Plant Signaling & Behavior
ISSN: (Print) 1559-2324 (Online) Journal homepage: http://www.tandfonline.com/loi/kpsb20
What lies ahead in post-genomics era Vijai Bhadauria & Sabine Banniza To cite this article: Vijai Bhadauria & Sabine Banniza (2014) What lies ahead in post-genomics era, Plant Signaling & Behavior, 9:4, e28503, DOI: 10.4161/psb.28503 To link to this article: http://dx.doi.org/10.4161/psb.28503
Published online: 08 Apr 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kpsb20 Download by: [218.67.78.114]
Date: 05 November 2015, At: 13:19
Perspective
Perspective
Plant Signaling & Behavior 9, e28503; April; © 2014 Landes Bioscience
What lies ahead in post-genomics era A perspective on genetic improvement of crops for fungal disease resistance Vijai Bhadauria* and Sabine Banniza* Crop Development Centre; University of Saskatchewan; Saskatoon, SK Canada
Downloaded by [218.67.78.114] at 13:19 05 November 2015
R
Keywords: Effectors, genome editing, lineage-exclusion, resistance breeding, resistance genes *Correspondence to: Vijai Bhadauria; Email: [email protected]; Sabine Banniza; [email protected] Submitted: 02/27/2014 Accepted: 03/11/2014 Published Online: 04/08/2014 Citation: Bhadauria V, Banniza S. What lies ahead in post-genomics era: A perspective on genetic improvement of crops for fungal disease resistance. Plant Signaling & Behavior 2014; 9:e28503; PMID: 24690770; http://dx.doi.org/10.4161/psb.28503
www.landesbioscience.com
esistance 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 funguslike 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 patterntriggered 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
Plant Signaling & Behavior e28503-1
Downloaded by [218.67.78.114] at 13:19 05 November 2015
Figure 1. Crop genetic improvement for disease resistance. QRLs, quantitative resistance loci; R, resistance genes, Vir, virulence target genes, RE, regulatory elements
for disease resistance of crops, and the transfer of such allelic diversity in elite cultivars can be accelerated via markerassisted 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
References
2. Fudal I, Ross S, Brun H, Besnard AL, Ermel M, Kuhn ML, Balesdent MH, Rouxel T. Repeat-induced point mutation (RIP) as an alternative mechanism of evolution toward virulence in Leptosphaeria maculans. Mol Plant Microbe Interact 2009; 22:93241; PMID:19589069; http://dx.doi.org/10.1094/ MPMI-22-8-0932
1.
Skamnioti P, Gurr SJ. Against the grain: safeguarding rice from rice blast disease. Trends Biotechnol 2009; 27:141-50; PMID:19187990; http://dx.doi. org/10.1016/j.tibtech.2008.12.002
e28503-2
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 DNAbinding 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 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. 3. Curtin SJ, Voytas DF, Stupar RM. Genome engineering of crops with designer nucleases. Plant Genome 2012; 5:42-50; http://dx.doi.org/10.3835/ plantgenome2012.06.0008
Plant Signaling & Behavior Volume 9
ISSN: (Print) 1559-2324 (Online) Journal homepage: http://www.tandfonline.com/loi/kpsb20
What lies ahead in post-genomics era Vijai Bhadauria & Sabine Banniza To cite this article: Vijai Bhadauria & Sabine Banniza (2014) What lies ahead in post-genomics era, Plant Signaling & Behavior, 9:4, e28503, DOI: 10.4161/psb.28503 To link to this article: http://dx.doi.org/10.4161/psb.28503
Published online: 08 Apr 2014.
Submit your article to this journal
Article views: 64
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kpsb20 Download by: [218.67.78.114]
Date: 05 November 2015, At: 13:19
Perspective
Perspective
Plant Signaling & Behavior 9, e28503; April; © 2014 Landes Bioscience
What lies ahead in post-genomics era A perspective on genetic improvement of crops for fungal disease resistance Vijai Bhadauria* and Sabine Banniza* Crop Development Centre; University of Saskatchewan; Saskatoon, SK Canada
Downloaded by [218.67.78.114] at 13:19 05 November 2015
R
Keywords: Effectors, genome editing, lineage-exclusion, resistance breeding, resistance genes *Correspondence to: Vijai Bhadauria; Email: [email protected]; Sabine Banniza; [email protected] Submitted: 02/27/2014 Accepted: 03/11/2014 Published Online: 04/08/2014 Citation: Bhadauria V, Banniza S. What lies ahead in post-genomics era: A perspective on genetic improvement of crops for fungal disease resistance. Plant Signaling & Behavior 2014; 9:e28503; PMID: 24690770; http://dx.doi.org/10.4161/psb.28503
www.landesbioscience.com
esistance 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 funguslike 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 patterntriggered 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
Plant Signaling & Behavior e28503-1
Downloaded by [218.67.78.114] at 13:19 05 November 2015
Figure 1. Crop genetic improvement for disease resistance. QRLs, quantitative resistance loci; R, resistance genes, Vir, virulence target genes, RE, regulatory elements
for disease resistance of crops, and the transfer of such allelic diversity in elite cultivars can be accelerated via markerassisted 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
References
2. Fudal I, Ross S, Brun H, Besnard AL, Ermel M, Kuhn ML, Balesdent MH, Rouxel T. Repeat-induced point mutation (RIP) as an alternative mechanism of evolution toward virulence in Leptosphaeria maculans. Mol Plant Microbe Interact 2009; 22:93241; PMID:19589069; http://dx.doi.org/10.1094/ MPMI-22-8-0932
1.
Skamnioti P, Gurr SJ. Against the grain: safeguarding rice from rice blast disease. Trends Biotechnol 2009; 27:141-50; PMID:19187990; http://dx.doi. org/10.1016/j.tibtech.2008.12.002
e28503-2
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 DNAbinding 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 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. 3. Curtin SJ, Voytas DF, Stupar RM. Genome engineering of crops with designer nucleases. Plant Genome 2012; 5:42-50; http://dx.doi.org/10.3835/ plantgenome2012.06.0008
Plant Signaling & Behavior Volume 9
