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Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS USA 76: 5269-5273

Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 11/1979; 76(10):5269-73. DOI: 10.1073/pnas.76.10.5269
Source: PubMed

ABSTRACT A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two populations or species. To express the degree of polymorphism in a population at the nucleotide level, a measure called "nucleotide diversity" is proposed.

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    • "The Dice coefficients were employed by using Simqual subprogram in similarity routine of software NTSYS-pc version 2.2 (Exeter Software, Setauket, NY, U.S.A.) software package. The estimation of genetic similarity (F) were calculated by following the method described elsewhere [11]. The resultant similarity matrix data was employed to construct a dendrogram by using Sequential Agglomerative Hierarchical Nesting (SAHN) based on unweighted pair-group method with an arithmetic average (UPGMA) to infer genetic relationships and phylogeny among cultivars. "
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    ABSTRACT: Salinity stress is the major constraint in rice production. Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) were used to find out salt tolerant rice genotypes. In this study three selected SSR markers viz. RM336, RM510 and RM3412 were used to screen the germplasm for salt tolerance. For genotyping rice germplasm, DNA was extracted from leaf samples using CTAB mini-prep method. The number of allele per locus was 10, with an average number of 10 per locus. The average gene diversity of overall SSR loci for the 25 genotypes was 0.8693, ranging from 0.8608 to 0.8768. The PIC values for 3 SSR markers varied from 0.8456 (RM336) to 0.8645 (RM510) with an average PIC of 0.8556. Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram, constructed from Nei's genetic distance produced three distinct clusters of 25 rice genotypes which is very much similar to Principal Component Analysis (PCA). It can be concluded that Jamai naru, Kajol shail, Hogla, Khak shail, Tal mugur, BINA dhan8 were salt tolerant compared to FL 478 because they showed a lower similarity value with FL 478. Marker RM510 showed the highest level of diversity due to high PIC value. This scientific information could be used for selection of suitable parents and development of salt tolerant rice varieties as well.
    • "The bands were visualized and photographed using Gel Documentation System (XR-Quantity One, Bio- Rad Laboratories). A similarity matrix was obtained after multivariate analysis using Nie and Li's coefficient (Nei and Li 1979). These similarity coefficients were used to generate a tree for cluster analysis using the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) method, using the software NTSYS 2.1 (Numerical Taxonomy and Multivariate Analysis System). "
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    ABSTRACT: Sixty six plants raised via direct shoot bud organogenesis from pre-plasmolysed leaf explants of Catharanthus roseus were assessed under in vivo conditions for their physio-morpho traits, tryptophan metabolism, genetic fidelity and alkaloid profile. Morphologically all plants were parent like except the three morpho-types i.e. broad cup-shaped leaves, dwarf phenotype and enlarged pink corona. Vindoline was detected in most of the plants in substantial amount while ajmalicine, ajmaline and catharanthine were detected in few plants only. More than eightfold increased vindoline (0.08 % dry wt.) was showed by plant no. 1, 4 and 39. Except plant no. 54, which accumulated the highest alkaloid content of 3.09 % dry wt. with tryptophan content of 0.0283 % dry wt., majority of the plants showed a negative correlation between total alkaloid content and tryptophan accumulation and strong positive correlation between tryptophan content and 5-methyltryptophan tolerance. ISSR and RAPD profile of seventeen randomly selected, field established plants was generated by using 10 ISSR and 60 RAPD primers. In RAPD, a total of 753 bands were detected, out of which 624 (82.87 %) were monomorphic. In ISSR profiling, a total of 205 bands were detected out of which 200 bands were monomorphic (97.56 %) and only 5 bands were found to be polymorphic. Highly significant data for the monomorphic banding pattern across all the three genotypes (p < 0.01) was observed. Principal components, AMOVA analysis and multivariate analysis using Nei and Li’s coefficient further validate the monomorphism. Thirteen plants having superior traits were grown in Random Block Design in field. The relevance of physiological and epigenetic changes occurred in the light of morpho-types and alkaloid profile of directly regenerated plants during in vitro to in vivo acclimatization in C. roseus is discussed.
    Plant Cell Tissue and Organ Culture 08/2015; DOI:10.1007/s11240-015-0841-0 · 2.61 Impact Factor
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    • "The AFLPSURV v.1.0 software (Vekemans et al. 2002) was used to estimate demographic statistics such as Nei 0 s gene diversity (Hj), pairwise differentiation among subpopulations (F ST ) and the percentage of polymorphic fragments per population (P) (Nei & Li 1979; Lynch & Milligan 1994). "
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    ABSTRACT: Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island diversification in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographic population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable "paleo-islands" of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographic clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between islands. We argue that volcanic eruptions and landslides after the merging of the paleoislands 3.5 million years ago played key roles in generating genetic boundaries within Tenerife, with the paleo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.
    Molecular Ecology 08/2015; DOI:10.1111/mec.13282 · 6.49 Impact Factor
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