MEKONNEN YESHITILA DEGEFU2025-12-312024https://etd.hu.edu.et/handle/123456789/188Morpho-Agronomical, Physiological, and Molecular Genetic Diversity of Amaranths (Amaranthus species) in Ethiopia The genus Amaranthus L. is one of the world's underutilized cosmo-politant and genetically potential orphan crops, with a diverse range of morphological characteristics and geographic distribution. It is one of the few dicotyledonous, non-grass mesophytes that uses specialized C4 annuals or short-lived perennials to produce significant amounts of edible small-seeded pseudo cereals. Amaranths are versatile plants with the potential for high yields. They have great photosynthetic performance as a result of eliminating the rival photorespiration mechanism. A diversified family of food crops known as amaranths is impressively adaptable to new environments despite a variety of biotic and abiotic constraints. Moreover, to maintain a healthy lifestyle and prevent disease, people are becoming more and more concerned with their diet and selective about the foods they eat. People are therefore moving away from the typical cereals and staple meals they have been eating for a long time and toward more nutrient-dense options. Regular cereals lack essential minerals, amino acids, a greater nutritional value, and contain gluten. As a result, pseudo-céréals, particularly amaranth, are excellent alternatives. The potential of Amaranthus spp. is still underexploited in Ethiopia. This is also evident from the limited genetic research and selection for desirable traits in amaranths. Consequently, the number of genotypes being cultivated is small, thus reducing the genetic variability of the elite germplasm and ultimately increasing potential vulnerability to biotic and abiotic stresses. In addition, the amaranth genotypes are poorly represented in gene banks. Moreover, the plant is being neglected due to a lack of extensive research, discrimination, ignorance, and, among other things, the long-term genetic growth of the plant in Ethiopia. As a result, there is a lack of data on its genetic diversity, necessitating this research. Therefore, it is important to broaden the germplasm collection of this crop and assess the genetic diversity existing within the germplasm to support future collection, conservation, and crop improvement programs. The objectives of the current study were to explore the potential of the genetic resources of amaranth genotypes for further conservation and exploitation and make it easier to incorporate them into breeding programs in order to increase productivity. In this study, one hundred twenty amaranth genotypes were evaluated over two years using an alpha lattice design with two replications using agro-morphological markers. The analysis of variance indicated that the mean square due to year and genotype-by-year interaction varied significantly for most measured traits. The estimates of variability, heritability, and genetic advance found in this study indicate high genetic diversity in amaranth genotypes and the strength of selection response for these traits in the population. Furthermore, the potential for amaranth improvement through appropriate selection is revealed by the existence of significant differences between the number of superior and inferior genotypes for the majority of examined traits. This suggests that these traits are governed more by additive gene action and that selection based on these traits might be successful in achieving the desired genetic gains for improvement. Aside from this, selection based on yield alone may not be effective for yield improvement in plant breeding initiatives. So yield should be considered along with potential yield contributing traits to progress the genetic gains during selection. On the other hand, the results revealed significant positive phenotypic and genotypic associations on leaf yield, with leaf area, leaf breadth, branch number, leaf number, plant height at flowering, and grain yield all having positive direct effects. Similar strong positive phenotypic and genotypic relationships were found for grain yield and grain sinking and filling rates. This study consequently shows the need for traits with significant positive indirect impacts via leaf area to be considered indirect selection criteria for improving leaf yield in amaranth genotypes. The grain sink filling rate also significantly improved grain yield indirectly at both the xxiv phenotypic and genotypic levels, mainly via days to flowering and leaf yield. This demonstrated that selection that mainly targeted days to flowering, leaf yield, and grain sink filling rate would ultimately boost the grain yield in amaranth genotypes. Principal component analysis showed that the first six principal components with eigenvalues greater than one contributed 80.41% of the variability. However, the first two principal components explained 52.42% of the total variation. The highest contributing traits in the first component were days to flowering, basal stem diameter, plant height at flowering, plant height at maturity, auxiliary inflorescence length, number of branches, terminal inflorescence lateral length, days to maturity, terminal inflorescence stalk length, leaf number, leaf length, top lateral branch length.. The traits with the greatest weight on the second component were leaf area, basal lateral branch length, leaf length, and leaf width, grain filling period, grain sinking filling rate, and grain yield. Therefore, selection based on these traits would be effective for yield improvement in amaranth genotypes. Additionally, the hierarchical clustering grouped all the genotypes into five clusters. The findings suggest that amaranth genotypes in Ethiopia have a lot of genetic variation, which might be used for future breeding and ought to be conserved. Twenty qualitative descriptors were utilized for a morphological diversity study for 120 amaranth genotypes. The overall mean of the Shannon diversity indices (H') was 0.61. The estimated diversity indices showed more intra-regional diversity (0.66) than inter-regional diversity (0.34), demonstrating the existence of gene flow between growing regions. Shannon-Weaver Diversity Index, ranged from 0.00 for auxiliary inflorescence to 1.94 for leaf coloration, with an overall mean of 19 characters (95%) that were found to have high diversity (>0.76) while auxiliary inflorescence was invariant. The hierarchical clustering grouped all the genotypes into three clusters. The first cluster included the most genotypes (58), followed by the