GENETIC DIVERSITY IN LIBERIAN AND GHANAIAN RICE (Oryza sativa L., Oryza glaberrima Steudi) GERMPLASM USING MORPHOLOGICAL AND SIMPLE SEQUENCE REPEAT (SSR) MARKERS

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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Item Type: Ghanaian Postgraduate Material  |  Attribute: 118 pages  |  Chapters: 1-5
Format: MS Word  |  Price: GH50  |  Delivery: Within 30Mins.
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