Genetic architecture of adult-plant resistance to stripe rust in bread wheat (Triticum aestivum L.) association panel.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.

Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm.

BACKGROUND: High-density single nucleotide polymorphisms (SNPs) are the most abundant and robust form of genetic variants and hence make highly favorable markers to determine the genetic diversity and relationship, enhancing the selection of breeding materials and the discovery of novel genes associated with economically important traits. In this study, a total of 105 barley genotypes were sampled from various agro-ecologies of Ethiopia and genotyped using 10 K single nucleotide polymorphism (SNP) markers. The refined dataset was used to assess genetic diversity and population structure. RESULTS: The average gene diversity was 0.253, polymorphism information content (PIC) of 0.216, and minor allelic frequency (MAF) of 0.118 this revealed a high genetic variation in barley genotypes. The genetic differentiation also showed the existence of variations, ranging from 0.019 to 0.117, indicating moderate genetic differentiation between barley populations. Analysis of molecular variance (AMOVA) revealed that 46.43% and 52.85% of the total genetic variation occurred within the accessions and populations, respectively. The heat map, principal components and population structure analysis further confirm the presence of four distinct clusters. CONCLUSIONS: This study confirmed that there is substantial genetic variation among the different barley genotypes. This information is useful in genomics, genetics and barley breeding.

Morphological variations of qualitative traits of barley (Hordeum vulgare L.) accessions in Ethiopia.

Ethiopian barley germplasm is a potential source of useful traits to fight the production challenges of barley farming and to enhance yield productivity in favorable and marginal environments. A study was carried out to assess the distribution and patterns of 17 qualitative trait variations among 85 Ethiopian barley accessions using an alpha lattice design with two replications. The Shannon-Weaver diversity (H') index was used to estimate morphological diversity. Fifteen morphological traits of barley accessions originating from various regions of origins and altitude ranges were polymorphic. However, two traits including stem branching and lemma awn were monomorphic. The highest (0.94) overall mean of H' was obtained for glume colour, kernel row and kernel shape. The estimated H' ranged from 0.41 to 0.99 across regions, and 0.52 to 0.99 across altitude ranges with an overall mean of 0.76. The analysis of variance of H' showed significant variation for most studied traits. Principal components analysis revealed that eight traits were the major loading on the first two principal components that describe 38.3% of the total morphological variance. Heat map analysis based on morphological traits of barley accessions was also grouped into three distinct clusters. Thus, the present finding confirmed that the Ethiopian barley accessions showed vast morphological variations across the region of origins and altitude ranges. Based on the result, further evaluation is ongoing to exploit specific gene variations through phenotyping and genotyping trait association.

Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072.

BACKGROUND: In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. Therefore, a computational survey was carried out for the Trametes hirsuta strain 072 genome with the open reading frames from the National Center for Biotechnology Information database. Seventeen functional sequences were used to analyze promoter regions and their regulatory elements. RESULT: The present study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two TSSs. Among these identified TSSs, a TSS with the highest predictive score was considered to determine a promoter region of the genes. Moreover, a total of five common candidate motifs such as MotI, MotII, MotIII, MotIV, and MotV were identified. Among these motifs, motif IV was investigated as the common promoter motif for 41.17% of genes that serve as binding sites for transcription factors (TFs) involved in the expression regulation of Trametes hirsuta strain 072 genes. Motif IV was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF using TOMTOM web server. Hence, it was revealed that MotIV might serve as the binding site mainly for the leucine zipper TF gene family to regulate a gene expression of Trametes hirsuta strain 072. Regarding CpG island determination, it was concluded that there is no CpG island in both promoter and gene body regions of the Trametes hirsuta strain 072 genome. CONCLUSIONS: This study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment.

In silico analysis of promoter region and regulatory elements of glucan endo-1,3-beta-glucosidase encoding genes in Solanum tuberosum: cultivar DM 1-3 516 R44.

