ABSTRACT

This chapter discusses linkage grouping and locus ordering. Locus ordering is to infer the relative order of the loci in a linkage group or locus locations on chromosomes. The chapter introduces different criteria for linkage grouping and locus ordering. It discusses methods for two-locus models and describes methods for determining locus order for three loci. Multiple-locus ordering statistics are usually extensions of the three-locus approaches. For a linkage group with more than three loci, the locus ordering problem can be partitioned into a number of three-locus ordering problems. Seriation for locus ordering was first introduced by Buetow and Chakravarti. Seriation is designed to obtain minimum sum of adjacent recombination fractions (SARF). Sampling and inadequate criteria and algorithms are error sources for determining locus order. Likelihood approaches have been used for locus ordering. Intuitively, likelihood ratios might be easily derived and used to measure the relative confidence of an estimated locus order.