Identification of polymorphisms in a region of chicken chromosome 3 associated with the performance of the fat deposition

Author(s)

Gabriel Costa Monteiro Moreira

• Document type: Master's Dissertation
• Press: Piracicaba.
• Institution: Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC)
• Defense date: 2014-02-12

Examining board members

Luiz Lehmann Coutinho; Clarissa Boschiero; Mônica Corrêa Ledur

• Advisor: Luiz Lehmann Coutinho

Abstract

Eighteen chickens from a parental generation used in a reciprocal cross with broiler and layer lines were sequenced by new generation technology with an average of 10-fold coverage. The DNA sequencing was performed by Illumina next generation platform. The genetic variants discovery was performed in a quantitative trait loci (QTL) region which was previously associated with abdominal fat weight and percentage in chicken chromosome 3 (GGA3) between the microsatellite markers LEI0161 and ADL0371 (33,595,706-42,632,651 bp). SAMtools software was used to detect 136,054 unique SNPs and 15,496 unique INDELs for the 18 chickens, and after quality filtration 92,518 unique SNPs and 9,298 unique INDELs were retained. One list of 77 genes was analised and genes related to lipid metabolism were searched. Variants located in coding region (386 SNPs and 15 INDELs) were identified and associated with important metabolic pathways. Loss of functional variants in the genes LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1 may be responsible for the QTL associated with fat deposition in chicken. (AU)

• FAPESP's process: 12/14965-5 - Identification of polymorphisms in a region of chicken chromosome 3 associated with the performance of the fat deposition
• Grantee: Gabriel Costa Monteiro Moreira
• Support Opportunities: Scholarships in Brazil - Master