Bioinformatics Tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review

Abstract

Genomics is the study of the complete genetic material of an organism. It would not be an exaggeration to say that we are at the peak of the genomics era as with the advent of high-throughput sequencing technologies we have an enormous amount of genomic data coming every day. Genomics assisted breeding (GAB) is becoming increasingly popular in the field of crop improvement. GAB utilizes available genomics information of different crops and their relatives for the purpose of plant breeding to produce improved varieties of the crops. Proper knowledge of these tools and databases helps in speeding up the process of plant breeding. The available tools can be categorized into several groups such as genetic diversity, Quantitative Trait Locus (QTL)/gene mapping, Next-Generation Sequencing (NGS) based Single Nucleotide Polymorphism (SNP) genotyping, Molecular breeding, Genome-Wide Association Studies (GWAS), Genomic Selection (GS), Marker-Assisted Recurrent Selection (MARS), Multiparent Advanced Generation Inter-Cross (MAGIC), etc. Most of the available tools are user friendly and where it is not, needs to be updated soon. There is an urgent need to develop the scientific resources and technical expertise for the proper and effective use of these tools. In this review, we have extensively covered the available tools and databases for the genomic assisted breeding and population genetics study of the plants. The details of these tools and databases along with their web links are also provided. We believe this review will be handy and useful for the scientists and researches of plant breeding, population genetics, and genomics.