Morphometric, Photosynthetic and Molecular Markers Based Genetic Diversity Study of the African Wild Rice (Oryza Longistaminata Chev. Et Roher) From Ethiopia
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2018-06-02
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Addis Ababa University
Abstract
MORPHOMETRIC, PHOTOSYNTHETIC AND MOLECULAR MARKERS BASED GENETIC DIVERSITY STUDY OF THE AFRICAN WILD RICE (Oryza longistaminata Chev. et Roher) FROM ETHIOPIA
Getachew Melaku Adane, PhD Dissertation
Addis Ababa University, June 2018
Rice which feeds more than half of the world human population is affected by environmental changes. Therefore, its productivity should be supplemented by the genetic resources from other wild relatives. The African wild rice, Oryza longistaminata Chev. et. Roher, which possess AA genome as the cultivated rice, is hypothesized as a good candidate for widening the cultivated rice gene pool. However, its status of genetic diversity and relationship with other Oryza members is still unresolved. So far, the genetic resource from this African species is underutilized for the breeding of cultivated rice. Even, characterization and evaluation of the different agro-morphological and photosynthetic traits of O. longistaminata are still untapped. To this end, assessing the morphometric, photosynthetic and molecular markers based genetic diversity and regional differentiation of the African wild rice (O. longistaminata) in Ethiopia is very important for efficient breeding and conservation schemes.
This study therefore, employed 67 SSR markers over 360 O. longistaminata accessions from 12 populations of Ethiopia, one O. longistaminata accession from Niger, 35 varieties of the Indica and Japonica subspecies of O. sativa, 25 accessions of four AA genome wild Oryza species, 8 accessions of five CC genome wild rice species and one Japonica weedy type for the assessment of genetic diversity and relatedness. In this study, evaluation of morphological differences and characterization of leaf gas exchange traits were done from the three replicates of 62 Ethiopian O. longistaminata accessions. The Restriction Associated DNA Sequencing xv
data from 87 O. longistaminata accessions of Ethiopia was also analyzed for their phylogenetic relationships and region based differentiation.
The eight morphometric and seven leaf gas exchange traits assessed in this study revealed a significant variation. Correlations between the evaluated morphological traits of the assessed accessions showed highly significant pairwise associations. The multivariate analysis from the eight morphological traits implicated population effect. In particular, the inter-population distances among the six populations of origin showed distinctness of the Amhara from the rest five Gambella populations. The Pearson pairwise correlation matrix for the seven leaf gas exchange traits revealed their inter-relationship. For instance, the rate of photosynthesis was positively and significantly (P < 0.001) correlated with all other traits except the intercellular CO2 concentration. Moreover, the accessions showed high photosynthetic rate with a minimum intercellular CO2 concentration, transpiration rate and stomatal conductance.
When the 12 O. longistaminata populations from Ethiopia were pooled as one, the 67 SSR markers showed (Na = 4.35, Ne = 1.91, Ho = 0.15, He = 0.38, F = 0.53 and PIC = 83.82). Such diversity indices implicated higher diversity than the rest AA and CC genome rice types. A highly significant (P> 0.001) genetic differentiation (Fst) = 0.299 was also observed among the 12 O. longistaminata populations of Ethiopia. However, the Analysis of Molecular Variance (AMOVA) showed the highest variance (38%) among accessions with in a population. PCA of the whole 430 accessions showed five main clusters and a clear geographic pattern was emerged for the 12 populations of O. longistaminata from Ethiopia. Population structuring and clustering through UPGMA and hierarchical clustering clearly separated the 12 Ethiopian O. longistaminata populations from other wild and cultivated rice types. Moreover, structure analysis from the SSR data indicated genetic distinctness in between the Amhara and Gambella regions. Dendrogram, DAPC, and population divergence xvi
(Fst) analysis from the 30,256 Single Nucleotide Polymorphisms (SNPs) generated by the Restriction Associated DNA Sequencing also showed genetic differentiation among the two regions.
In conclusion, the high diversity status of the Ethiopian O. longistaminata populations and their genetic distinctness to other Oryza species or in particular to O. sativa is an ideal opportunity for their utilization in diverse rice improvement programs. Moreover, the low transpiration rate and stomatal conductance records with a maximum Carboxylation Efficiency of the O. longistaminata accessions showed their environmental adaptability and high water use efficiency. The high Photosynthetic rate observed in the assessed accessions implicated that O. longistaminata could be used as a genetic resource for the photosynthetic improvement of rice cultivars. Therefore, the very efficient carbon balance mechanism and adaptation potential of O. longistaminata can be utilized for developing rice varieties and hybrids with higher yield even under harsh environment conditions.
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Morphometric, Photosynthetic, Molecular Markers Based, Genetic Diversity