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Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens
Author(s) -
Moreira G. C. M.,
Godoy T. F.,
Boschiero C.,
Gheyas A.,
Gasparin G.,
Andrade S. C. S.,
Paduan M.,
Montenegro H.,
Burt D. W.,
Ledur M. C.,
Coutinho L. L.
Publication year - 2015
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12263
Subject(s) - indel , quantitative trait locus , biology , genetics , single nucleotide polymorphism , candidate gene , chromosome regions , gene , chromosome , family based qtl mapping , microsatellite , gene mapping , allele , genotype
Summary Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative trait loci ( QTL ) related to fat deposition have been detected, the resolution for these regions is low and functional variants are still unknown. The current study was conducted aiming at increasing resolution for a region previously shown to have a QTL associated with fat deposition, to detect novel variants from this region and to annotate those variants to delineate potentially functional ones as candidates for future studies. To achieve this, 18 chickens from a parental generation used in a reciprocal cross between broiler and layer lines were sequenced using the Illumina next‐generation platform with an initial coverage of 18X/chicken. The discovery of genetic variants was performed in a QTL region located on chromosome 3 between microsatellite markers LEI 0161 and ADL 0371 (33 595 706–42 632 651 bp). A total of 136 054 unique SNP s and 15 496 unique INDEL s were detected in this region, and after quality filtering, 123 985 SNP s and 11 298 INDEL s were retained. Of these variants, 386 SNP s and 15 INDEL s were located in coding regions of genes related to important metabolic pathways. Loss‐of‐function variants were identified in several genes, and six of those, namely LOC 771163 , EGLN 1 , GNPAT , FAM 120B , THBS 2 and GGPS 1, were related to fat deposition. Therefore, these loss‐of‐function variants are candidate mutations for conducting further studies on this important trait in chickens.