MY RESEARCH

GENETIC MAPS / LINKAGE MAPS

Linkage maps describes the linear order of markers within linkage groups. Ordering is based on recombination frequency and represented as centimorgans (cM). Linkage maps are prerequisite for genome assembly and/or QTL mapping. For assembly of genome, the contigs will be arranged to scaffolds/chromosomes based on the relative order and position of markers. The linkage map also provides information on linked markers to a trait that can be used for marker-assisted selection in breeding programs.

ASSOCIATION MAPPING

GWAS/ LD Mapping is a method of mapping QTL based on historic linkage disequilibrium to link phenotypes to genotypes. AM is applicable to natural as well as synthetic populations. Precision of the associations are greater in AM than that of the conventional linkage mapping. AM is based on LD, which in turn is dependent on various factors like history of population, diversity, structure, recombination and the trait variation.

QTL MAPPING

QTL Mapping is a statistical method that links phenotypic data and genotypic data (molecular markers) to find the genetic basis of variation in complex traits. We can identify the number, interaction, and precise location of these regions.

DEMOGRAPHY

The patterns of nucleotide diversity within and among populations are influenced by evolutionary forces, such as mutation, population structure, gene flow, selection, and recombination. Demographic parameters such as effective population size, population divergence times, gene flow rates between populations collectively define biogeographic history of a species.

DOMESTICATION GENOMICS

Domestication is the process of selecting for desirable traits, by which humans altered the morphology and allele frequency of genes. Understanding the genomics of domestication can help identify genes that are responsible for trait variation usually by comparing the domesticated forms to the wildtypes.

POPULATION GENOMICS

It is the study of DNA variation of subpopulations along with the structure, geographical distribution and diversity. Subpopulations evolve when they get adapted to a new environment, genes get selected along the way that are needed for survival to new environment (Natural selection). Further domestication (selection by humans for desired traits for hundreds of years and artificial selection (breeders’ selection) further change the landscape of the genome.

COMPARATIVE GENOMICS

It is a field of biological research in which the genomic features of different organisms are compared to get a better understanding the evolutionary relationship between organisms. Include studying the synteny, homologs, conservation of genes etc

PHYLOGENOMICS/PHYLOGENETICS

Phylogenomics is using genome data to understand evolution. Here we compare entire genomes or entire set of genes to predict gene function, understand the evolutionary relationships, gene family evolution, whole genome duplications, estimating species trees. Phylogenetics is the use of few genes/sequences to estimate evolutionary relationships between individuals or groups of organisms.

TRANSCRIPTOMICS

It is the study of transcriptome, sum of all RNA transcripts, result of DNA transcription. RNA-seq tabulates all genes, identifies structure of genes, splicing patterns, relative abundances, post-transcriptional modifications, and quantification of expression levels during development and under different treatment conditions.

FUNCTIONAL GENOMICS

It is the study of how genes and intergenic regions affects the phenotype. Involves narrowing down to a small list of candidate genes or regions to analyze in more detail. Involves a combination of genomics and epigenomics, transcriptomics, proteomics, and metabolomics.

MICROBIOME ANALYSIS

Microbiome is the study of microbial communities found in and on the human body to understand the role of microbes in health and disease. 16S and ITS ribosomal RNA (rRNA) sequencing are common amplicon sequencing methods used to identify and compare bacteria or fungi present within samples. Phylogeny, within and between diversity, relative abundances are used for interpretation.

CANCER GENOMICS

It is the study of cancer genomes to understand biology of cancer that helps diagnose and treat the disease