Breeding and biotechnological interventions for trait improvement: status and prospects

Abstract

Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.

Keywords: Gene editing; Genomics-assisted breeding; Molecular markers; RNA interference; Speed breeding; Transgenics.

Fig. 1

Timeline of significant achievements in the deployment of approaches, including overexpression of candidate genes, genome sequencing, use of RNAi and genome editing for trait improvement in major species, namely rice, wheat, tomato and soybean

Fig. 2

Mapping of quantitative trait loci associated with complex agronomic traits and their application in genomics-assisted breeding. Linkage analysis in mapping population segregating for desired phenotype conquer QTL identification which generally employs in MAS

Fig. 3

Diagrammatic representation of the application of speed breeding in genomic-assisted breeding. Speed breeding significantly reduces the length of breeding cycle and accelerates the process of crop improvement. Conventional marker-assisted breeding (MAB) approximately takes 7–8 years to release an improved cereal variety while speed-breeding-assisted MAB would be completed within 3–4 years

Fig. 4

Strategies for crop improvement through biotechnological approaches. a Overexpression leads to greater transcription of target gene which can be translated into protein; b RNA interference leads to downregulation of target gene; c Gene editing through CRISPR/Cas9 leads to insertions or deletions at target site which gives rise to mutations

Fig. 5

Application of functional and comparative genomics in marker-assisted breeding and biotechnological approaches for crop improvement. The candidate gene(s) identified from functional genomic studies can be introduced through genetic engineering or targeted modify through genome editing technology in crop species for improved agronomic traits. The other approach is through molecular breeding which employ molecular markers to identify genomic region associated with desired traits during breeding programme