Burra, Dharani, et al.
(författare)
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RNAseq and Proteomics for Analysing Complex Oomycete Plant Interactions
- 2016
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Ingår i: Current Issues in Molecular Biology. - : MDPI AG. - 1467-3037 .- 1467-3045. ; 19, s. 73-87
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Forskningsöversikt (refereegranskat)abstract
- The oomycetes include some of the most devastating plant pathogens. In this review we discuss the latest results from oomycete and plant studies with emphasis on interaction studies. We focus on the outcomes of RNAseq and proteomics studies and some pitfalls of these approaches. Both pathogenic interactions and biological control are discussed. We underline the usefulness of studies at several levels of complexity from studies of one organism, up to two or more and within agricultural fields (managed settings) up to wild ecosystems. Finally we identify areas of future interest such as detailed interactome studies, dual RNAseq studies, peptide modification studies and population/meta omics with or without biological control agents.
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| 8. |
- Chawade, Aakash, et al.
(författare)
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Lignocellulolytic and Chitinolytic Glycoside Hydrolases: Structure, Catalytic Mechanism, Directed Evolution and Industrial Implementation
- 2020
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Ingår i: Industrial Applications of Glycoside Hydrolases. - Singapore : Springer Singapore. - 9789811547669 ; , s. 97-127
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Bokkapitel (refereegranskat)abstract
- Lignocellulolytic and chitinolytic glycoside hydrolases are commonly used enzymes in commercial processes and thus are well documented for their vital role in agriculture, textile, paper, food, biofuel and healthcare sectors. Ongoing research is targeted to further enhance the applicability of these vital enzymes in the above mentioned sectors. In this regard, an up-to-date knowledge of enzymatic structure, catalytic mechanism and several modern approaches like recombinant technology, chemical and enzymatic pre-treatment, enzyme immobilization and directed evolution for the improvement of enzymes production, activity and stability is highly required. This review provides an up-to-date information and discussion on the various lignocellulolytic and chitinolytic glycoside hydrolases regarding the vital aspects of the enzymes viz. catalytic mechanism, structural features, directed evolution approaches, current applications and under research potential applications.
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| 9. |
- Cleary, Michelle, et al.
(författare)
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Susceptibility of common tree species in Sweden to Phytophthora cactorum, P. cambivora and P. plurivora
- 2017
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 47
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Tidskriftsartikel (refereegranskat)abstract
- In Sweden, invasive Phytophthora pathogens have been recognized as a growing threat to urban and production forests, calling for an urgent update of regeneration strategies for infested areas. Stem inoculation tests were performed to test the relative susceptibility of common conifer and broadleaved tree species Pinus sylvestris, Picea abies, Larix x eurolepis, Betula pendula, Quercus robur, Fagus sylvatica, Populus trichocarpa and Tilia cordata to the root pathogens Phytophthora cactorum, P. cambivora and P. plurivora commonly isolated from Swedish soils. Results indicate that all the species tested were susceptible and formed lesions following stem inoculation with all three Phytophthora species, but to varying degrees. Of particular interest are the high levels of susceptibility in P. trichocarpa to all three Phytophthora species compared to other tested tree species.
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| 10. |
- Gebeyehu Demissie, Adane, et al.
(författare)
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RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
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