marker-assisted selection in wheat - ictsd

Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishhighlights issues that might be importantto applications of MAS in developingcountries. Although molecular markers maybe used for a wide range of different tasks,such as to quantify the genetic diversityand relationships within and betweenagricultural populations (e.g. livestockbreeds), to investigate biological processes(such as mating systems, pollen movementor seed dispersal in plants) or to identifyspecific genotypes (e.g. cloned forest trees),these applications are not considered here.Background to MASMolecular markersAll living organisms are made up of cellsthat are programmed by genetic materialcalled DNA. This molecule is made up ofa long chain of nitrogen-containing bases(there are four different bases – adenine [A],cytosine [C], guanine [G] and thymine [T]).Only a small fraction of the DNA sequencetypically makes up genes, i.e. that code forproteins, while the remaining and majorshare of the DNA represents non-codingsequences, the role of which is not yetclearly understood. The genetic material isorganized into sets of chromosomes (e.g.five pairs in Arabidopsis thaliana; 30 pairs inBos taurus [cow]), and the entire set is calledthe genome. In a diploid individual (i.e.where chromosomes are organized in pairs),there are two alleles of every gene – onefrom each parent.Molecular markers should not be consideredas normal genes as they usually donot have any biological effect. Instead, theycan be thought of as constant landmarksin the genome. They are identifiable DNAsequences, found at specific locations of thegenome, and transmitted by the standardlaws of inheritance from one generationto the next. They rely on a DNA assay,in contrast to morphological markers thatare based on visible traits, and biochemicalmarkers that are based on proteins producedby genes.Different kinds of molecular markersexist, such as restriction fragment lengthpolymorphisms (RFLPs), random amplifiedpolymorphic DNA (RAPDs) markers,amplified fragment length polymorphisms(AFLPs), microsatellites and single nucleotidepolymorphisms (SNPs). They maydiffer in a variety of ways – such as theirtechnical requirements (e.g. whether theycan be automated or require use of radioactivity);the amount of time, moneyand labour needed; the number of geneticmarkers that can be detected throughoutthe genome; and the amount of geneticvariation found at each marker in a givenpopulation. The information provided tothe breeder by the markers varies dependingon the type of marker system used. Each hasits advantages and disadvantages and, in thefuture, other systems are likely to be developed.More details on the individual markersystems are provided in Chapter 3.From markers to MASThe molecular marker systems describedabove allow high-density DNA markermaps (i.e. with many markers of known location,interspersed at relatively short intervalsthroughout the genome) to be constructedfor a range of economically importantagricultural species, thus providing theframework needed for eventual applicationsof MAS.Using the marker map, putative genesaffecting traits of interest can then be detectedby testing for statistical associationsbetween marker variants and any trait ofinterest. These traits might be geneticallysimple – for example, many traits for diseaseresistance in plants are controlled by one ora few genes (Young, 1999). Alternatively,