Dagnachew, Lule (2015) Assessment of Genetic Diversity, Genotype by Environment Interaction, Blast (Magnaporthe Oryzae) Disease Resistance, and Marker Development for Finger Millet Germplasm from Ethiopia and Introduced. PhD thesis, Addis Ababa University.
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Abstract
Finger millet (Eleusine coracana subsp. coracana) is extensively cultivated in the tropical and subtropical regions of Africa and India. It is the major staple food for millions of resource poor people and plays an important role in the dietary habits and economy of subsistence farmers inhabiting arid and semi-arid regions of Africa and India. The crop is adapted to adverse agro-ecological conditions with minimal inputs, tolerant to moisture stress, produced on marginal land where other crops cannot perform and tolerant to acidic soils. Breeding efforts in finger millet has been limited and farmers are growing unimproved and low yielding cultivars. Improvement in any crop usually involves exploiting the genetic variability in specific traits of interest. Moreover, the use of multiple data sets, such as morphological, biochemical and molecular in combination with appropriate statistical methods are essential to identify inter and intra-species variation to develop improved cultivars. One hundred and five finger millet accessions, collected from the major finger millet producing regional states of Ethiopia (Amhara, Benishangul Gumuz, Oromia, Tigray and Southern Nations Nationalities and Peoples Region (SNNP)), supplemented by 39 introduced accessions from Kenya, Zambia, Zimbabwe and Eritrea and six improved varieties, were evaluated in the field at Gute and Arsi Negele during 2011 to assess the genetic diversity and eco-geographical patterning. The analysis of variance indicated that the mean square due to environment and genotype were highly significant (P≤0.01) for all quantitative traits except ear weight for the latter case. Erect type growth habit, open ear type, light green ear (glumes) color, enclosed grains by glumes, lower spikelet density and purple black seed color were the predominant phenotypic classes for the traits recorded in the present study. Cluster analysis for both qualitative and quantitative phenotypic traits indicated that finger millet accessions from neighboring regions of Ethiopia, neighboring African countries and proximity in altitude classes shared strong similarity. Principal component analysis at population level, geographical locations and agro-ecologies of origin indicated that grain yield per plant, thousand grain weight, days to heading, days to maturity, lodging index and biomass weight per plant were the most important traits contributing to the overall variability, implying that breeding efforts on those traits can meet the objectives in improving the trait. The higher heritability coupled with higher genetic advance noted for ear weight (71.14%), lodging index (53.49), finger length (41.94%), thousand grain weights (28.88) and grain yield per plant (26.34) indicated the ease of phenotypic selection for the improvement of those traits. About 68.4% of the total traits association showed positive correlation. The 150 finger millet test accessions were also evaluated using a set of 20 SSR markers. Results showed variable genetic polymorphism with an average polymorphic information content of 0.57. A total of 188 alleles were recorded with an average of 9.89 alleles per locus. Analysis of molecular variance revealed 69.52% variation within populations and 30.48% among populations. Relatively higher within accession polymorphism were recorded for accessions from Oromia (21.10%), Amhara (16.93%) and Tigray (13.43%) regional states of Ethiopia. Weighted neighbor joining-based clustering grouped the 138 accessions for which the SSR markers worked well, into three major clusters apart from the main node, and accessions collected from the same region or the same altitude classes did not often group entirely together within a given major cluster or sub cluster. Likewise, analysis of population structure distinguished the 138 finger millet accessions in to three subpopulation ( = 3) with the highest ∆K of around 300. The first, second and the third group comprised of accessions from the different geographical locations and the improved varieties with membership proportion 22.9%, 38.5% and 38.6%, respectively. Magnaporthe oryzea, a fungal pathogen that attacks more than 50 gramineous species, is well known to cause immense yield loss, and is particularly severe on rice and finger millet. A total of 225 finger millet materials were evaluated for blast resistance/tolerance on a sick plot supplemented with artificial inoculation at Bako Agricultural Research Center in 2011. The analyses of variance revealed the mean square due to genotypes were highly significant (P≤0.01) for leaf, sheath, neck and head blast. Based on the head blast disease severity index, the 225 test materials were classified into five groups: only one accession (Acc. BKFM0031) was resistant (head blast severity score of < 3 at maturity with both head blast severity index and relative area under disease progress curve (RAUDPC) values of less than 21%), 10 accessions were moderately resistant with blast severity index of 21-40%, the remaining 214 was in a range of moderately susceptible to highly susceptible. About 66% of the most susceptible accessions gave grain yield below the average (11.29 g/plant), indicating that grain yield reduction in most accessions were due to blast infection. Finger millet accessions collected from the same region showed different levels of disease reaction, implying that diversified materials are produced within a country or region. Both correlation and regression analysis revealed highly significant (P≤0.01) negative association of head blast to grain yield. An average of 63.2% yield loss was recorded due to head blast disease during the severe infection periods of 2011 as estimated using different yield loss assessment models. Identification of adaptable, stable and high yielding genotypes under varying environmental conditions are the first steps in plant breeding prior to release of a cultivar and this has direct bearing on the adoption of the variety, its productivity and total production of the crop. To this end, a total of 30 advanced finger millet genotypes were evaluated against two standard checks (Gute and Taddesse) across four locations (Arsi Negele, Assosa, Bako and Gute) in the 2012 and 2013. Additive Main effect and Multiplicative Interaction (AMMI), Genotype and Genotype by Environment Interaction (GGI) biplot analysis and, Eberhart and Russell model revealed that Acc. 203544 was stable and high yielding (3.16 ton ha-1) with a yield advantage of 13.7% over the best standard check, Gute (2.78 ton ha-1), and thus recommended for possible release with wider environmental adaptability. Moreover, Acc. 242111 (3.08 ton ha-1) and BKFM0051 (3.07 ton ha-1) were high yielding, but showed narrow stability and thus recommended for possible release for specific environments. Single strand conformation polymorphism (SSCP) analysis detected that only one marker was polymorphic among the thirteen primers designed from Rice Orthologous Genes with finger millet for blast resistant. Sequence analysis of this polymorphic marker (Pi9F2) for eight representative finger millet accessions and 15 clone samples revealed the average contigs measurement of 891bp and nucleotide distribution of 30.9% Thymine (T), 28.1% Adenine (A), 24.2% Cytosine (C) and 16.8% Guanine (G). Multiple sequence alignment of those sequence revealed two possible SNPs at consensus positions 460 (G/A) and 780 (G/C) in a window of 66 bp, where the consensus residue is G at both positions. Overall, this study showed the presence of divers finger millet accessions that deserve sustainable conservation and use in breeding program and generated information on the extent of genetic variation among finger millet accessions and eco-geographical regions using multiple markers. Besides, the study has of the preliminary contribution in the application of molecular tools for diversity analysis and thus variety development and identified accessions with variable level of blast tolerance for further utilization in breeding and other genomic research activities.
| Item Type: | Thesis (PhD) |
|---|---|
| Uncontrolled Keywords: | Finger millet (Eleusine coracana subsp. coracana), Additive main effect and multiplicative interaction (AMMI), Area Under Disease Development Curve (AUDPC), Heritability, Magnaporthe oryzae, polymorphism, Simple Sequence Repeat (SSR), Single strand confirmation polymorphism (SSCP). |
| Subjects: | Q Science > Q Science (General) Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QK Botany |
| Divisions: | Africana |
| Depositing User: | Selom Ghislain |
| Date Deposited: | 25 Sep 2018 12:51 |
| Last Modified: | 25 Sep 2018 12:51 |
| URI: | http://thesisbank.jhia.ac.ke/id/eprint/5642 |
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