Comparative genomics is the study of similarities and differences at the genomic level to make inferences about the functions and evolution of various biological processes. This is an important field to study genome evolution, sequence collinearity, and transfer of information from extensively studied model organisms to species of commercial interest. This approach provides insights into gene function, gene regulation, and the genetic basis of complex traits. 

The key techniques used in comparative genomics include genome sequencing, sequence alignment, phylogenetic analysis, and annotation, helps to identify the homologous genes, gene families, and structural variations. Comparative genomics has various applications in crop breeding such as identifying genes of interest, enhancing nutritional quality and reliability of marker-assisted breeding etc. A study utilized comparative genomics and meta-quantitative trait loci (MQTLs) analysis to identify stable QTLs and functional genes controlling wheat grain yield, quality traits, and micronutrient content. By analysing 735 QTLs from 27 mapping populations, 449 QTLs were consolidated into 100 MQTLs with significantly reduced confidence intervals. The majority of these MQTLs were in non-telomeric regions, with key findings including the co-localization of QTLs for grain yield, thousand kernel weight, grain protein content, and micronutrients. This study also identified orthologous MQTLs across wheat, rice, and maize, highlighting candidate genes that can be targeted for crop improvement programs. Rice and wheat, both from the Poaceae family, share genetic homology that can be leveraged to enhance crop traits. Comparative genomics between rice and wheat helps to identify candidate wheat genes, understand their functions, and develop molecular markers for breeding. This knowledge facilitates the transfer of desirable traits between crops through genetic engineering, gene editing, or wide crossing. Blast disease, caused by Magnaporthe grisea, significantly limits finger millet production. Due to limited genome data, comparative genomics is crucial for identifying blast resistance genes using SSR markers. In this study, 58 SSRs were developed, identifying four QTLs for finger blast and one for neck blast resistance across 190 genotypes. Resistant alleles, mainly found in exotic genotypes like VHC3997 and VHC3996, offer the potential for breeding blast-resistant cultivars, with identified markers useful for gene cloning, fine mapping, and marker-assisted breeding. In plant breeding, comparative genomics has emerged as a powerful tool to enhance the efficiency and precision of breeding programs, facilitating the development of crops with improved traits by providing essential tools for improving crop resilience, productivity, and quality.

REFERENCES: 

1 BABU, B. K., DINESH, P., AGRAWAL, P. K., SOOD, S., CHANDRASHEKARA, C., BHATT, J. C. AND KUMAR, A., 2014, Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs. PloS One, 9(6):99-182.

 2 SHARIATIPOUR, N., HEIDARI, B., TAHMASEBI, A. AND RICHARDS, C., 2021, Comparative genomic analysis of quantitative trait loci associated with micronutrient contents, grain quality, and agronomic traits in wheat (Triticum aestivum L.). Front. Plant Sci., 12:709-817. 

3 WIJERATHNA-YAPA, A., BISHNOI, R., RANAWAKA, B., MAGAR, M. M., REHMAN, H. U., BHARAD, S. G., LORENC, M. T., RAMTEKEY, V., GOHAR, S., LATA, C. AND HARUN-OR-RASHID, M., 2023, Rice–wheat comparative genomics: Gains and gaps, Crop. J., 12(2):656-669.