Integrating omics databases for enhanced crop breeding

Abstract

Crop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes underlying plant traits and their interactions. This review highlights the importance of integrating omics databases in crop plant breeding, discusses available omics data and databases, describes integration challenges, and highlights recent developments and potential benefits. Taken together, the integration of omics databases is a critical step towards enhancing crop plant breeding and improving global food security.

Genomic Analysis of Romanian Lycium Genotypes: Exploring BODYGUARD Genes for Stress Resistance Breeding

“…With growing market demand for goji berries, comprehensive molecular research has been initiated to identify valuable genes in both cultivated and wild goji berry plants, aiming to enhance future breeding programs [1,33,[43][44][45][46]. Crop breeding aims to develop new plant varieties with improved traits such as increased yield, disease resistance, and nutritional quality [47]. High-throughput technologies, including genomics, transcriptomics, and metabolomics, have opened up a new phase in crop breeding, enhancing the efficiency and precision of this process [47,48].…”

“…Crop breeding aims to develop new plant varieties with improved traits such as increased yield, disease resistance, and nutritional quality [47]. High-throughput technologies, including genomics, transcriptomics, and metabolomics, have opened up a new phase in crop breeding, enhancing the efficiency and precision of this process [47,48]. The last two decades have seen a significant growth in both the volume and quality of publicly available plant genomes, with a higher efficiency of genome sequencing, assembly, and annotation [48][49][50].…”

BGRS: bioinformatics of genome regulation and data integration

“…Experimental studies of gene regulation at transcription level led to the development of the databases on transcription factor regulation – TRRD and TRANSFAC [ 3 ]. The series of bioinformatics tools for the transcription factor binding sites prediction and integrations to the databases has been developed [ 4 – 6 ]. We have published papers on such tools following the rise of high-throughput sequencing technologies and corresponding growth of the experimental data [ 7 , 8 ].…”

“…Note the satellite society meetings held in parallel to main BGRS event, such as Russian-German Virtual Bioinformatics Network, Sino-Russian workshops on bioinformatics [ 1 , 17 ] ( http://www.zjbioinformatics.org/meetings/2020/index.html ; http://glab.hzau.edu.cn/subpages/RESOURCES/meeting.php ). Current join international projects such as “Smart Crop” [ 6 ] raised from these workshops.…”

“…In the special issue we present work by Haoyu Chao and co-authors [ 6 ] on plant bioinformatics raised from the joint Russian-Chinese research project on integrating omics data from crop plants (“Smart Crop” – Cognitive Platform for Reconstruction, Visualization and Analysis of Stress Response Networks based on ANDSystem and Multiomics in Rice and Wheat).…”