SylbV01-00-00. pmd

III. Credit Hours
: 3(2+1)
IV. Why this course ?
The genomic revolution has generated detailed population genetic data. Big data
samples of complete genome sequences of many individuals from natural populations
of many species have transformed population genetics inferences on samples of loci
to population genomics: the analysis of genome-wide patterns of DNA variation
within and between species. Molecular analyses of this is essentially to be taught
to students.
V. Aim of the Course
Students would be provided insights into organization and structure of genetic
variation in plant populations and practical skills in molecular diversity analyses.
VI. Theory
Unit I
The genetic structure of populations – Genetic transmission in populations, the
Hardy-Weinberg principle and estimating allele frequencies, testing of departures
from Hardy-Weinberg proportions, inbreeding and self-fertilization, analyzing the
genetic structure of populations: Bayesian F-statistics, Nei’sGst, Weir &
Cockerham’s, the Wahlund Effect and Wright’s F-statistics.
Unit II
Natural selection, genetic drift, mutations – The genetics of natural selection,
estimating viability, Selection at one locus with many alleles, fertility selection and
sexual selection, Selection component analysis, genetic drift- mutation, migration
and genetic drift, selection and genetic drift; the coalescent.
Unit III
Quantitative genetics – introduction to quantitative genetics, resemblance among
relatives, partitioning variance, evolution of quantitative traits, simultaneous
evolution of several quantitative traits, mapping quantitative trait loci, introduction
to linkage disequilibrium and association analysis.
Unit IV
Molecular evolution – introduction to molecular population genetics, the neutral
theory of molecular evolution, patterns of nucleotide and amino acid substitutions,
detecting selection on nucleotide polymorphisms; patterns of selection on nucleotide
polymorphisms, Tajima’s D, Fay’s and Wu’s H, and Zeng et al’s E, introduction to
population genomics and challenges.
Unit V
Evolution in multigene families, phylogeography, analysis of molecular variance
(AMOVA), nested clade analysis, basics of cladistic analysis.
VII. Practical
• Calculating gene and genotypic frequencies;
• Testing of HWE;
• Estimation of allele frequencies under forces of selection, mutation and migration;
• Calculation of inbreeding coefficient;

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Plant Sciences–Plant Genetic Resources
149
• Estimation of linkage disequilibrium;
• Quantifying genetic variation at the molecular level, analysis of molecular variance;
• Hypothesis testing in molecular evolution, estimation of evolutionary parameters.