Botany - Mphil Thesis

Permanent URI for this collectionhttps://kr.cup.edu.in/handle/32116/30

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Development and chacterization of genomic microsatellite markers in rhdodendron arboreum
(Central University of Punjab, 2014) Choudhary, Shruti; Bhardwaj, Pankaj
Rhododendron arboreum, a key species inhabiting Indian Himalayas, has ecological and economic importance. Global climate change and anthropogenic activities can pose a threat to the biodiversity richness. Population genetics characteristics are the fundamentals of conservation and management practices. However, no genetic background for the species is presently available. To provide an insight into the population structure of the species, an effective marker resource was developed. A genomic library enriched for microsatellites was constructed using biotin- streptavidin hybridization technique, followed by sequencing of positive clones. With 54% enrichment rate, 41 primers were designed from SSR clones, consisting of perfect or interrupted repeats of AG/CT, AC/GT motifs. 38 loci showed successful amplification on genotypes of three populations with number of alleles ranging from 2 to 14, observed and expected heterozygosity of 0.167 to 0.933 and 0.422 to 0.917, respectively and average polymorphic information content of 0.104 to 0.811. A high gene flow (Nm= 5.436) demonstrated high genetic diversity within the populations. 19 loci displayed significant deviations from Hardy Weinberg equilibrium. Overall no linkage disequilibrium and bottleneck was detected among sampled populations. DARwin and STRUCTURE analysis grouped the populations into two original clusters and admixed genetic stock irrespective of their geographical locations. These novel loci will support further genotyping studies in R. arboreum.
Development and characterization of genomic microsatellite markers in Melia azedarach
(Central University of Punjab, 2014) Thakur, Sapna; Bhardwaj, Pankaj
Melia azedarach is ecologically imperative species known for its innumerable biological benefits such as antiviral, anthelminthic, antibacterial, etc. In this study, we developed 43 genomic microsatellite markers from (AG)n enriched library and subsequently employed 23 of them for genetic diversity and population structure analysis of Melia azedarach growing in Indian Thar desert. Fourteen populations encompassing 95 genotypes were selected for analysis and we found a moderate level of diversity (Na = 3.211, Ho = 0.558, He = 0.549, P = 94.41%) in them. Gene diversity (h) among population pairs varied from 0.566 to 0.714 with very low overall genetic differentiation (F = 0.021). The highest value of ΔK estimated using STRUCTURE indicated 2 subpopulations (K=2) and admixed cluster occupied maximum area (75.79%) under Bar plot. Genetic distance based UPGMA dendrogram also identified 2 major clusters among 14 Melia azedarach populations. UNJ tree based on genetic dissimilarity clustered genotypes from different population together. No significant correlation between geographical and genetic distance was found in present study (Rxy = 0.261, P = 0.18). Allele frequency distribution under “mode-shift” indicator was normal L-shaped, suggesting populations under study are not experiencing any recent bottleneck. This study laid the foundation for more precise inference about the biogeography and management of M. azedarach in the Indian Thar Desert
Development and charaterization of UGMS markers for genetic diversity analysis in Rhododendron arboreum
(Central University of Punjab, 2013) Sharma, Gagan; Bhardwaj, Pankaj
Rhododendron arboreum is an ecologically important species growing in Himalayan regions. It is widely popular due to its medicinal potential, edible, sacred & economic value, however very little is known about its genetic diversity. The development and characterization of UGMS markers will provide a major impact on genetic diversity analysis. Total 792 (615 singletons and 177 contigs) unigenes were predicted from 1,241 publicly available EST database from NCBI (http://www.ncbi.nlm.nih.gov/) site in R.catawbiense by clustering of 2 - 33 random EST sequences. From 50 SSR contained Unigenes, 36 UGMS primers were designed for the cross amplification approach and six pairs of microsatellite primers were produced clear PCR amplification. The cross related species/genera transferability rate was 16.66% from R.catawbiense to R.arboreum. The polymorphism information content (PIC) ranged from 0.2756 to 0.9212 with an average of 0.5765.The average observed heterozygosity (Ho) was 0.8666 i.e. greater than average expected heterozygosity (He) was 0.6792. The genetic diversity was found with an average of 0.6222 within population of R.arboreum and genetic diversity found with an average of 0.3436 among the population.This study revealed the insight of abundance & distribution of microsatellite in the expressed region of the Rhododendron arboreum genome.
Genetic diversity and polpulation analysis of melia azaderach L. by Rapd markers in bathinda and adjoing regions
(Central University of Punjab, 2013) Navgeet; Bhardwaj, Pankaj
Melia azedarach L. is an ecologically imperative species growing in Thar Desert. Biological effects such as antiviral, anthelminthic, antibacterial etc. makes it important, yet a little is known about its genetic diversity and structure. In this study, 30 RAPD primers were employed for DNA profiling of 47 individuals representing 6 populations from different geographic locales. A total of 87 bands were scored with an average of 2.9 bands per primer. The PIC ranged from 0.1195 to 0.4998 with an average of 0.4160. Nei's genetic diversity (h) and Shannon's information index (I) ranged from 0 to 0.5 and 0 to 0.6931 with an average Nei's genetic diversity of 0.2422. The gene flow (Nm) 1.4381 and the genetic diversity of 0.2381 at species level demonstrated overall high level of genetic diversity. Cladistics analysis using DARwin and Bayesian cluster analysis using STRUCTURE placed 47 individuals into two main clusters or original genetic stocks (K=2) which showed little or no association with the geographic origin. The lack of clear assignment of individuals to geographic regions of sampling and consideration of different populations in the same genetic cluster suggests a recent common evolutionary history.
Population analysis of media azesarach L. by RAPD markers in the region of rajasthan
(Central University of Punjab, 2013) Ahmad, Kamal; Bhardwaj, Pankaj
Melia azedarach L is ecologically imperative species growing in Thar Desert. Biological effects such as antiviral, anthelminthic, antibacterial, etc. makes it important, yet a little is known about its genetic diversity and structure. In this study, we employed 30 RAPD primers for DNA profiling of 91 individuals representing 8 geographically isolated populations. A total of 98 bands were scored with an average of 3.2 bands per primer. The PIC ranged from 0.0681 to 0.5351 with an average of 0.4103. Nei's genetic diversity (h) and Shannon's information index (I) ranged from 0.1237 to 0.2375 and 0.1845 to 0.3500 respectively with average Nei'sgenetic diversity of 0.2570. The gene flow (Nm) 0.9295 and the genetic diversity of 0.3498 at species level demonstrated overall high level of genetic diversity. Cladistics analysis using DARwin and Bayesian cluster analysis using STRUCTURE placed 44 individuals into two main clusters or original genetic stocks (K = 2) which show little or no association with the geographic origin. The lack of clear assignment of individuals to geographical regions of sampling and consideration of different populations in the same genetic cluster suggests a recent common evolutionary history. M. azedarach is a good reforestation tree because of its fast growth and drought hardy nature. This study adds a foundation for more precise inference about the biogeography and management in the reforestation projects in the Thar Desert.