title: A fast expectation-maximum algorithm for fine-scale QTL mapping.
abstract: The recent technology of the single-nucleotide-polymorphism (SNP) array makes it possible to genotype millions of SNP markers on genome, which in turn requires to develop fast and efficient method for fine-scale quantitative trait loci (QTL) mapping. The single-marker association (SMA) is the simplest method for fine-scale QTL mapping, but it usually shows many false-positive signals and has low QTL-detection power. Compared with SMA, the haplotype-based method of Meuwissen and Goddard who assume QTL effect to be random and estimate variance components (VC) with identity-by-descent (IBD) matrices that inferred from unknown historic population is more powerful for fine-scale QTL mapping; furthermore, their method also tends to show continuous QTL-detection profile to diminish many false-positive signals. However, as we know, the variance component estimation is usually very time consuming and difficult to converge. Thus, an extremely fast EMF (Expectation-Maximization algorithm under Fixed effect model) is proposed in this research, which assumes a biallelic QTL and uses an expectation-maximization (EM) algorithm to solve model effects. The results of simulation experiments showed that (1) EMF was computationally much faster than VC method; (2) EMF and VC performed similarly in QTL detection power and parameter estimations, and both outperformed the paired-marker analysis and SMA. However, the power of EMF would be lower than that of VC if the QTL was multiallelic.
authors.affiliation: Life Science College, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China. fangming618@126.com
authors.forename: Ming
authors.initials: M
authors.lastname: Fang
mesh_terms: D000465:Algorithms; D000483:Alleles; D040582:Inheritance Patterns / Q000235:genetics; D016013:Likelihood Functions; D009154:Mutation / Q000235:genetics; D020161:Physical Chromosome Mapping / Q000379:methods*; D040641:Quantitative Trait Loci / Q000235:genetics*; D013997:Time Factors