Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
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Genome Wide Association Study to Identity QTL for Growth Taits in Hanwoo

전장 유전체 연관분석을 통한 한우 성장 연관 양적형질좌위 (QTL) 탐색

  • Received : 2012.09.03
  • Accepted : 2012.10.26
  • Published : 2012.10.31
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Abstract

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sires using bovine 10K mapping chip in Hanwoo (Korean cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cut-off p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, a single marker regression analysis was implemented in this study. SNP was assumed to be in LD with QTL in close proximity and the effect evaluated was additive effect (QTL allele substitution effect). The number of significant SNP at a threshold of P<0.001 was 3, 5, 5 and 4 loci for live weight at 6, 12, 18 and 24 months, respectively. For live weight at different ages, significant SNP were spread out across chromosome but some of significant SNP (rs29012453 and rs29012456 on BTA24) had shown highly significant effects. As for the distribution of size of SNP effects, few loci for live weight at different age had moderate effects (6~11%) but most of significant loci had small effects (2 to 5% of additive genetic variance) against total additive genetic variance. In conclusion, live weight at different age might be affected by few loci with moderate effect and many loci with small effects across genome in Hanwoo.

본 연구는 한우 거세우 266두에서 유전자형 결정이 완료된 4,522개의 SNP를 이용하여 한우 성장형질 (6, 12, 18 및 24개월령 체중)에 대한 양적형질좌위 (QTL)을 탐색 하였다. 각 SNP와 성장형질과의 연관성 분석은 회귀분석 (single marker regression)을 이용하여 수행하였으며, 통계적 유의성은 P-value (P<0.001)로 설정하였다. 그 결과, 6개월체중에서 3개 좌위, 12개월 체중에서는 5개 좌위, 18개월체중에서 5개좌위 그리고 24개월체중에서 4개 좌위가 통계적 유의차를 보였다. 통계적 유의차를 보인 SNP의 상가적 유전분산을 분석한 결과, 몇몇 SNP에서는 6~11% 정도의 상가적 유전효과를 보였으며, 대부분의 SNP들은 2~5%로 매우 작은 효과를 보였다.

Keywords

References

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