marker-assisted selection in wheat - ictsd

Chapter 15 – Marker-assisted selection in forestry species 285IntroductionTree breeding offers a unique set ofchallenges associated with long generationtimes, outcrossing breeding systems and arelatively short history of genetic improvement.Breeding populations are often onlyone or two generations from the wild state.This has the advantage over crop breedingof providing vast stores of genetic variationthat can be utilized in tree improvement.Tree breeding programmes have generallyrelied on testing and selecting large numbersof genotypes derived from multiple geneticbackgrounds, the maintenance of highgenetic diversity in production forests,and sexual propagation and capture ofadditive genetic variation through recurrentselection (Strauss, Lande and Namkoong,1992). Inbreeding depression and longgeneration intervals have precluded the useof inbred lines, although research into theirdevelopment continues (Wu, Abarquezand Matheson, 2004). The greatest use ofinterspecific hybrids in operational treebreeding has been with introduced species;for example, Pinus elliottii x P. caribaea inAustralia (Nikles, 1996), hybrid eucalyptsin South Africa, Brazil and the Congo(Eldridge et al., 1993), Acacia mangiumx A. auriculiformis in Viet Nam (Kha,Hai and Vinh, 1998) and hybrid poplarsin temperate regions. These programmesoften rely on clonal propagation fordeployment.The goal of commercial tree breeding isto increase the quantity and quality of woodproducts from plantations. Productionof industrial timber was estimated at2.8 thousand million cubic metres in 2004and has been increasing at an average annualrate of 2.4 percent since 1998 (FAOSTAT)with much of the recent increase beingdue to rapid economic growth in China.Consumption of fuelwood is increasing ata similar rate (Carson, Walter and Carson,2004). Rising demand together withrestrictions on the supply of timber fromnative forests mean that increases in forestproductivity will be required. To date,increased production has been achievedby expanding the area of plantations,particularly in tropical regions wherehigh growth rates can be achieved. Gainshave also been made using conventionalbreeding, but further productivity increasesare required to reduce pressure on nativeforests and limit the increases in land arearequired for plantations. MAS has thepotential to enhance plantation productivityif the relationship between genetic variationin gene sequences and phenotypic variationin traits can be demonstrated.The relatively long generation timesand poor juvenile-mature trait correlationsin forest trees have promoted interest inMAS to accelerate breeding through earlyselection. MAS relies on identifying DNAmarkers which explain a high proportionof additive variation in phenotypic traits.Initially, research focused on the use ofDNA markers in genome-wide linkageanalysis of progeny arrays (Lander andBotstein, 1989). By identifying patternsof co-segregation in complex traits andpolymorphic markers (QTL), these studiesaimed to reveal causative regions of thechromosome or gene that were inheritedintact over a few generations. The QTLapproach can be used for marker-aidedbreeding within families. The low successrate in validating QTL in different geneticbackgrounds and environments (Neale,Sewell and Brown, 2002) led to a changein research focus towards population-levelassociation mapping. This approach seeksto find alleles of genes that affect thephenotype directly (Neale and Savolainen,2004), and relies on the retention of much