ABSTRACT
Rice is an important staple food crop that feed over half of
the global population and it has become the cereal that provides a major source
of calories for the urban and rural poor in Africa. However, little attention
has been paid to the improvement of Liberian and Ghanaian rice germplasm
evaluation and the genetics of some quality traits. The need for increasing
rice cultivation depends not only on cultural/traditional practices but also on
their inbuilt genetic potential to withstand stresses. Therefore, these
varieties have to be collected and evaluated for their exploitable genetic
variability and conserved. The first step in achieving this is to evaluate and
characterize available rice germplasm or genotypes at both morphological and
molecular levels to reveal important traits or accessions of interest to plant
breeders for crop improvement. In experiment, arranged in Completely Randomized
Design was conducted to study the genetic variability among and within 48
genotypes or accessions obtained from Central Agricultural Research Institute
(CARI), Suakoko, Liberia and Plant Genetic Resources Research Institute
(PGRRI), Bunso, Ghana. DNA was extracted from 48 plants per accession without
bulking to check the purity of the accession using the 16 SSR markers. Field
data taken included 28 qualitative and 14 quantitative traits scored using the
IRRI descriptor list. Analysis of variance revealed highly significant
difference (P≤ 0.01) among the accessions for all quantitative traits studied
except for grain width. Qualitative data revealed some variations among the
traits. Four significant principal components analysis were identified and
accounted for 55.3%. PC1 had Eigen-value of 0.44 explaining 18.5% of the total
variation. Next was PC2 which had 0.31 as its Eigen-value, explained 14.5% to
the total variation. Correlation analysis indicated that length of ligule was
highly significant and positive with leaf width of blade. Similar observation
was made with grain length and length of ligule. The SSR markers were highly
informative as generated by the powerMarker V3.25 software. At the similarity coefficients 90%, the highly distance genetic
diversity was found between two accessions, ACSS37 and ACSS1. Cluster X was the
largest of all the clusters while Clusters VII and VIII were the second largest
clusters with 7 accessions each. The outcome of this study should be useful to
manage the gremplasm conservation and future rice genetic improvement. However,
all the accessions may be cultivated over time at different locations on the
field to ascertain their stability and purity.
TABLE OF CONTENTS
ABSTRACT
LIST OF ABBREVIATIONS
TABLE OF CONTENTS
LIST OF TABLES
LIST OF FIGURES
LIST OF APPENDICES
LIST OF PLATES
CHAPTER ONE
1.0 INTRODUCTION
1.1 Main objective
1.2 Specific objectives
CHAPTER TWO
2.0 LITERATURE REVIEW
2.1 Botany, Classification
and Taxonomy of Rice
2.2 Socio-economic importance
of rice
2.3 Rice production and
productivity in West Africa
2.4 Rice production in Ghana
2.5 Morphological diversity
of rice
2.6 Grain yield and characters associated with grain yield in rice
2.7 Germplasm Collection and Characterization
2.8 Core Collection and Their Use in Germplasm Management
2.9 Conservation of Genetic Materials and Importance of Genetic
Diversity Studies in Rice
2.10 Genetic diversity or
characterization studies
2.11 Genetic erosion
2.12 Molecular diversity of
rice
2.6.1 DNA based molecular
techniques in genetic diversity studies
2.13 Genetic Distance
2.14 Multivariate Techniques
for Interpretation of Genetic Distance
2.14.1 Cluster analysis
2.14.2 Principal Component
Analysis (PCA)
CHAPTER THREE
3.0 MATERIALS AND METHODS
3.1 Experimental Sites
3.2 Seed Sources
3.3 Evaluation of morphological characteristics of the rice
genotypes
3.4 Soil used for the pot experiment
3.5 Experimental setup for morphological characterization
3.6 Agronomic Practices
3.7 Harvesting
3.8 Morphological characters evaluated
3.8.1 Standard evaluation
system for rice data collection
3.8.2 Qualitative characters
3.8.3 Quantitative characters
measured
3.8.3.1 Culm diameter at
basal Internode (DABI)
3.8.3.2 Flag Leaf length and
width
3.8.3.3 Leaf width and length
of blade
3.8.3.4 Leaf length of ligule
(LOL)
3.8.3.5 Panicle number per
plant (PNPP)
3.8.3.6 Plant height
3.8.3.7 Productive tillers/
Plant
3.8.3.8 Awn length (mm)
3.8.3.9 Panicle length of
main axis (cm)
3.8.3.10 100 Grain weigh
3.8.3.11 Grain length
3.8.3.12 Grain Width
3.9 Morphological data
analysis
3.10 Laboratory Experiment:
Evaluation of 48 Rice Genotypes from Liberia and Ghana using SSR Markers
3.10.1 Molecular Analysis
