Browsing by Author "MIHERETU FUFA GELETA"

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    GENETIC DIVERSITY AND GENOME-WIDE ASSOCIATION MAPPING IN TETRAPLOID WHEAT (TRITICUM TURGIDUM SPP.) GERMPLASM OF ETHIOPIA
    (Hawassa University College of Agriculture, 2024) MIHERETU FUFA GELETA
    Genetic Diversity and Genome-Wide Association Mapping in Tetraploid Wheat (Triticum turgidum spp.) Germplasm of Ethiopia PhD Dissertation Miheretu Fufa Geleta Hawassa University, 2024 Ethiopia is a center of diversity for Tetraploid wheat (Triticum turgidum spp.) species, which hold ample genetic variation; howevr, the country remains a net importer of wheat due to a huge gap between production and consumption. The present study was aimed to investigate the extent and pattern of diversity based on phenotypic traits, grain quality traits, and molecular markers; and Genome-Wide association studies for phenotypic and grain quality traits. Diversity assessment at the entire genotypes based on the qualitative traits revealed intermediate (0.60±0.01) diversity and high diversity concerning glum color (0.78), spike density (0.61), and seed color (0.86); however, low diversity for awndness (0.15). All qualitative traits showed highly significant (p<0.001) variation across regions of collections and altitudinal classes; however, only spike density was significantly (p<0.05) different at the species level. Within populations diversity was higher than between population diversity. Analysis of variance based on the quantitative traits revealed highly significant variation (p<0.001) among genotypes and for genotype by location interaction in all traits except for the number of effective tillers per plant. The observed mean and range values of the phenotypic traits revealed high variability in the accessions. Phenotypic Coefficient of Variation (PCV) and Genotypic Coefficient of Variation (GCV) values were high for grain yield, biomass yield, and harvest index. The estimates of heritability (H2 ) ranged from 41.78 to 84.62 % respectively for grain yield and the number of seeds per spikelet. High genetic advance as a percentage of mean was observed for the number of seeds per spikelet, the number of effective tillers per plant, grain yield, biomass yield, and harvest index. The number of seeds per spikelet gave a high value of genetic advance and heritability implying high genetic gain from its selection. Grain yield showed a highly significant (p<0.001) negative correlation with days to booting and days to maturity and a positive correlation with the remaining quantitative traits. The combined ANOVA based on the grain quality traits revealed a highly significant variation (p < 0.001) among the genotypes and for genotype by location interaction for all traits. The genotypes showed a wide range in their thousand kernel weight, zeleny index, and vitreousness percentage. Grain yield and protein content, respectively, showed high and low values of PCV and GCV; however, an intermediate value of PCV and GCV was observed for gluten content and thousand kernel weight. Zeleny index and vitreousness percentage showed high PCV and intermediate GCV; however, protein content showed low PCV and GCV. The estimate of broad sense heritability (H2 ) ranged from 33.57 % for vitreousness percentage to 66.36 % for zeleny index. The values of genetic advance and GAM observed were respectively high for grain yield (31.94, 26.91) and zeleny index (31.89, 29.34); intermediate for thousand kernel weight (18.27, 16.59), gluten content (15.70, 13.55), and vitreousness percentage (15.75, 12.97) and low for protein content (9.81, 8.44). Grain yield showed a highly significant positive correlation with thousand kernel weight (0.43***) and vitreousness percentage (0.19**) and positive correlation, but not significant, with protein content, gluten content, and zeleny index. xxi Principal component analysis (PCA) based on phenotypic traits showed that the first and second principal components (PC) respectively accounted for 19.74% and 15.96 of the total variation in the entire genotypes, respectively. The first five principal components combined explained 61.21 % based on the entire genotypes. On the other hand, PCA of grain quality traits showed that the first and second PCs respectively accounted for 34.12 % and 20.65% of the total variation and the three PCs explained 69.11% of the total variation in the entire genotypes. Eleven landraces and eleven improved varieties were top performing based on their grain yield and grain quality traits. Clustering based on phenotypic traits and grain quality traits respectively grouped the whole genotypes into seven and six clusters without clear regional grouping. Furthermore, the genetic diversity and population structure were investigated for the study panel as well as the landraces based on 10349 DArTSeq markers distributed across A and B genomes. The study panel was clustered into two populations: pop1 and pop2 respectively comprising 150 landraces and 3 released varieties and 19 released varieties and 12 landraces pop2 being more diverse than pop1; likewise, landraces were clustered into two subgroups. Analysis of molecular variance (AMOVA) revealed highly significant (P<0.001) variation between populations and within populations the latter being higher than the former implying that more attention should be given to individual accessions within populations to explore the existing genetic diversity. Little to moderate genetic differentiation (Fst) was respectively reported for the landraces (0.028) and the study panel (0.117) implying no significant differentiation among populations. High gene flow (1.297-8.818) was recorded based on DArTSeq markers at all level. PCA based on DArTSeq markers grouped the released varieties and the landraces separately in the study panel; however, PCA of the landraces did not show clear groupings. 127 genotypes were reported to have one or more private alleles at 755 loci, an indication of key adaptive genes at these loci to be exploited in breeding programs. In conclusion, high genetic diversity was detected in Ethiopian tetraploid wheat germplasm, which could be utilized for future wheat breeding programs. The landraces ETW115 and ETW135 and the released varieties (Tesfaye and Bekelcha) could be used in a crossing program owing to their maximum genetic distance. Analysis of genome-wide LD in the whole collection showed that 44.98% of the total marker pairs had a significant LD (p<0.01) with a mean r2 value of 0.129791. 44.59% (18668) and 8.62% (3609) of the significant marker pairs showed r2 values above 0.2 and 0.7, respectively, indicating a higher level of LD in the genome. The number of significant marker pairs observed was higher in the B genome (24.44%) than the A genome (20.54%). GWAS identified 44 SNPs, two of which are pleiotropic, across chromosome 1A, 2A, 2B, 3A, 3B, 4B, 5A, 5B, 6A, 6B, and 7B that were significantly (FDR <0.05) associated with some of the traits studied. Thirty-five QTLs were reported while the remaining 9 QTLs were found to be novel, which need to be validated for further use in the breeding program. We also identified several candidate genes, potentially regulating the traits, and encoding various proteins involved in plant growth and development. Hence, this study highlights the significance of the Ethiopian tetraploid wheat gene pool for improving tetraploid wheat globally; thus, a breeding strategy focusing on accumulating favorable alleles at these loci could improve tetraploid wheat production in Ethiopia and beyond