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

Abstract

Genomics is the study of complete genetic material of an organism. It would not be an exaggeration to say that we are at the peak of 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 categorize in 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 of the hour 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.

A Machine Learning Based Computational Method for Prediction of Functional SNPs in Rice Genome

“…Among all the nucleotide variants, Single Nucleotide Polymorphism (SNP), the DNA sequence polymorphism at the genomic level caused by variant of a single nucleotide, is the most common genetic variant, and SNP is also the most prevalent and stable type of genetic diversity that exists in most organisms [6][7][8]. As SNP genotyping is becoming faster and more cost-effective, it is widely used as the genetic marker for diversity study and molecular breeding in plants [9,10]. However, the number of SNP in rice genome is very huge, with nearly 32M [11], thus bringing a very large obstacle to conducting genomic studies.…”

MILNP: Plant lncRNA–miRNA Interaction Prediction Based on Improved Linear Neighborhood Similarity and Label Propagation

“…Although predictions about lncRNA-miRNA interactions exist, most of them are not about plants (Jiang et al, 2018(Jiang et al, , 2019Ayachit et al, 2020;Banerjee et al, 2020;Ma et al, 2020;Qazi et al, 2020;Shen et al, 2020;Aglawe et al, 2021). The confirmed plant lncRNA-miRNA interactions are very limited and have been barely covered.…”