Genomics-Assisted Breeding: A new era in crop development

By Suraj Nair, Lead (TechSprouts), Ankur Capital

Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses. With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding. High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits. Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterisation, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding (GAB). With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.

Agriculture remains the mainstay of human civilisation, providing sustenance and livelihoods across the globe. However, the growing population along with deteriorating climatic conditions have raised serious questions about current agricultural practices. Frequent droughts, heatwaves and floods have resulted in crop losses, lower yields and diminished nutritional quality. Traditional agricultural practices which are highly water-intensive and resource-consuming, have become highly unsustainable. This has created an ever-increasing demand for improved seeds and crop varieties, whether to increase yields for a growing population, enhance climate resilience with the onset of anthropomorphic climate change, or to protect against a plethora of pests.

Conventional plant breeding techniques, although long-standing, have drawbacks. One key disadvantage is the lengthy and expensive process of variety development, which can take over a decade. It involves laborious experiments, field trials, and the analysis of individual traits. This manual process is cumbersome.

Over the past decade, the agricultural industry has exhibited gradual signs of change. One prominent trend in agricultural research and development over the past two decades has been the rapid emergence and adoption of advanced seed breeding tools as well as genetic editing techniques, such as CRISPR. These techniques enable us to sequence a plant’s genome and analyse its growth and behaviour at a more granular level. The advancements in sequencing techniques, bioinformatics, and the ability to manipulate large datasets have led to the advent of a new paradigm: genomics-assisted breeding (GAB).

GAB relies on genomic data, which has been extensively accumulated since the sequencing of rice in 2006. The availability of this data has significantly improved gene-mapping strategies, particularly in our ability to correlate genomic data with phenomic performance. This understanding has expedited the process of trait discovery, making it possible to breed plants with specific traits in mind. For example, it is now feasible to develop a new rice variety with enhanced amylose content through targeted breeding efforts.

GAB can take one of two broad forms: the first is a highly advanced form of conventional varietal creation achieved through controlled crosses between specific parent plants, and the second is through direct genetic modification of plants with the aim of introducing desirable traits. Both approaches offer great versatility, allowing for the breeding of novel traits in crops, even without genetic engineering. An example of this is HarvestPlus, an international research programme that has developed hybrid corn varieties with reduced vitamin A deficiency.

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By Suraj Nair, Lead (TechSprouts), Ankur CapitalFood