A new method of QTL identification for undersaturated maps

A K A Pamplona, M. Balestre, Leticia De Castro Lara, J, B. Santos , J.S.S. Bueno Filho

Research output: Contribution to journalArticlepeer-review

Abstract

In many species, low levels of polymorphism prevent the assembly of linkage maps that are used to identify genetic markers related to the expression of quantitative trait loci (QTLs). This study compared two methods of locating QTLs in association studies that do not require a
previous estimation of linkage maps. Method I (MI) was a Bayesian multiple
marker regression and Method II (MII) combined multiple QTL mapping
and “moving away from markers”. In this method, markers are not directly
regressed to the phenotype, but are used as pivots to search for QTLs
along the genome. To compare methods, we simulated 300 individuals
from an F2 progeny with two levels of marker loss (20 and 80%). A total
of 165 markers and seven QTLs were spread along 11 chromosomes
(roughly emulating the genetic structure of the common bean, Phaseolus
vulgaris). A real data example with 186 progenies of a F2:4 generation of
the species was analyzed using 59 markers (17 simple sequence repeats,
31 amplified fragment length polymorphisms, and 11 sequence-related
amplified polymorphisms). MII was more precise than MI for both levels of
marker loss. For real data, MII detected 17 candidate positions for QTLs, whereas MI did not detect any. MII is a powerful method that requires further studies with actual data and other designs such as crossover, and genome-wide studies.
Original languageEnglish
JournalGenetics and molecular research
DOIs
Publication statusPublished - 25 Sep 2015

Keywords

  • Bayesian regression
  • Genome-wide
  • Multiple marker
  • QTL analysis

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