| 1. |
- Ortiz Rios, Rodomiro Octavio, et al.
(författare)
-
Oil crops for the future
- 2020
-
Ingår i: Current Opinion in Plant Biology. - : Elsevier BV. - 1369-5266 .- 1879-0356. ; 56, s. 181-189
-
Forskningsöversikt (refereegranskat)abstract
- Agriculture faces enormous challenges including the need to substantially increase productivity, reduce environmental footprint, and deliver renewable alternatives that are being addressed by developing new oil crops for the future. The efforts include domestication of Lepidium spp. using genomics-aided breeding as a cold hardy perennial high-yielding oil crop that provides substantial environmental benefits, expands the geography for oil crops, and improves farmers’ economy. In addition, genetic engineering in Crambe abyssinica may lead to a dedicated industrial oil crop to replace fossil oil. Redirection of photosynthates from starch to oil in plant tubers and cereal endosperm also provides a path for enhancing oil production to meet the growing demands for food, fuel, and biomaterials. Insect pheromone components are produced in seed oil plants in a cost-effective and environmentally friendly pest management replacing synthetically produced pheromones. Autophagy is explored for increasing crop fitness and oil accumulation using genetic engineering in Arabidopsis.
|
|
| 2. |
- Brhanie Mesfin, Haftom, et al.
(författare)
-
Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources
- 2022
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
-
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.
|
|
| 3. |
- Brhanie Mesfin, Haftom, et al.
(författare)
-
Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses
- 2022
-
Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09-0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.
|
|
| 4. |
- Dida, Mulatu Geleta, et al.
(författare)
-
High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes
- 2020
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11
-
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.
|
|
| 5. |
- Dueholm, Bjørn, et al.
(författare)
-
Cookability of 24 pea accessions-determining factors and potential predictors of cooking quality
- 2024
-
Ingår i: Journal of the Science of Food and Agriculture. - : John Wiley & Sons. - 0022-5142 .- 1097-0010. ; 104:6, s. 3685-3696
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Cooking time and cooking evenness are two critical quantities when determining the cooking quality (termed cookability) of pulses. Deciphering which factors contribute to pulse cookability is important for breeding new cultivars, and the identification of potential cookability predictors can facilitate breeding efforts. Seeds from 24 morphologically diverse pea accessions were tested to identify contributing factors and potential predictors of the observed cookability using a Mattson cooker. Size- and weight-based measures were recorded, and seed-coat hardness was obtained with a penetrometer. Content of protein, starch (amylose and amylopectin), and phytate was also determined.RESULTS: Distinct differences were found between wrinkled and non-wrinkled seeds in terms of water-absorption capacity, seed-coat hardness, and plunger-perforation speed. Potential predictive indicators of cooking time and cooking evenness were seed-coat hardness (r = 0.49 and r = 0.38), relative area gained (r = -0.59 and r = -0.8), and percentage of swelled seeds after soaking (r = -0.49 and r = -0.58), but only for non-wrinkled seeds. Surprisingly, the coefficients of variation for the profile area of both dry and swelled seeds appeared to be potential cookability predictors of all pea types (correlation coefficients around r = 0.5 and supported by principal component analysis). However, no strong correlation was observed between cookability and protein, starch, or phytate levels.CONCLUSION: Using three types of instruments together with chemical components enabled the identification of novel cookability predictors for both cooking time and cooking evenness in pea. This study unveils the diverse quantitative aspects influencing cookability in pea. Considering both cooking time and cooking evenness, as well as seed-coat hardness, underscores the multifaceted nature of pulse cookability and offers important insights for future breeding strategies to enhance pea cultivars. (c) 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
|
|
| 6. |
- Enyew, Muluken Birara, et al.
(författare)
-
Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers
- 2022
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy-Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.
|
|
| 7. |
- Enyew, Muluken Birara, et al.
(författare)
-
Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor
- 2022
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.
|
|
| 8. |
- Enyew, Muluken Birara, et al.
(författare)
-
Genotype by environment interaction, correlation, AMMI, GGE biplot and cluster analysis for grain yield and other agronomic traits in sorghum (Sorghum bicolor L. Moench)
- 2021
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16
-
Tidskriftsartikel (refereegranskat)abstract
- Genotype by environment (GxE) interaction is a major factor limiting the success of germplasm selection and identification of superior genotypes for use in plant breeding programs. Similar to the case in other crops, GxE complicates the improvement of sorghum, and hence it should be determined and used in decision-making programs. The present study aimed at assessing the GxE interaction, and the correlation between traits for superior sorghum genotypes. Three hundred twenty sorghum landraces and four improved varieties were used in alpha lattice experimental design-based field trial across three environments (Melkassa, Mieso and Mehoni) in Ethiopia. Phenotypic data were collected for days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT) and grain yield (GY). The results revealed that the variance due to genotype, environment and GxE interaction were highly significant (P < 0.001) for all traits. GY and PAWT were highly affected by environments and GxE whereas DTF, PALH, PAWD and PH were mainly affected by genotypic variation. Therefore, multi-environment testing is needed for taking care of G x E interaction to identify high yielding and stable sorghum landraces. GY and PAWT revealed highly significant positive correlations indicating the possibility of effective selection of the two traits simultaneously. Among the studied populations, South Wello, West Hararghe and Shewa zones had highly diverse genotypes that were distributed across all clusters. Hence, these areas can be considered as hotspots for identifying divergent sorghum landraces that could be used in breeding programs. Melkassa was the most representative environment whereas Mieso was the most discriminating. Five genotypes (G148, G123, G110, G203 and G73) were identified as superior across the test environments for grain yield with farmer-preferred trait, such as plant height. The identified stable and high yielding genotypes are valuable genetic resources that should be used in sorghum breeding programs.