BACKGROUND: Potato (Solanum tuberosum L.) is one of the most important food crops in the world. Pathogens remain as one of the major constraints limiting potato productivity. Thus, understanding of gene regulation mechanism of pathogenesis-related genes such as glucan endo-1,3-beta-glucosidase is a foundation for genetic engineering of potato for disease resistance and reduces the use of fungicides. In the present study, 19 genes were selected and attempts were made through in silico methods to identify and characterize the promoter regions, regulatory elements, and CpG islands of glucan endo-1,3-beta-glucosidase gene in Solanum tuberosum cultivar DM 1-3 516 R44. RESULTS: The current analysis revealed that single transcription start sites (TSSs) were present in 12/19 (63.2%) of promoter regions analyzed. The predictive score at a cutoff value of 0.8 for the majority (84.2%) of the promoter regions ranged from 0.90 to 1.00. The locations for 42% of the TSSs were below -500 bp relative to the start codon (ATG). MßGII was identified as the common promoter motif for 94.4% of the genes with an E value of 3.5e-001. The CpG analysis showed low CpG density in the promoter regions of most of the genes except for gene ID102593331 and ID: 102595860. The number of SSRs per gene ranged from 2 to 9 with repeat lengths of 2 to 6 bp. Evolutionary distances ranged from 0.685 to 0.770 (mean = 0.73), demonstrating narrower genetic diversity range. Phylogeny was inferred using the UPGMA method, and gene sequences from different species were found to be clustered together. CONCLUSION: In silico identified regulatory elements in promoter regions will contribute to our understanding of the regulatory mechanism of glucan endo-1,3-beta-glucosidase genes and provide a promising target for genetic engineering to improve disease resistance in potatoes.

In silico analysis of promoter region and regulatory elements of mitogenome co-expressed trn gene clusters encoding for bio-pesticide in entomopathogenic fungus, Metarhizium anisopliae: strain ME1.

BACKGROUND: Pest control strategies almost entirely rely on chemical insecticides, which cause environmental problems such as biosphere deterioration and emergence of resistant pests. Bio-pesticide is an alternative approach, which uses organisms such as entomopathogenic fungi, Metarhizium anisopliae, to control pests. Screening such potential organism at a molecular level and understanding their gene regulation mechanism is an important approach to reduce emergence of pesticide resistance and worsening of the biosphere. Understanding promoter regions which play a pivotal role in gene regulation is crucial. In particular, identification of the promoter regions in M. anisopliae Strain ME1 remains poorly understood. To our knowledge, the mitogenome trn gene clusters of M. anisopliae Strain ME1 were not characterized. Here, we used machine learning approach to identify and characterize the promoter regions, regulatory elements, and CpG island densities of 15 protein coding genes of entomopathogenic fungi, M. anisolpliae Strain ME1. RESULTS: The current analysis revealed multiple transcription start sites (TSS) for all utilized sequences, except for promoter region genes of Pro-cob and Pro-nad5. With reference to the start codon (ATG), 85.3% of TSS was located above - 500 bp. Based on the standard predictive score at cut off value of 0.8a, the current study revealed 54.7% of predictive score greater than or equal from 0.9 promoter prediction score. Expectation maximization algorithm output identified five candidate motifs. Nonetheless, of all candidate motifs, MtrnI was revealed as the common promoter region motif with a value of 76.9% both in terms of size of binding sites and with an E value of 9.1E-054. Accordingly, we perceived that MtrnI serve as the binding site for tryptophan cluster with P value 0.0044 and C4 type zinc fingers functions as the binding site to regulate gene expression of M. anisopliae Strain ME1. The analysis revealed that mitogenome trn gene clusters of M. anisopliae Strain ME1 showed homologues evolutionary ancestor supported with a bootstrap value of 100%. CONCLUSION: Identified common candidate motifs and binding transcription factors through in silico approach are likely expected to contribute for better understanding of gene expression and strain improvement of M. anisopliae Strain ME1 for its bio-pesticides role.

Genetic Diversity of Tef [Eragrostis tef (Zucc.)Trotter] as Revealed by Microsatellite Markers.