3.10.2 DNA extraction and
purification
3.10.3 DNA quality control
3.10.4 Polymerase chain
reaction with molecular markers
3.10.5 Agarose gel
electrophoresis
3.10.6 Gel scoring of DNA
fragment
3.11 Molecular Data Analysis
CHAPTER FOUR
4.0 RESULTS
4.1 Morphological Characters
4.1.1 Qualitative characters
4.1.2 Morpho-agronomic
analysis of quantitative characters
4.2 Phenological Studies of Some Early Reproductive Traits among
Rice Accessions
4.3 Phenological Studies of Some Late Reproductive Traits among
Rice Accessions
4.4 Principal Component Analysis (PCA)
4.5 Cluster Analysis of the Morphological Data
4.6 Peason Correlation among the Quantitative Traits
4.7 Summary Statistics about the SSR Markers Used
4.7.1 Evaluation of SSR
markers in rice varieties using the dendrogram
CHAPTER FIVE
5.0 DISCUSSION
5.1 Qualitative Characters
5.2 Flag Leaf (Attitude of Blade)
5.3 Awning Characteristic
5.4 Plant Height
5.5 The Culm (DABI)
5.6 Grain Length and Grain Width
5.7 Panicle (Attitude of Blade, Main Axis and Secondary Branching)
5.8 Productive Tillers per Plant Type
5.9 Core Collection
5.10 Principal Component
Analysis (PCA)
5.11 Evaluation of the SSR
Markers in Rice Genotypes using Dendrogram
CHAPTER SIX
6.0 CONCLUSION AND
RECOMMENDATION
6.1 Conclusions
6.2 Recommendations
REFERENCES
CHAPTER ONE
1.0 INTRODUCTION
Rice (Oryza sativa L., 2n = 24), a
member of Poaceae (Gramineae) is the world’s most important staple food crop
that feeds over half of the global population (Khush, 2005). It is cultivated
in tropical and subtropical regions. Rice is grown in more than 114 countries,
over an area of 161.4 m ha in a wide range of ecosystems under varying
temperature and water regimes with the production of 466.7 mt (on milled basis)
(FAO, 2011). According to Nwanze et al. (2006) approximately 20 million farmers
are engaged in rice production in sub-Sahara Africa (SSA) and about 100 million
people depend on it directly for their livelihoods on the continent.
Rice is rapidly becoming a staple
food in the African diet; and its production in SSA continues to be outpaced by
consumption as a result of low and stagnated production. Imported rice accounts
for 50 percent of sub-Saharan Africa’s rice requirement (FAO, 2006a). Rice is
no longer a luxury food but has become the cereal that constitutes a major
source of calories for the urban and rural poor. Rice production in SSA has
been bedeviled with conditions such as environmental degradation due to
pesticide usage, excessive water usage, and nutrient contamination, methane
emission and ammonia volatilization and these conditions require urgent
attention (Newmah, 2010).
A wide range of technologies are,
however, available and can be used as tools for reducing these adverse
consequences of rice production but they are, however, not extended to majority
of rice growers or farmers (FAO, 2006b). Self-sufficiency in rice production
is, however, declining as demand increases. Little attention has been paid to
the improvement of Liberian and Ghanaian rice germplasm evaluation and the
genetics of some quality traits. Thus, there is very little information
available on the genetic diversity of Liberian and Ghanaian rice germplasm for
crop improvement and conservation purposes. There is an urgent need to increase
and improve the production of rice in Africa in order to meet up with the high
demand. The need for increasing rice cultivation depends not only on
cultural/traditional practices, but also, on their inbuilt genetic potential to
withstand stresses. A successful breeding programme will depend on the genetic
variability of a crop for achieving the goals of improving the crop and
producing high yielding varieties (Padulosi, 1993). The first step in achieving
this is to evaluate and characterize available rice germplasm or genotypes at
both morphological and molecular levels; as phenotypic and genotypic diversity
will reveal important traits or accessions of interest to plant breeders
(Singh, 1989).
1.1 Main objective
The overall objective of this study
is to evaluate the genetic and morphological variability of rice germplasm from
Liberia and Ghana using morphological and simple sequence repeat (SSR) markers.
1.2 Specific objectives
To assess the extent of genetic
diversity and relatedness among rice germplasm collections in Liberia and Ghana
at both the morphological and molecular levels.
To estimate correlations among
measured quantitative traits.
To identify some morphological
traits that are discriminating and contribute most to the total variability
among rice germplasm accessions using principal components analysis.
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