Genomics-assisted breeding 2.0 for sustainable agriculture

By Rajeev Varshney

Accelerating genetic gains through genomics-assisted breeding 2.0 approaches will deliver higher produce for smallholder farmers while ensuring sustainable agriculture and environmental protection.

Ecological agriculture takes cognizance of the fact that the “symptoms” point to a larger problem facing us – poor agricultural practices resulting in a poor ecosystem that affects crop production, yield, soil fertility, etc. There is a need for a holistic approach that can address these shortcomings and provide an overall solution for the challenges faced in the global agricultural landscape. The world needs to adopt and increasingly deploy modern scientific tools and practices into our crop breeding programs to accelerate the delivery of improved crop varieties in farmers’ fields.

In an open access feature review published recently by Cell Press in the 25th Anniversary Issue of Trends in Plant Science, Feeding the World: The Future of Plant Breeding, scientists from the International Crops Research Institute for the Semi-Arid Tropics, Murdoch University (Australia), ICAR- Indian Institute of Pulses Research, Iowa State University (USA), Leibniz Institute of Plant Genetics & Crops Plant Research (Germnay), Huazhong Agricultural University (China) and Cornell University (USA) present a comprehensive approach of designing future crops. This approach has been dubbed “genomic breeding” or genomics- assisted breeding (GAB) 2.0.

The strategy is to optimize crop genomes with the accumulation of beneficial alleles and purging of deleterious alleles for designing future crops. In the coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner while ensuring sustainable and environmental protection.

GAB: The Game-Changer

Fifteen years ago, Genomics-Assisted Breeding (GAB) was presented as a milestone future approach in the 10th Anniversary Issue of Trends in Plant Science, Feeding the World: Plant Biotechnology Milestones. It was envisaged in 2005 that GAB will be a gamechanger for the development and delivery of improved crops varieties (high yielding and resistant to pest and disease, and abiotic stresses).

The success stories we have today speak for themselves. For instance, GAB has expedited timelines of breeding progress across a range of crop species, with the development of more than 130 publicly bred cultivars of different crops. The majority of the noteworthy crop products delivered by GAB include improved cultivars with elevated resistance levels against important diseases such as bacterial blight and blast in rice and rust in wheat, etc.

Key products with biotic stress resistance in some cereal and legume crops through GAB

• Rice: improved rice varieties with resistance to blast and bacterial blight disease

• Wheat: improved varieties resistance to stress response and other agronomic and quality-related traits

• Pearl millet: improved variety with higher resistance to downy mildew

• Barley: improved lines with resistance to eyespot, barley yellow mosaic viruses, and barley powdery mildew

• Soybean: several soybean cyst nematode and multiple disease resistant genotypes

• Groundnut: introgression lines showing higher yield and increased rust resistance

• Chickpea: high-yielding and Fusarium wilt and blight resistant varieties

Among abiotic stresses, tolerance to submergence, salinity and drought remained the key target traits for improvement using GAB. Similarly, several varieties with higher nutrition quality have been developed in many crops through GAB. These varieties include higher grain protein content wheat varieties, improved fragrance and intermediate amylose content rice varieties, quality protein maize cultivars, high oleic acid content groundnut varieties, etc.

Recent advances in genome sequencing, genetic diversity analysis, phenotyping and genome editing technologies can identify and accumulate superior alleles for targets traits in crop improvement.

Key advances in upstream science technologies for accelerating crop improvement

• Availability of reference genomes and genome-wide surveys on comprehensive diversity panels pave the way to associate the allelic variation with phenotypes.

• Methods are now available to evaluate the genetic worth of the vast genetic resources archived in gene banks and streamline application of these resources in crop improvement programs.

• Precise genome editing technologies in concert with enhanced trait architectures enable innovative solutions to engineer complex trait variation.

• High-throughput phenotyping methods are beginning to alleviate the challenge of accurate, precise and large-scale measurements of plant performance.

• Optimized speed breeding protocols remain crucial to accelerating breeding advance when applied with genomic breeding approaches.

• Sustaining gains from genomic breeding mandates fast-tracking exploitation of the minor effect alleles, accumulation of favorable alleles and purging of deleterious alleles.

Development of disease resistant, pest-resistant, abiotic stress tolerant and better quality/nutrition varieties through GAB 2.0 is expected to reduce application of pesticides, insecticides and fertilizers in growing these varieties. Such varieties are also expected to deliver higher produce to farmers while ensuring sustainable agriculture and environmental protection. The plant breeding community will continue to be armed not only with a vast array of data but also with the proper tools and technologies to decipher and implement the knowledge to feed a growing world.