Genetic variability is the fundamental prerequisite of any crop-breeding program to develop superior cultivars. There are about 350 Eragrostis1 species, of which, tef is the only species cultivated for human consumption. Currently, the Ethiopian Biodiversity Institute (EBI) collected over five thousand tef accessions from different geographical regions, diverse in terms of climate and elevation, which are uncharacterized yet. The objective of this study was to evaluate the genetic diversity among 64 tef accessions using 10 selected polymorphic simple sequence repeats (SSRs) markers. A total of 314 alleles were detected with an average of 14.5 alleles per locus and amplicon size ranged from 90 bp-320 bp. The mean value of polymorphic information content (PIC) was 0.87, appearing polymorphic for all loci. The lowest Fst value (0.05) was recorded among the studied tef populations. The mean value of major allele frequency and the number of effective alleles were 0.33 and 3.32, respectively. The mean value of gene flow (Nm) and Shannon's information index (I) was 4.74 and 1.65, respectively. The observed (Ho) and expected (He) heterozygosities varied from 0.34 to 0.56 and from 0.58 to 0.76, respectively. The cluster analysis has grouped the 64 tef accessions into three distinct clusters based on their similarity. The PCoA analysis showed that clustering is basing on the geographical origin of accessions. Analysis of molecular variance revealed 56%, 39% and 5% of the total variation due to variation within populations, among individuals and among populations, respectively. Structure bar-plot also inferred three gene pools, but with high level of admixtures. Thus, the present study shows that the identified tef accessions could be of great interest for the initiation of a planned breeding and conservation programs.

In silico analysis of promoter regions and regulatory elements (motifs and CpG islands) of the genes encoding for alcohol production in Saccharomyces cerevisiaea S288C and Schizosaccharomyces pombe 972h.

BACKGROUND: The crucial factor in the production of bio-fuels is the choice of potent microorganisms used in fermentation processes. Despite the evolving trend of using bacteria, yeast is still the primary choice for fermentation. Molecular characterization of many genes from baker's yeast (Saccharomyces cerevisiaea), and fission yeast (Schizosaccharomyces pombe), have improved our understanding in gene structure and the regulation of its expression. This in silico study was done with the aim of analyzing the promoter regions, transcription start site (TSS), and CpG islands of genes encoding for alcohol production in S. cerevisiaea S288C and S. pombe 972h-. RESULTS: The analysis revealed the highest promoter prediction scores (1.0) were obtained in five sequences (AAD4, SFA1, GRE3, YKL071W, and YPR127W) for S. cerevisiaea S288C TSS while the lowest (0.8) were found in three sequences (AAD6, ADH5, and BDH2). Similarly, in S. pombe 972h-, the highest (0.99) and lowest (0.88) prediction scores were obtained in five (Adh1, SPBC8E4.04, SPBC215.11c, SPAP32A8.02, and SPAC19G12.09) and one (erg27) sequences, respectively. Determination of common motifs revealed that S. cerevisiaea S288C had 100% coverage at MSc1 with an E value of 3.7e-007 while S. pombe 972h- had 95.23% at MSp1 with an E value of 2.6e+002. Furthermore, comparison of identified transcription factor proteins indicated that 88.88% of MSp1 were exactly similar to MSc1. It also revealed that only 21.73% in S. cerevisiaea S288C and 28% in S. pombe 972h- of the gene body regions had CpG islands. A combined phylogenetic analysis indicated that all sequences from both S. cerevisiaea S288C and S. pombe 972h- were divided into four subgroups (I, II, III, and IV). The four clades are respectively colored in blue, red, green, and violet. CONCLUSION: This in silico analysis of gene promoter regions and transcription factors through the actions of regulatory structure such as motifs and CpG islands of genes encoding alcohol production could be used to predict gene expression profiles in yeast species.

Phylogeography and conservation genetics of a giant lobelia (Lobelia giberroa) in Ethiopian and Tropical East African mountains.

Lobelia giberroa is a giant rosette plant growing in the afro-montane belt of the afro-alpine environment, a unique and little-studied ecosystem occupying the high mountains of eastern Africa. We analysed amplified fragment length polymorphisms (AFLPs) from 11 mountain systems in Ethiopia and Tropical East Africa to infer the phylogeographical history of the species. A total of 191 individuals were investigated from 25 populations. Principal coordinate analysis and population structure analyses revealed three major phylogeographical groups: the Ethiopian mountains and one group on each side of the Rift Valley in Tropical East Africa, respectively: Elgon-Cherangani and Kenya-Aberdare-Kilimanjaro-Meru. Analysis of Molecular Variance showed 55.7% variance among the three groups, suggesting an old divergence. Together with a clear geographical substructure within the main groups, this pattern indicates gradual expansion and supports the montane forest bridge hypothesis, stating that the area occupied by forest was larger and more continuous in previous interglacials and earlier in the present interglacial. Genetic diversity was lower in Ethiopia than in the other two main groups, possibly due to an ancient founder effect when Ethiopia was colonized from the south.