In:
Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 28 ( 2012-07-10)
Abstract:
Breeding and genetic engineering of crop species, such as cassava, is a slow and laborious process. It is therefore highly advantageous to first identify the most promising resistance gene before attempting to introduce it to farmer-preferred crop varieties. The most promising resistance gene will be one that recognizes a highly conserved pathogen-specific molecule. Our results demonstrate the next major advance in plant breeding and genetics: the ability to assess genomic variability in a pathogen population a priori and to identify the most highly conserved potential targets for disease resistance strategies. Looking forward, our results set the stage for pathogen population monitoring, whereby through continual sampling, we will be able to identify the appearance of novel pathogen strains that threaten to overcome current resistance strategies before they have a chance to spread. As the host–pathogen arms race continues, this type of genomic surveying will be an essential step to meet the nutritional requirements of our rapidly increasing human population. Specifically, this research focused on the bacterial phytopathogen Xanthomonas axonopodis pv. manihotis ( Xam ), the causal agent of cassava bacterial blight (CBB). Cassava is a staple food source in the tropics and is of particular importance in developing countries ( Fig. P1 ). Moreover, CBB is the most important bacterial disease of cassava, resulting in significant crop losses. We generated genome sequences using the Illumina next-generation sequencing platform for 65 temporally and geographically diverse Xam strains. Next, we used an extensive database of animal and plant pathogen type three effector proteins to identify the complete effector repertoire for each Xam strain. Although effector arsenal size did not correlate particularly well with overall virulence levels, we were able to identify a core set of effectors that have been maintained in Xam over 70 y of evolution, across three continents and 11 countries. Sequence analysis further compared effector alleles and identified genes that are particularly highly conserved on a population level. We propose that these highly conserved and genetically static effectors will be ideal targets for developing resistance strategies for breeding sustainable and durable disease resistance. A resistance gene may become ineffective if a subset of the pathogen population does not contain the recognized effector or maintains alternative alleles that are not recognized by the cognate host resistance gene ( 3 , 4 ). Consequently, our ability to predict the durability of a given resistance gene is hindered by an incomplete understanding of the genetic variability within a pathogen population. However, with the advent of Illumina next-generation sequencing combined with computational biological pipelines for effector prediction, we are now in a position to overcome this challenge by analyzing bacterial pathogens with small genomes (5 Mb). Full genome sequencing can be accomplished at a cost of less than $120.00 USD per strain, and the repertoire of effectors for each sequenced strain can be determined. Thus, we are now in a position to deduce the effector content of important bacterial pathogens on a population level, and the most highly conserved effectors become the best potential targets for durable resistance strategies. Sir Rowland Biffen (1874–1949), building upon Gregor Mendel’s (1822–1884) work on inheritance, demonstrated that resistance to yellow rust of wheat was controlled by a single gene, revolutionizing the field of plant breeding ( 1 ). Soon thereafter, work by Henry Harold Flor (1900–1991) and others led to the “gene-for-gene” model, in which induction of a resistance response was traceable to a single pathogen gene that matched a single resistance gene in the host ( 2 ). To this day, the introgression of resistance genes from wild species into agronomic crops is the preferred method of crop protection by geneticists, farmers, and consumers. Unfortunately, history has shown that most single genes for disease resistance are rapidly “defeated” in the field by pathogens that mutate to avoid recognition. We report here the results of next-generation sequence analysis of a significant bacterial plant pathogen that identifies ideal targets for developing resistance strategies for breeding sustainable and durable disease resistance.
Type of Medium:
Online Resource
ISSN:
0027-8424
,
1091-6490
DOI:
10.1073/pnas.1208003109
Language:
English
Publisher:
Proceedings of the National Academy of Sciences
Publication Date:
2012
detail.hit.zdb_id:
209104-5
detail.hit.zdb_id:
1461794-8
SSG:
11
SSG:
12
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