marker-assisted selection in wheat - ictsd

Chapter 12 – Marker-assisted selection in dairy cattle 205scored from the centromere. Chromosomesare denoted with the prefix “BTA” (B.taurus). Similar to other mammals, thebovine DNA includes 3×10 9 base pairs(bp), and the map length is approximately3 000 cM. The human genome is estimatedto encode 20 000–25 000 protein-codinggenes (International Human GenomeSequencing Consortium, 2004), and it canbe assumed that the number of genes inother mammals, including cattle, should bequite similar. Thus, a single map unit, onaverage, includes approximately eight genesand one million bp.As in other animal species, microsatellitesare still the marker of choice for mapconstruction due to their prevalence andhigh polymorphism. Although singlenucleotide polymorphisms (SNPs) aremuch more prevalent, genetic maps basedon SNPs are still in the future. Morethan 50 000 SNPs have been identified inhumans, but only several thousand havebeen validated in cattle (www.afns.ualberta.ca/Hosted/Bovine%20Genomics/), andrates of polymorphism are generallyunknown. With the completion of the sixfoldcoverage of the bovine genome bythe Bovine Genome Sequencing Project atBaylor College of Medicine (www.hgsc.bcm.tmc.edu/projects/bovine/) many moreSNPs will be identified.Several genetic maps are available on theinternet. The United States Meat AnimalResearch Center (MARC) (www.marc.usda.gov/) includes thousands of markers,chiefly microsatellites. The ArkDB databasesystem, hosted at Roslin Institute,includes data from several published maps(www.thearkdb.org/). The CommonwealthScientific and Industrial Research Organization(CSIRO) livestock industries cattlegenome marker map is built upon dataprovided by the University of Sydney’scomparative location database (www.livestockgenomics.csiro.au/perl/gbrowse.cgi/cattlemap/). This map combined all publicly-availablemaps into a single integratedmap that currently includes 9 400 markers.Methods of QTL detectionsuitable for commercial dairycattle populationsDetection of QTL requires generation oflinkage disequilibrium (LD) between thegenetic markers and QTL. In plants, this isgenerally accomplished by crosses betweeninbred lines but, for the reasons noted inthe introduction, this is not a viable optionfor dairy cattle in developed countries, inwhich all analyses must be based on analysisof the existing population. Detection ofQTL in developing countries is consideredbelow. For advanced commercial populations,the “daughter” and “granddaughter”designs, which make use of the existenceof large half-sib families, are most appropriatefor QTL analysis (Weller, Kashi andSoller, 1990). These designs are presentedin Figures 2 and 3.Both designs are similar to the backcrossdesign for crosses between inbred lines inthat only the alleles of one parent are followedin the progeny. Thus, similar to thebackcross design, dominance cannot beestimated. These designs differ from crossesbetween inbred lines in that several familiesare analysed in which the linkage phasebetween QTL and genetic markers maydiffer. In addition, any specific QTL will beheterozygous in only a fraction of the familiesincluded in the analysis. Thus, QTLeffects must be estimated within families,and these designs are therefore less powerfulper individual genotyped than designsbased on crosses between inbred lines.The granddaughter design has theadvantage of greater statistical power per