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Introduction. The establishment of the new science of genomics in the 1980s has revolutionized biological research into a completely new era






The establishment of the new science of genomics in the 1980s has revolutionized biological research into a completely new era. This revolution is enabling scientists through the use of powerful new tools to know the sequence of the entire genome, to understand the structure and function of every single gene, to study the organization and evolution of any sequence and to deter- mine the molecular bases of genetic varia- tion. Undoubtedly, the Human Genome Plan (HGP) and other similar genome pro- grammes on model organisms (e.g. Arabidopsis and rice as model plant organ- isms) have been playing the leading role in the incredible developments in this area. Among the special focuses and major objec- tives in these genomic programmes are the characterization, isolation and manipula- tion of the agriculturally important disease resistance (R) genes responsible for defend- ing against diseases caused by various pathogens (Takken and Joosten, 2000).

Dozens of plant R genes have been iso- lated from various plant species or crops


 

since the fi rst four were published (Martin et al., 1993; Bent et al., 1994; Jones et al., 1994; Whitham et al., 1994): Pto from tomato resistant to Pseudomonas syringae pv. tomato, N from tobacco resistant to tobacco mosaic virus (TMV), RPS2 from Arabidopsis resistant to Pseudomonas syringae pv. tomato and Cf-9 from tomato resistant to Cladosporium fulvum. A few excellent reviews have been written on plant R genes regarding their structure, function, evolution, organization, classifi - cation, defence mechanisms, and so on (Ellis et al., 2000; Takken and Joosten, 2000; Young, 2000; Lehmann, 2002). Briefl y, there are six major classes of R genes (Table 13.1), fi ve classifi ed earlier plus a new class from RPW8 in Arabidopsis (Xiao et al., 2001). Most R gene products have the LRR (leucine-rich repeat) domain, and also largely are in the NBS (nucleotide- binding site)–LRR form. Two groups of NBS–LRR R genes were clearly distin- guished by the conserved amino acid motifs in the NBS domain. One group, which was comprised of sequences encoding an N-ter- minal domain with homology to Toll/inter-


 

© CAB International 2007. Citrus Genetics, Breeding and Biotechnology (ed. I.A. Khan) 287


Table 13.1. Classes of resistance genes, classifi ed by their structural domains.

Class Example of R genes Structural domain description First reference

 
 

PK Pto Serine/threonine protein Martin et al., 1993 kinase with myristoylation site

TIR–NBS–LRR N, RPP1, RPP10, Cytoplasmic protein with Whitham et al., RPP14, L6, L1-12, homologies to Toll cytoplasmic 1994

M, RPP5, RPS4 domain, apoptotic ATPases

CED4 and Apaf1, and C-terminal LRRs

CC–NBS–LRR RPS2, Prf, RPM1, Cytoplasmic protein with Bent et al., 1994

RPS5, RPP8, Mi, homologies to CC,

I2, Dm3, Pi-B, Xa1 apoptotic ATPases CED4 and

Apaf1, and C-terminal LRRs (also called LZ–NBS–LRR)

LRR–TM Cf-9, Cf-2, Cf-4, Cf-5, Transmembrane protein with

Hcr9-4E, HSIpro-1 extracellular LRRs (eLRRs) Jones et al., 1994 LRR–TM–PK Xa21 Transmembrane protein;

extracellular LRRs, Song et al., 1995 cytoplasmic (LRR kinase)

SA–CC RPW8.1, RPW8.2 Putative signal anchor (SA) Xiao et al., 2001

 
 

for membrane insertion, and putative CC domain

Genes in bold are the fi rst reported in each class.

LRR = leucine-rich repeat; NBS = nucleotide-binding site; TIR = Toll/interleukin-1 receptor; CC

= coiled-coil; LZ = leucine zipper; PK = protein kinase.

 

 


leukin-1 receptor (TIR), surprisingly was entirely absent from monocot plants. The other group was found in both monocot and dicot plants. The conservation of R gene structural domains provides not only an informative guide for isolation of other R genes, but also a broad potential to enable use of natural genetic resistance more effi - ciently by rapid transfer of genes among crops for specifi c resistance breeding objec- tives.

Citrus is one of the most important fruit crops widely planted in the tropical and subtropical zones of the world. It is a major source of revenue in many regions of the developed world, as well as an important nutrient source in some less industrialized areas. However, in every growing region of the world, cultivated citrus species are sus- ceptible to various diseases or pests,


including but not limited to citrus tristeza virus (CTV), citrus nematode (Tylenchulus semipenetrans), Phytophthora species, citrus canker (Xanthomonas axonopodis), viroids, phytoplasmas, etc. that can result in tremendous economic losses of citrus production. Traditional genetic manipula- tion methods and conventional hybridiza- tion breeding programmes, which are time consuming and labour intensive, have been proven ineffective or irrelevant for many citrus breeding objectives. Such goals as breeding disease-resistant cultivars of most species are nearly impossible to achieve because of high genetic heterozygosity, long periods of juvenility and little genetic knowledge of the inheritance of most traits. Most scion cultivar groups, specifically sweet oranges, grapefruit, most lemons and


 


many mandarins, have diversified by somatic mutations and not through sexual recombination and segregation; these groups, by virtue of their limited genetic base in addition to the other breeding impediments, are not amenable to genetic manipulation through hybridization strate- gies. Other characters, such as nucellar embryony, self-incompatibility or large tree size in most citrus varieties, will signifi - cantly increase the difficulties because these characters generally reduce the possi- bilities of obtaining genetic information on the transmission and heritability of useful agronomic traits in citrus. The rapidly developed molecular marker technology and MBC (map-based cloning) approach in the past several years have greatly acceler- ated understanding of the citrus genome (Durham et al., 1992; Cai et al., 1996; Liou et al., 1996) and the genetics of several agri- culturally important single gene or quanti- tative trait loci (QTLs) related to disease, pest and stress resistances (Cai et al., 1994; Gmitter et al., 1996, 1997; Deng et al., 1997,

2000; Fang et al., 1997, 1998; Ling et al., 2000). The polymorphic DNA markers closely linked to an important specifi c trait can greatly facilitate early selection (called marker-assisted selection; MAS) and mini- mize costs associated with plant size and juvenility. Genetic transformation methods allow trait-specifi c modifi cation of commer- cial cultivars, including those listed above for which sexual hybridization is precluded as a strategy for improvement. We will sum- marize the advances in MBC of the single dominant CTV resistance gene, designated Ctv (Gmitter et al., 1996), and in characteri- zation of a major citrus nematode resistance QTL, named Tyr1 (Ling et al., 2000). We will discuss the cloning and characteriza- tion of other R genes within the citrus genome, through a strategy based on sequence homologies among plant R genes in general, and provide information on the distribution of R genes and resistance gene


candidates (RGCs). Finally, the chapter will conclude with consideration of the future prospects for manipulating disease resist- ance through genomic approaches.

 

 






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