Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
LI Emeagi, TL Thomas, LE Uduak, TE Konyeme and OU Udensi*
The tremendous therapeutic, nutritional and economic importance of tea plant (Camellia sinensis (L.) O. Kuntze) cannot be overemphasized. However, the precise determination of its Deoxyribonucleic Acid (DNA) polymorphisms and genetic diversity, especially using DNA sequence dataset obtained through molecular characterization assay is an important strategy in planning and designing breeding programs for the Mambilla tea. In the present study, we reported here that the Simple Sequence Repeats (SSR) marker of Histone Gene (H2A.Cs) amplicons revealed distinct band profiles, mean Heterozygosity (He) were 0.277 ± 0.051, 0.214 ± 0.070, 0.274 ± 0.078, 0.385 ± 0.043 and 0.262 ± 0.078 respectively. Five tea populations showed narrow Genetic Distance (GD) and very close Genetic Identity (GI). Phylogenetic analysis showed that two distinct clusters were generated with 6 tea clones in cluster 1 and 38 tea clones in cluster 11, but there was no marked pattern of clustering as the different populations were mixed up together with bootstrap values showing common ancestral relationship. Analysis of Molecular Variance (AMOVA) result revealed 99.9% within population variation and 0.1% among population variation while PCoA generated six clusters with percentage of variation in the tea populations as 65.93%, 33.61% and 0.46% (1st, 2nd and 3rd axes) respectively. Nucleotide frequencies were A (23.14%), T (32.53%), C (19.38%) and G (24.95%) while transition/transversion rate ratios are k1=14.562 for purines and k2=0.183 for pyrimidines. The overall transition/transversion bias Ratio (R)=3.414, R= (A*G*k1+T*C*k2)/((A+G)*(T+C)). Our result also showed that only the gene sequence of tea clone obtained from Bangoba (BAN3) did not evolve with the same pattern of substitution with other gene sequences of other tea clones using Monte Carlo test. We also reported the degree of differentiation among the five tea populations, which indicated that Fixation Index (FST) estimation was 67.81% (0.6781) (Karaka population (germplasm))>61.33% (0.6133) (cultivated population)>Bangoba tea population (0.5984)˃0.5810 (Kasalasa population)˃(0.5032) (Kusuku population). Structure analysis revealed that the populations were genetically similar with percentage of membership of the sample in each of the 5 population clusters as Kusuku (19.4%), Bangoba (15.2%), Kasalasa (25.5%), Kakara (15.8%) and cultivated population was 24.2%, respectively. The present study suggests that the tea populations in the Mambilla Plateau is very homogeneous and needs introduction of new elite genotype/germplasm for breeding and improvement.
Published Date: 2024-06-13; Received Date: 2024-05-14