marker-assisted selection in wheat - ictsd

Chapter 10 – Strategies, limitations and opportunities for marker-assisted selection in livestock 169IntroductionSince the 1970s, the discovery of technologythat enables identification and genotypingof large numbers of genetic markers, andresearch that demonstrated how this technologycould be used to identify genomicregions that control variation in quantitativetraits and how the resulting QTL could beused to enhance selection, have raised highexpectations for the application of gene-(GAS) or marker-assisted selection (MAS)in livestock. Yet, to date, the application ofGAS or MAS in livestock has been limited(see e.g. review by Dekkers, 2004 and thecase study chapters that follow). However,recent further advances in technology,combined with a substantial reduction inthe cost of genotyping, have stimulatedrenewed interest in the large-scale applicationof MAS in livestock.Successful application of MAS inbreeding programmes requires advances inthe following five areas:• Gene mapping: identification and mappingof genes and genetic polymorphisms.• Marker genotyping: genotyping of largenumbers of individuals for large numbersof markers at a reasonable cost for bothQTL detection and routine applicationfor MAS.• QTL detection: detection and estimationof associations of identified genes andgenetic markers with economic traits.• Genetic evaluation: integration of phenotypicand genotypic data in statisticalmethods to estimate breeding values ofindividuals in a breeding population.• MAS: development of breeding strategiesand programmes for the use of moleculargenetic information in selection and matingprogrammes.This chapter outlines the main strategiesfor the application of MAS in livestock andidentifies and discusses the limitations andopportunities for successful MAS in commercialbreeding programmes. It concludesby discussing limitations and opportunitiesfor applying MAS in developing countries.Markers and linkagedisequilibriumOver the past decades, a substantial number ofalternate types of genetic markers have becomeavailable to study the genetic architecture oftraits and for their use in MAS, includingrestriction fragment length polymorphisms(RFLPs), microsatellites, amplified fragmentlength polymorphisms (AFLPs) and singlenucleotide polymorphisms (SNPs). Detailedinformation on these markers can be foundelsewhere in this publication. Althoughalternate marker types have their ownadvantages and disadvantages, dependingon their abundance in the genome, degreeof polymorphism, and ease and cost ofgenotyping, what is crucial for their usefor both QTL detection and MAS is theextent of linkage disequilibrium (LD) thatthey have in the population with loci thatcontribute to genetic variation for the trait.Linkage disequilibrium relates to dependenceof alleles at different loci and is centralto both QTL detection and MAS. Thus, athorough understanding of LD and of thefactors that affect the presence and extent ofLD in populations is essential for a discussionof both QTL detection and MAS.Linkage disequilibriumConsider a marker locus with alleles M andm and a QTL with alleles Q and q that ison the same chromosome as the marker,i.e. the marker and the QTL are linked. Anindividual that is heterozygous for bothloci would have genotype MmQq. Allelesat the two loci are arranged in haplotypeson the two chromosomes of a homologous