Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models

Autor(es)

Mollinari, Marcelo ^[1] ; Franco Garcia, Antonio Augusto ^[2]

Afiliação do(s) autor(es)

^[1] North Carolina State Univ, Dept Hort Sci, Bioinformat Res Ctr, Raleigh, NC 27695 - USA

^[2] Univ Sao Paulo, ESALQ, Dept Genet, Piracicaba, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: G3-GENES, GENOMES, GENETICS; v. 9, n. 10, p. 3297-3314, OCT 2019.
• Citações Web of Science: 1

Resumo

Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations. (AU)

• Processo FAPESP: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
• Beneficiário: Anete Pereira de Souza
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOEN - Temático
• Processo FAPESP: 13/12245-8 - Desenvolvimento de modelos estatísticos para o mapeamento de QTLs utilizando marcadores SNPs em autopoliploides, com aplicações em cana-de-açúcar
• Beneficiário: Marcelo Mollinari
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 12/17009-8 - Mapeamento de QTLs utilizando marcadores SNPs em autopoliploides, com aplicações em cana-de-açúcar
• Beneficiário: Marcelo Mollinari
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado