Detection of QTL for Carcass Quality on Chromosome 6 by Exploiting Linkage and Linkage Disequilibrium in Hanwoo
1
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA) 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM) method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA), and marbling score (Marb), respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp) with the most significant evidence for linkage (p<10-5). Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp) was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.
Abstract
The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA) 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM) method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA), and marbling score (Marb), respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp) with the most significant evidence for linkage (p<10-5). Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp) was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.
참고문헌 (20)
- Blott, S., "Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition", Genetics, 163, pp.253~266 (2003)
- Druet, T., "A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping", Genetics, 184, pp.789~798 (2010)
- Druet, T., "Fine mapping of quantitative trait loci affecting female fertility in dairy cattle on BTA03 using a dense single-nucleotide polymorphism map", Genetics, 178, pp.2227~2235 (2008)
- Garrick, D. J., "The nature, scope and impact of genomic prediction in beef cattle in the United States", Genet. Sel. Evol, 43, pp.17~ (2011)
- Hubbard, T. J., "Ensembl 2009", Nucleic Acids Res, 37(Database issue), pp.D690~D697 (2009)
- Khatkar, M. S., "Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel", BMC Genomics, 9, pp.187~ (2008)
- JongJoo Kim, "Evaluation of a New Fine-mapping Method Exploiting Linkage Disequilibrium: a Case Study Analysing a QTL with Major Effect on Milk Composition on Bovine Chromosome 14", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 15(9), pp.1250~1256 (2002), 아세아·태평양축산학회
- Y.-M. Lee, "A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 23(4), pp.417~424 (2010), 아세아·태평양축산학회
- Y.-M. Lee, "Detection of Quantitative Trait Loci for Growth and Carcass Traits on BTA6 in a Hanwoo Population", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 23(3), pp.287~291 (2010), 아세아·태평양축산학회
- Y.S. Lee, "Identification of Candidate SNP (Single Nucleotide Polymorphism) for Growth and Carcass Traits Related to QTL on Chromosome 6 in Hanwoo (Korean Cattle)", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 21(12), pp.1703~1709 (2008), 아세아·태평양축산학회
- Y. Li, "Application of Linkage Disequilibrium Mapping Methods to Detect QTL for Carcass Quality on Chromosome 6 Using a High Density SNP Map in Hanwoo", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 24(4), pp.457~462 (2011), 아세아·태평양축산학회
- Matukumalli, L. K., "Development and characterization of a high density SNP genotyping assay for cattle", PLoS One, 4(4), pp.e5350~ (2009)
- McClure, M. C., "A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle", Anim Genet, 41, pp.597~607 (2010)
- Meuwissen, T. H., "Prediction of identity by descent probabilities from marker-haplotypes", Genet. Sel. Evol, 33, pp.605~634 (2001)
- Meuwissen, T. H., "Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping", Genetics, 161, pp.373~379 (2002)
- Mizoguchi, Y., "Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population", Anim. Genet, 37, pp.51~54 (2006)
- "Annual Research Report" (2009)[URL]
- Setoguchi, K., "Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate", BMC Genet, 10, pp.43~ (2009)
- Sun, Y. V., "A scan statistic for identifying chromosomal patterns of SNP association", Genet. Epidemiol, 30, pp.627~635 (2006)
- Visscher, P. M., "A note on the asymptotic distribution of likelihood ratio tests to test variance components", Twin Res. Hum. Genet, 9, pp.490~495 (2006)