second (47), and the third cluster contained the fewest (15). The study unequivocally demonstrated that, even when the genotypes were grouped into a small number of clusters, there was still enough divergence within the clusters to demonstrate the genotypes of amaranth to have a high genetic diversity. These results indicate that there is substantial genetic diversity among Ethiopian amaranth genotypes, which should be safeguarded and may be utilized in breeding in the future. The results of the analysis of variance showed that all examined physio-morphological parameters, except the rate of photosynthesis and stomata conductance, had mean squares that varied considerably (P < 0.001) owing to genotypes. The estimates of genetic variability, heritability, and expected genetic advance indicated high genetic diversity among amaranth genotypes, with a significant selection pressure for these traits in the population to produce better genotypes for improved amaranth. Selection based on desirable features such as leaf-to-air vapor pressure deficit, transpiration rate, chlorophyll a, chlorophyll b, total chlorophyll, carotenoid, leaf area, plant height, leaf number, and root weight can be useful in achieving the intended genetic gains for improvement since these traits appear to be more controlled by additive gene activity. Thus, selection in amaranth genotypes may consider these desired yield-related features. Moreover, the study showed that certain genotypes (ALE-073) exhibited better intercellular CO2 concentration (Ci), leaf-to-air vapor pressure deficit (VPD), transpiration rate (E), and leaf number (LN), resulting in better grain yield. Understanding the relationship between LA and E can help in selecting crops for high E and may provide an avenue to improve leaf yield. Furthermore, some of the selected genotypes in this study could be used as potential parents for improving the genetic gain in amaranth breeding programs. The study concluded that there was additive gene action present since the Ch a, Ch b, TCh, and Tca markers exhibited 100% heritability. This showed that the use of these characteristics for selection, which indicated a potentially exploitable variation, would be more effective and successful in the long run in breeding programs than the use of other traits for splitting generations. Hierarchical clustering grouped all the genotypes into seven clusters. The sixth cluster had the fewest genotypes (6), while the seventh cluster had the greatest number of genotypes (35) and was followed by Cluster Five (25), Cluster Three (22), Cluster One (14), Cluster Two (11), and Cluster Four (7). High leaf and grain yield-producing genotypes were grouped into the sixth cluster. The second cluster (C2) was characterized by high mean values for LA, LY, and GY. The maximum and significant genetic divergence was found between clusters C4 and C6 (D2 =103.44) and the least non-significant genetic divergence was found between clusters C5 and C7 (D2 =17.00). The first six PCs with eigenvalues greater than one accounted for 79.30% of the total variation in amaranth genotypes. The cumulative variance of 39.40% xxv was explained by 1st two principal components (PC1 and PC2) with eigenvalues greater than 1. Component 1 with a variance of 21.11 had a contribution from root length, root weight, total chlorophyll, and carotenoid while principal component 2 accounting for18.29% total variability had a contribution from transpiration rate, rate of net photosynthesis, chlorophyll b and, stomata conductance. The remaining variability of 13.02%, 11.33%, 9.37%, and, 6.17 % was consolidated in PC3, PC4, PC5, and PC6. These give scope for the selection of parents for breeding programs from these clusters, genetic divergence, and principal components to realize high genetic variation and novel combinations for yield incremen t. The present study was conducted to determine the genetic diversity and population structure of 40 amaranth genotypes using four inter-simple sequence repeat (ISSR) markers. The polymorphic information content (PIC), marker index (MI), resolving power (RP) and effective multiplex ratio (EMR) showed average values of 0.46, 10.41, 4.74, and 4.22 per primer, indicating high polymorphism values. The degree of polymorphism among the genotypes ranged from 0.00% for the Amhara population to 100% for the Southern Nations, Nationalities, and Peoples' Region population, with a grand mean of 70.83+11.34%. The observed number of alleles (Na), effective number of alleles (Ne), expected heterozygosity (He ), and genetic diversity estimated by Shannon’s information index (I) were 1.51, 1.50, 0.28 and 0.42, among collection regions, respectively. The total genetic diversity, Ht (0.400+0.006), and the average intrapopulation genetic diversity, Hs (0.285+0.004). A high level of gene flow (Nm = 2.12) between populations implies the presence of gene flow (Nm > 1) and reflects high genetic differentiation (Gst = 0.281). The analysis of molecular variance showed that the maximum value of genetic variation was found within populations (99%), whereas a low value of genetic variance was observed among populations (1%). The structure analysis, principal coordinate analysis (PcoA), and unweighted pair-group method with arithmetic averages (UPGMA) analysis clustered the 40 amaranths genotypes into four distinct subpopulations. The majority of genotypes (35%) were clustered in Pop2, mainly obtained from Southern Nations, Nationalities, and Peoples' regions constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. The findings of this study provide important and relevant information for future breeding and conservation efforts of amaranths. Therefore, the use of molecular markers would be valuable for the effective utilization of amaranth in breeding programs. In conclusion, the characterization of the genotypes using the molecular marker, and phenotypic traits compositions indicated the presence of diversity and variation among Ethiopian amaranth genotypes. The results from these studies suggest possibilities for identification of amaranth genotypes superior for leaf and grain yield, indicating the need for the initiation of a planned breeding program. The outcome of this study provided new insights into the genetic diversity and population structure in Ethiopian amaranth genetic resources for designing an effective collection and conservation strategies for efficient utilization in future breeding.en-USagro-morphologicalamaranthsagro-physiologicalbreedingdiversitygenotypesmolecular markerqualitative traitsThesis