Applications of Bioinformatics to Plant Biotechnology

Abstract

Bioinformatics encompasses many tools and techniques that today are essential for all areas of research in the biological sciences. New databases with a wealth of information about genomes, proteins, metabolites, and metabolic pathways appear almost daily. Particularly, for scientists who carry out research in plant biology, the amount of information has multiplied exponentially due to the large number of databases available for many individual plant species. In this sense, bioinformatics together with next generation sequencing and 'omics' approaches, can provide tools for plant breeding and the genetic engineering of plants. In addition, these technologies enable a better understanding of the processes and mechanisms that can lead to plants with increased tolerance to different abiotic stress conditions and resistance to pathogen attack, as well as the development of crop varieties with improved nutritional quality of seeds and fruits.

Bioinformatics approaches and applications in plant biotechnology

“…With the aid of software, it is possible to formulate predictive hypothesis and incorporate the desired phenotypes from a complex combination into plants by looking at those genetic markers which score well and gives a higher reliability in breeding [2,15]. Other than genome sequence information, databases which store the information of metabolites also play a crucial role in the study of interaction with proteomics and genomics to reflect the changes in phenotype and specific function of an organism [1]. Some of the most widely used metabolomics databases for plants and crops such as Metlin (http:// metlin.…”

“…edu), provides multiple metabolite searching and about 240,000 metabolites, nearly 72,000 high-resolution MS/ MS spectra, and PlantCyc (https:// plant cyc. org/), a database which stores information about biochemical pathway and their catalytic enzyme and genes from plants [1,16]. Moreover, single-nucleotide polymorphism markers also benefit from the revolution of NGS and other sequencing technologies.…”

“…Bioinformatics played a crucial role in many areas of biology as its applications provide various types of data, including nucleotide and amino acid sequences, protein domains and structure as well as expression patterns from various organisms [3]. Similarly, the field of plant biotechnology has also taken advantages of bioinformatics, which Tan et al Journal of Genetic Engineering and Biotechnology (2022) 20:106 provides full genomic information of various plant species to allow for efficient exploration into plants as biological resource to humans [1,3,4]. The intention of this article is to describe some of the key concepts, tools, and its applications in bioinformatics that are relevant to plant biotechnologies.…”

“…Over the past decades, the term ‘bioinformatics’ has become a buzzword in all areas of research in biological science. With the continuous development and advancement in molecular biology, the explosive growth of biological information required a more organized, computerized system to collect, store, manage, and analyse the vast amount of biological data generated in the experiments from all fields [ 1 ]. Bioinformatics, as a new emerging interdisciplinary field for the past few decades, has many tools and techniques that are essential for efficient sorting and organizing of biological data into databases [ 1 , 2 ].…”

Detecting QTL and Candidate Genes for Plant Height in Soybean via Linkage Analysis and GWAS

“…It was difficult to predict candidate genes and design marker-assisted selection for PH. With the continuous development of molecular markers, high-throughput and high-density single nucleotide polymorphism markers (SNPs) were used as major markers for linkage analysis for mapping QTL (Adewusi et al, 2017;Gomez-Casati et al, 2017;Zhang et al, 2019;Karikari et al, 2020;Tian et al, 2020;Salari et al, 2021;Silva et al, 2021). In order to construct effective linkage intervals to identify QTL, SNP bin maker technology were gradually used in construction of linkage map.…”