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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

A model for quantitative trait loci mapping, linkage phase, and segregation pattern estimation for a full-sib progeny

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Author(s):
Gazaffi, Rodrigo [1] ; Margarido, Gabriel R. A. [2] ; Pastina, Maria Marta [3] ; Mollinari, Marcelo [2] ; Garcia, Antonio Augusto F. [2]
Total Authors: 5
Affiliation:
[1] Univ Fed Sao Carlos, Ctr Agr Sci, BR-13600970 Araras, SP - Brazil
[2] Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz ESALQ, BR-13400970 Sao Paulo - Brazil
[3] Embrapa Maize & Sorghum, Nucleus Appl Biol, BR-35701970 Sete Lagoas, MG - Brazil
Total Affiliations: 3
Document type: Journal article
Source: Tree Genetics & Genomes; v. 10, n. 4, p. 791-801, AUG 2014.
Web of Science Citations: 12
Abstract

Quantitative trait loci (QTL) mapping is an important approach for the study of the genetic architecture of quantitative traits. For perennial species, inbred lines cannot be obtained due to inbreed depression and a long juvenile period. Instead, linkage mapping can be performed by using a full-sib progeny. This creates a complex scenario because both markers and QTL alleles can have different segregation patterns as well as different linkage phases between them. We present a two-step method for QTL mapping using full-sib progeny based on composite interval mapping (i.e., interval mapping with cofactors), considering an integrated genetic map with markers with different segregation patterns and conditional probabilities obtained by a multipoint approach. The model is based on three orthogonal contrasts to estimate the additive effect (one in each parent) and dominance effect. These estimatives are obtained using the EM algorithm. In the first step, the genome is scanned to detect QTL. After, segregation pattern and linkage phases between QTL and markers are estimated. A simulated example is presented to validate the methodology. In general, the new model is more effective than existing approaches, because it can reveal QTL present in a full-sib progeny that segregates in any pattern present and can also identify dominance effects. Also, the inclusion of cofactors provided more statistical power for QTL mapping. (AU)

FAPESP's process: 12/13272-6 - Development of statistical models for genome wide association studies to identify Genotype-Environment interaction for water stress in sorghum
Grantee:Rodrigo Gazaffi
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 10/00083-5 - Association mapping, linkage disequilibrium and population structure in sugarcane
Grantee:Maria Marta Pastina
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 08/54402-4 - Development of a model to build genetic maps in autopolyploides, with applications in sugarcane
Grantee:Marcelo Mollinari
Support type: Scholarships in Brazil - Doctorate