Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo Korean Cattle
Coimbra, Joao Carlos; Pinto, Iraja Damiani; Wurdig, Norma Luiza; Do Carmo, Dermeval Aparecido
Genes and Genomics 34(1): 43-49
2012
ISSN/ISBN: 1976-9571
DOI: 10.1007/s13258-011-0081-6
Accession: 036328254
Meat quality traits are the most economically important traits affecting the beef industry in Korea. We performed a whole genome quantitative trait locus (QTL) mapping study of carcass data in Hanwoo Korean cattle. Two hundred sixty-six Hanwoo steers from 65 sires were genotyped using a 1K Affymetrix SNP chip. The average SNP interval across the bovine genome was 1.5Mb. Associations between each individual SNP and four carcass traits [carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling (MAR)] were assessed using a linear mixed model of each trait. Combined linkage and linkage disequilibrium analysis (LDLA) detected six potential QTL on BTA4, 6, 13, 16, 17, and 23 at the chromosome-wise level (P<.5). Two MAR QTL were detected at 52.2 cM of BTA6 and 46.4 cM of BTA17. We identified three genes (ARAP2, LOC53946, and LOC511424) in the QTL region of BTA6 and seven genes (RPS14, SCARB1, LOC78213, BRI3BP, AACS, DHX37, and UBC) in the QTL region of BTA17. One significant QTL for CWT was detected at 1 cM on BTA4 and the corresponding QTL region spanned 1.7 cM from 99.7 to 11.4 cM. For EMA QTL, one significant QTL was detected at 3.9 cM of BTA23 and the most likely QTL interval was 1.4 cM, placing 15 candidate genes in the marker bracket. Finally, two QTL for BFT were identified at 68 cM on BTA13 and 24 cM on BTA16. The LPIN3 gene, which is functionally associated with lipodystrophy in humans, is located in the BFT QTL on BTA13. Thus, two potential candidate genes, acetoacetyl-CoA synthetase (AACS) and lipin (LPIN), were detected in QTL regions on BTA17 for MAR and BTA13 for BFT, respectively. In conclusion, LDLA analysis can be used to detect chromosome regions harboring QTL and candidate genes with a low density SNP panel, yielding relatively narrow confidence intervals regarding location.