marker-assisted selection in wheat - ictsd

Chapter 9 – Molecular marker-assisted selection for resistance to pathogens in tomato 155making crosses and backcrosses, and theselection of the desired resistant progeny,make it difficult to respond adequately tothe evolution of new virulent pathogens.Moreover, several interesting resistances aredifficult to use because the diagnostic testsoften cannot be developed due to the challengeposed by inoculum production andmaintenance. In addition, where symptomsare detectable only on adult plants and/orfruits, diagnostic tests can be particularlyexpensive and difficult to perform.Since the 1980s, the use of molecularmarkers has been suggested as a tool forbreeding many crops, including tomato.In the last two decades, molecular markershave been employed to map and tag majorgenes and quantitative trait loci (QTL)involved in monogenic and polygenicresistance control, known respectively asvertical and horizontal resistance. To date,more than 40 genes (including many singlegenes and QTL) that confer resistanceto all major classes of plant pathogens havebeen mapped on the tomato molecular map(Table 2) and/or cloned from Solanaceousspecies, as reported by Grube, Radwanskiand Jahn (2000). Since then, other resistancegenes together with resistance geneanalogues (RGAs), which are structurallyrelated sequences based on the proteindomain shared among cloned R genes(Leister et al., 1996), have been added to themap. A molecular linkage map of tomatobased on RGAs has also been constructedin which 29 RGAs were located on nine ofthe 12 tomato chromosomes (Foolad et al.,2002; Zhang et al., 2002). Several RGA lociwere found in clusters and their locationscoincided with those of several knowntomato R genes or QTL. This map providesa basis for further identifying and mappinggenes and QTL for disease resistance andwill be useful for MAS.In fact, independently of the type ofmarker used for selection, by making itpossible to follow the gene under selectionthrough generations rather than waitingfor phenotypic expression of the resistancegene, markers tightly linked to resistancegenes can greatly aid disease resistanceprogrammes. In particular, genetic mappingof disease resistance genes has greatlyimproved the efficiency of plant breedingand also led to a better understanding of themolecular basis of resistance.DNA marker technology has been usedin commercial plant breeding programmessince the early 1990s, and has proved helpfulfor the rapid and efficient transfer ofuseful traits into agronomically desirablevarieties and hybrids (Tanksley et al., 1989;Lefebvre and Chèvre, 1995). Markers linkedto disease resistance loci can now be usedfor MAS programmes, thus also allowingseveral resistance genes to be cumulated inthe same genotype (“pyramiding” of resistancegenes), and they may be also usefulfor cloning and sequencing the genes. Intomato, several resistance genes have beensequenced to date, among them Cf-2, Cf-4, Cf-5, Cf-9, Pto, Mi, I2, and Sw5. Thesecloned R genes now provide new tools fortomato breeders to improve the efficiencyof breeding strategies, via MAS. AlthoughMAS is still not used routinely for improvingdisease resistance in many importantcrops (Michelmore, 2003), it is being usedby seed companies for improving simpletraits in tomato (Foolad and Sharma, 2005).Furthermore, while the deep knowledgeof the tomato genome and the availabilityof a high-density molecular map for thisspecies (Pillen et al., 1996) should providefurther opportunities to acceleratebreeding through MAS, the time-consumingand expensive process of developingmarkers associated with genes of inter-