marker-assisted selection in wheat

Chapter 8 – Marker-assisted selection in maize 123molecular marker technology. PCR-basedmarkers require little DNA, allowing samplingof young seedlings and very earlyselection and thereby optimization ofbreeding schemes. PCR-based marker protocolsare very amenable to automation andminiaturization and improvements to protocolsresulted in considerable reductionsin both cost and time required to producedata points. The first two PCR-basedmarker systems were random amplified polymorphicDNA (RAPDs), and amplifiedfragment length polymorphisms (AFLPs).Detailed descriptions and critical assessmentsof these two systems can be found inWelsh and McClelland (1990), Williams etal. (1990), Penner et al. (1993), Ragot andHoisington (1993), Skroch and Nienhuis(1995) and Jones et al. (1997) for RAPDs,and in Vos et al. (1995), Jones et al. (1997)and Castiglioni et al. (1999) for AFLPs.They are also described in other chaptersof this book.Simple sequence repeats (SSRs) or microsatellitesrapidly became the marker ofchoice in maize, almost entirely displacingRFLPs and previously developed PCRbasedmarker systems. Polymorphism ofSSRs is due to variable numbers of shorttandem repeats, often two or three basepairs in length and usually flanked byunique regions (Tautz, 1989). SSRs arevery reproducible (Jones et al., 1997) andco-dominant (Shattuck-Eidens et al., 1990;Senior and Heun, 1993; Senior et al., 1996)and are therefore very suitable for maizeMAS applications.Many additional variations of PCRbasedmarker systems have been developedand a thorough review can be found inMohan et al. (1997).All the DNA-based marker systems describedto date are gel-based systems, a majorconstraint for automation. Single nucleotidepolymorphisms (SNPs) (Lindblad-Toh etal., 2000) can be revealed in many waysincluding allele-specific PCR, primerextension approaches, or DNA chips, all ofwhich are not gel-based. SNPs can generallybe scored as co-dominant markers, exceptin the case of insertion-deletion polymorphisms.Although allelic diversity at SNPs isusually limited to two alleles, this limitationcan be offset by the abundance of SNPs andthe analysis of haplotypes, combinations ofgenotypes at several neighbouring SNPs.Haplotype analyses increase informativeness(Ching et al., 2002), although at someexpense because two to four SNPs have tobe genotyped where one SSR sufficed. SNPgenotyping can be highly miniaturized andautomated, thereby reducing the cost andallowing the production of very large numbersof data points. With genetic mapscontaining several thousand mapped SNPs,these have become the marker of choice forprivate maize MAS programmes.DNA marker technology has been adynamic and often expensive componentof the infrastructure needed for MAS. Forexample, one corporation indicated havingspent tens of millions of United Statesdollars to develop an automated systemfor detecting RAPDs, a technology thatwas never suited for MAS in a large maizebreeding programme. Later, another corporationspent an even greater amount ofmoney to acquire technology for matrixassistedlaser desorption/ionization time offlight (MALDI-TOF) analysis of amplifiedDNA fragments. These technologies wereeither rapidly replaced or never used. Suchdecisions would have bankrupted mostnational maize programmes or a coupleof centres belonging to the ConsultativeGroup on International AgriculturalResearch (CGIAR). Fortunately, this areaof infrastructure has matured somewhat