fast expectation-maximum algorithm for fine-scale QTL mapping

• Published in: Theoretical and applied genetics Vol. 125; no. 8; pp. 1727 - 1734
• Main Author: Fang, Ming
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.12.2012; Springer; Springer Nature B.V
• Subjects: Agriculture; Algorithms; Alleles; Biochemistry; Biomedical and Life Sciences; Biotechnology; Chromosome mapping; Gene loci; Genetic algorithms; Genetic aspects; genetics; genome; Genomes; genotype; Genotype & phenotype; Haplotypes; Inheritance Patterns; Inheritance Patterns - genetics; Life Sciences; Likelihood Functions; Maximum likelihood method; methods; Mutation; Mutation - genetics; Original Paper; Physical Chromosome Mapping; Physical Chromosome Mapping - methods; Physiological aspects; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Power; Probability; Quantitative trait loci; Quantitative Trait Loci - genetics; single nucleotide polymorphism; Time Factors; variance; China; Quantitative Trait Locus Locus; Quantitative Trait Locus; Quantitative Trait Locus Effect; Quantitative Trait Locus Allele; Putative Quantitative Trait Locus
• ISSN: 0040-5752; 1432-2242; 1432-2242
• DOI: 10.1007/s00122-012-1949-9

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.