|
|
| 9. |
- Enyew, Muluken Birara, et al.
(författare)
-
Novel sources of drought tolerance in sorghum landraces revealed via the analyses of genotype-by-environment interactions
- 2022
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Globally, sorghum is the fifth most important crop, which is used for food, feed and fuel. However, its production and productivity are severely limited by various stresses, including drought. Hence, this study aimed to determine the responses of different drought-tolerance related traits in the Ethiopian sorghum germplasm through multi-environment field trials, thereby identifying novel sources of germplasm that can be used for breeding the crop for drought-tolerance. Three hundred twenty sorghum landraces and four improved varieties were grown at three sites within drought-prone areas (Melkassa, Mieso and Mehoni) in Ethiopia. The targeted traits were chlorophyll content at flowering (CHLF), chlorophyll content at maturity (CHLM), green leaf number at flowering (GLNF), stay-green (SG), flag leaf area (FLA), peduncle length (PDL), and panicle exertion (PAE). Multi-variate analyses of the collected data revealed the presence of high phenotypic variation in all traits. The combined and AMMI Analysis of variance showed that phenotypic variation due to the genotypes was higher for SG, CHLM, CHLF and GLNF and lower for FLA, PE and PDL in comparison with variation due to the environments or genotype by environment interactions. High broad sense heritability was observed for CHLF, CHLM, SG, GLNF, FLA, and PDL, whereas PAE showed moderate heritability. Due to the high heritability of chlorophyll content and the relatively small effect of environmental factors on it, it could serve as a criterion for selecting desirable genotypes for drought-tolerant breeding in sorghum. It has been found that chlorophyll content has a significant positive correlation with stay-green and grain yield, indicating that high chlorophyll content contributes to increasing grain yield by delaying the process of leaf senescence. The analyses of AMMI, GGE biplot, and genotype selection index revealed that several sorghum landraces outperformed the improved varieties with respect to CHLF, CHLM, and SG. Such landraces could serve as novel sources of germplasm for improving drought tolerance through breeding.
|
|
| 10. |
- Gebeyehu Demissie, Adane, et al.
(författare)
-
Characterization of oilseed crop noug (Guizotia abyssinica) using agro-morphological traits
- 2021
-
Ingår i: Agronomy. - : MDPI AG. - 2073-4395. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- Noug (Guizotia abyssinica) is an outcrossing oilseed crop that serves as a source of edible oil and other nutrients although its seed yield is generally low. The analysis of agro-morphological traits in relation to seed and oil yields is important for improving the productivity of this crop. The present study aimed at assessing the variation and heritability of quantitative (10) and qualitative (6) traits in noug based on 60 landrace accessions collected from wide geographic area in Ethiopia. The field trial was conducted at two sites in Ethiopia using a square lattice design. The analysis of variance revealed significant variation (p < 0.05) among these accessions. The highest broad-sense heritability (H-2) was recorded for days to 10% flowering (DTF10; 85.4%), whereas number of capitula per plant (NCPP) and number of seeds per capitulum (NSPC) showed medium heritability (H-2 = 38.5% and 31.6%, respectively). NCPP and NSPC showed a highly significant (p < 0.01) positive and negative genotypic correlation with days to flowering, respectively. These three traits showed very low genotypic coefficient of variation (<1%). In the case of qualitative traits, small capitulum, large flower, green leaf, green stem and course leaf margin showed significant association with higher number of seeds per plant (NSPP). Euclidean distance-based cluster analysis revealed that the clustering pattern of the accessions poorly correlates with the geographic distance between sample collecting sites. Similarly, no clear clustering pattern of accessions was revealed by principal component analysis (PCA) that explained 66.3% and 53.6% of the total variation of quantitative traits and qualitative traits, respectively. The oil content of these accessions was previously investigated and accessions with high oil content show large differences in terms of days to flowering, NSPP and thousand seed weight (TSW). Among the accessions included in this research, Hr_B21; Gj_C17, Sh_14 and Gr_F15 Gj_G18 and Tg-R13 are top ranking, as they have at least one the following highly desirable traits: early maturity, high oil content, NSPP and TSW. Hence, crossbreeding of their selected genotypes would lead to the development of new cultivars that combine early maturity and both high seed and oil yields.
|
|
