| 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. |
- Campbell, Bruce M., et al.
(författare)
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Agriculture production as a major driver of the Earth system exceeding planetary boundaries
- 2017
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Ingår i: Ecology & Society. - 1708-3087. ; 22:4
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Tidskriftsartikel (refereegranskat)abstract
- We explore the role of agriculture in destabilizing the Earth system at the planetary scale, through examining nine planetary boundaries, or safe limits: land-system change, freshwater use, biogeochemical flows, biosphere integrity, climate change, ocean acidification, stratospheric ozone depletion, atmospheric aerosol loading, and introduction of novel entities. Two planetary boundaries have been fully transgressed, i.e., are at high risk, biosphere integrity and biogeochemical flows, and agriculture has been the major driver of the transgression. Three are in a zone of uncertainty i.e., at increasing risk, with agriculture the major driver of two of those, land-system change and freshwater use, and a significant contributor to the third, climate change. Agriculture is also a significant or major contributor to change for many of those planetary boundaries still in the safe zone. To reduce the role of agriculture in transgressing planetary boundaries, many interventions will be needed, including those in broader food systems.
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| 3. |
- Dida, Mulatu Geleta, et al.
(författare)
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High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes
- 2020
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F2 mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft L. campestre whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F2 individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1–Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events during the evolution of n = 8 karyotype in ancestral species shared by Lepidium and Arabidopsis to n = 5 karyotype in A. thaliana. This study generated highly useful genomic tools and resources for Lepidium that can be used to accelerate its domestication.
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| 4. |
- Ortiz Rios, Rodomiro Octavio
(författare)
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Introduction
- 2020
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Ingår i: Plant Genetic Conservation. - 9780521001304 ; , s. 3-44
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Bokkapitel (refereegranskat)
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| 5. |
- Hammenhag, Cecilia, et al.
(författare)
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Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop
- 2018
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits.Results: Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine nonsynonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum.Conclusions: There is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.
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| 6. |
- Hegay, Sergay, et al.
(författare)
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Comparing genetic diversity and population structure of common beans grown in Kyrgyzstan using microsatellites
- 2012
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Ingår i: Scientific Journal of Crop Science. - 2322-1690. ; 1, s. 63-75
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Tidskriftsartikel (refereegranskat)abstract
- Common bean (Phaseolus vulgaris L.) is an important export crop in Kyrgyzstan. The aim of this study was to assess the extent of genetic diversity, determine the population structure, and relate to the main gene pools grown in Kyrgyzstan. Twenty-eight common bean accessions (including five Kyrgyz cultivars, and main references from the Mesoamerica and South America) were evaluated with microsatellites. Nine polymorphic microsatellites were used to estimate genetic diversity and heterozygosity. The number of alleles per microsatellite locus ranged from 2 to 4 and there were a total of 24 alleles. The observed heterozygosity of each accession over all loci ranged from 0 to 0.11 (with an average of 0.01), while the expected average heterozygosity was 0.05, which could reflect the self-pollinating breeding behavior of common beans. The analysis of molecular variance further revealed that 94.71% of the total variation was accounted by differences among accessions (Fst =0.947; p<0.001). Cluster analysis grouped accessions in two gene pools: 16 belong to the Andean and 12 to the Mesoamerican gene pool. The microsatellites separated accessions in Mesoamerican gene pool from Durango and Jalisco races, which were grouped together. We also observed that the most divergent accessions were the Kyrgyz cultivars, which may be related to the Mesoamerican races. Andean accessions were less diverse than Mesoamerican accessions in this study. This research confirms the ability of microsatellites to differentiate common bean accessions, even using a small sample size, and to be able to assign modern cultivars to their gene pools or races.
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| 7. |
- Ortiz Rios, Rodomiro Octavio
(författare)
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Genetic Diversity Measurement
- 2020
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Ingår i: Plant Genetic Conservation. - 9780521001304 ; , s. 114-132
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Bokkapitel (refereegranskat)
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| 8. |
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| 9. |
- Ortiz Rios, Rodomiro Octavio
(författare)
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Musa
- 2011
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Ingår i: Wild Crop Relatives: Genomic and Breeding Resources, Tropical and Subtropical Fruits. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783642204463 ; , s. 97-128
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 10. |
- Ortiz Rios, Rodomiro Octavio
(författare)
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Planning Plant Conservation
- 2020
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Ingår i: Plant Genetic Conservation. - : Cambridge University Press. - 9780521001304 ; , s. 135-185
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Bokkapitel (refereegranskat)
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