| 1. |
- Desta, Zeratsion Abera, et al.
(författare)
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Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F-2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that similar to 57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.
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| 2. |
- Desta, Zeratsion Abera, et al.
(författare)
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Genetic diversity and structure found in samples of Eritrean bread wheat
- 2014
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Ingår i: Plant Genetic Resources. - 1479-2621. ; 12, s. 151-155
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Tidskriftsartikel (refereegranskat)abstract
- Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat.
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| 3. |
- Desta, Zeratsion Abera, et al.
(författare)
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Genomic selection: genome-wide prediction in plant improvement
- 2014
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Ingår i: Trends in Plant Science. - : Elsevier BV. - 1360-1385 .- 1878-4372. ; 19, s. 592–601-
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Forskningsöversikt (refereegranskat)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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| 4. |
- Desta, Zeratsion Abera
(författare)
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Genomic tools and molecular breeding approaches for the domestication of field cress (Lepidium campestre L.)
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Field cress (Lepidium campestre L.) is a biennial self-pollinated plant with a small genome size. The ever-increasing global population alongside climate change prompts urgent actions to save the ecosystem. Domesticating multi-purpose species such as field cress could be considered as part of the solution to mitigate the challenges posed by climate change and population growth. In addition to the oil producing potential, the domestication of field cress in arable lands has multitude effects – such as protecting environmental contamination and contributing as food and feed uses. In clues of these potentials, identifying the genomic variation underlying important traits using genomic tools is pivotal approach in field cress domestication. The main goal of the research in this thesis was to develop genomic tools for field cress domestication, specifically aiming at constructing the genetic linkage map, identifying the quantitative trait loci (QTL) underpinning domestication traits, and elucidating the common genetic variants associated with the seed yield as well as seed oil, protein, and moisture contents in field cress. An integrated mapping approach were performed to developing the first genetic linkage map for field cress. Relying on the linkage map, the identification of domestication QTL using linkage analysis as well as common variants using genome-wide association study (GWAS) were succeeded. Furthermore, the developed linkage map will be used in guiding to develop the reference genome using whole-genome sequencing (WGS) in field cress. Given further functional genomic efforts, the identified QTL and single variants could facilitate the process of domestication and genomicsassisted breeding in field cress, including the use of evolving approaches such as genome-wide prediction in the field cress.
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| 5. |
- Desta, Zeratsion Abera, et al.
(författare)
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Molecular mapping and identification of quantitative trait loci for domestication traits in the field cress (Lepidium campestre L.) genome
- 2020
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540.
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Tidskriftsartikel (refereegranskat)abstract
- Lepidium campestre (L.) or field cress is a multifaceted oilseed plant, which is not yet domesticated. Moreover, the molecular and genetic mechanisms underlying the domestication traits of field cress remain largely elusive. The overarching goal of this study is to identify quantitative trait loci (QTL) that are fundamental for domestication of field cress. Mapping and dissecting quantitative trait variation may provide important insights into genomic trajectories underlying field cress domestication. We used 7624 single nucleotide polymorphism (SNP) markers for QTL mapping in 428 F-2 interspecific hybrid individuals, while field phenotyping was conducted in F-2:3 segregating families. We applied multiple QTL mapping algorithms to detect and estimate the QTL effects for seven important domestication traits of field cress. Verification of pod shattering across sites revealed that the non-shattering lines declined drastically whereas the shattering lines increased sharply, possibly due to inbreeding followed by selection events. In total, 1461 of the 7624 SNP loci were mapped to eight linkage groups (LGs), spanning 571.9 cM map length. We identified 27 QTL across all LGs of field cress genome, which captured medium to high heritability, implying that genomics-assisted selection could deliver domesticated lines in field cress breeding. The use of high throughput genotyping can accelerate the process of domestication in novel crop species. This is the first QTL mapping analysis in the field cress genome that may lay a foundational framework for positional or functional QTL cloning, introgression as well as genomics-assisted breeding in field cress domestication.
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