Harnessing crop biodiversity and genomics assisted pre-breeding approaches for next generation climate-smart varieties

Authors: VIKRAM, PRASHANT - Shree Guru Gobind Singh Tricentenary University; SEHGAL, DEEPMALA - Jealott Hill International Research; PRASAD, MANOJ - University Of Delhi; Singh, Sukhwinder; RAMAN, HARSH - Wagga Wagga Agricultural Institute

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/27/2024
Publication Date: 3/6/2024
Citation: Vikram, P., Sehgal, D., Prasad, M., Singh, S., Raman, H. 2024. Harnessing crop biodiversity and genomics assisted pre-breeding approaches for next generation climate-smart varieties. Frontiers in Plant Science. 15: Article 1387016. https://doi.org/10.3389/fpls.2024.1387016.
DOI: https://doi.org/10.3389/fpls.2024.1387016

Interpretive Summary: Agricultural innovation is paramount to broadening the genetic diversity of crops, focusing on enhancing yield, tolerance to biotic and abiotic stress factors nutritional value and adaptation to new environments, especially in response to climate change. Leveraging diverse genetic resources, including on-farm diversity and germplasm maintained in Gene Banks including local landraces, and secondary, and tertiary gene pools has become imperative. Advanced genomics tools and technologies offer promising avenues for varietal development through knowledge enrichment which is instrumental in strategizing breeding programs. By integrating underutilized and unlocking genetic diversity by identifying and incorporating novel alleles, the genetic base of cultivated varieties can be broadened. This approach, termed "genomics-assisted-pre-breeding," encompasses diversity analysis, functional genomics, and structural genomics, in combination with advanced statistical tools necessary for crop improvement. Embracing "genomics-assisted-pre-breeding" is critical for breeders worldwide to meet global food, fuel and fibre demands. Moving beyond the Green Revolution means looking towards innovative strategies that harness the full potential of crop biodiversity to meet future food demands.

Technical Abstract: Wheat is one of the most widely grown crops in the world and unveiling its genetic diversity is important for genetic improvement programs. Ali et al. (2022) investigated a set of 422 wheat accessions including synthetic derivatives, cultivars and breeding lines for nucleotide diversity, population structure, and selection signatures in a breeding program?. The study identified 32 unique genome regions which were subjected selection pressure. Among these regions, B, D & A genomes contribute 50%, 29% and 21% respectively. Interestingly, these regions harboured genes/QTLs controlling adaptive traits including vernalization, adaptability, disease resistance, and yield-components. Miazzi et al. (2022) investigated the relationships between the Tunisian durum landraces (Triticum turgidum L. ssp. durum Desf.) and the modern cultivars. This study identified candidate genes such as transcription factors AP2/EREBPs, zinc finger CONSTANS, and FLOWERING LOCUS T (FT-B1) for plant and spike architecture. Furthermore, distinct genes related to grain composition, disease resistance proteins (NPS-LRR and RPM), and nucleotide-binding site and leucine-reach repeat proteins in response to biotic stress were identified. In another study, Mulugeta et al. (2023) assessed genetic diversity, population structure, and linkage disequilibrium in five hundred (500) lines including landraces, cultivars and breeding lines from China and, identified regions under selection. With 65 loci under balancing selection and 17 under directional selection, the genomic scan employing the Fst outlier test identified 85 selection signatures. Potential candidate genes were linked to grain yield, plant height, host plant susceptibility to diseases, heading date, grain quality, and phenolic content when they co-localized with genomic regions showing significant selection signals. The genotypes were grouped into five subpopulations, with clustered landraces from geographically non-adjoining environments.