What lies ahead in post-genomics era

Abstract

Resistance breeding, especially for the lineage-exclusion (LEB) is essential to meet the caloric demand of ever-growing population as diseases, especially caused by fungal and fungus-like pathogens are posing a visible and imminent threat to sustainable world food supply. This article provides a fresh perspective on the application of genomics in the LEB.

An estimated 20% of yield is lost in crops, such as rice, wheat, corn, oilseed and legumes to fungal pathogens (causative agents of notorious diseases, such as rice blast, rusts, blights, blackleg and anthracnose),¹ which would be sufficient to meet the caloric demands of people equivalent to the annual population growth rate of world (1.17% or 83 million people). Therefore, broad-spectrum, durable and environmental friendly disease management strategies are required to ensuring sustainable global food supply.

With the advent of next generation sequencing technologies (developed by Illumina/Solexa, Roche, Pacific Biosciences, Life Technologies, Helicos BioSciences), we are witnessing an era of genomics where the number of crops and their pathogens being sequenced and re-sequenced, and/or genotyped is increasing exponentially. One of the next challenges will be the processing and translation of this plethora of information into genetic improvement of crops to obtain varieties with broader disease resistance spectra. Translational genomics offers solutions by capturing diversity, such as single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) in fungal effectors (Ef; with virulence and/or avirulence activity), and their cognate resistance (R) and/or virulence (host) target (Vir; guardee) genes, as well as transcriptional and post-transcriptional regulatory elements (RE, expression determinants) in crops. Mapping such variations in corresponding genomes not only provides a mechanistic glimpse into the molecular arms race between R, Vir and RE on the one side, and Ef on the other side, but also lays the foundation for lineage-exclusion molecular breeding (LEB). Plants possess a bi-layered inducible immunity system consisting of pathogen-associated molecular pattern-triggered immunity (PTI) and effector- triggered immunity (ETI), which is compromised by evolving fungal effectors. Pathogenic races of a fungal pathogen secrete effectors to evade recognition by manipulating the immune system of a plant species or cultivar during the arms race, with the result that resistance rapidly erodes. Fungal pathogens, such as Leptosphaeria maculans, the causative agent of blackleg disease on oilseed rape possess the capability to mutate their effectors via repeat-induced point mutation within a year, which contributes to virulence and makes resistance ineffective.² The LEB likely repairs, reinforces or replaces weaken PTI and ETI via introgression of novel genetic components, such as quantitative resistance loci containing R and/or Vir and/or RE into elite varieties. Therefore, looking for novel natural allelic variations in germplasm (including wild relatives in primary, secondary and tertiary gene pools) is a key to improve and expand the genetic base for disease resistance of crops, and the transfer of such allelic diversity in elite cultivars can be accelerated via marker-assisted selection, such as SNPs (Fig. 1). Such introgression may be cumbersome because of sterility problems or issues with the normal development of embryos that result in embryo abortion. However, some of these problems can be overcome by using bridging parents and embryo rescue techniques. An alternative to this molecular breeding approach can be the direct deployment of R genes by genetic engineering or editing, which allows site-directed DNA manipulations in the genomes of crops. Insertion or stacking of R and/or Vir genes or RE at a specific chromosomal position requires double stranded break (DSB) through nucleases (such as zinc finger and transcriptional activator-like effector nuclease) followed by the repair of DSB via homologous recombination of a cassette containing gene(s) conferring resistance and up- and downstream sequences flanking to the DBS site. Such nucleases contain a DNA-binding domain and an endonuclease domain, and therefore it is extremely important to engineer nucleases specific to a site wherein higher transcription (expression) level of incorporated gene(s) could be achieved. Stacking of R genes at a single location simplifies its introgression into cultivated varieties by crossing as they are linked and therefore confer durable resistance.³

Figure 1. Crop genetic improvement for disease resistance. QRLs, quantitative resistance loci; R, resistance genes, Vir, virulence target genes, RE, regulatory elements

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

We acknowledge the financial support from the Saskatchewan Agriculture Development Fund and the Saskatchewan pulse growers.