Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

Seung Hwan Lee; Bong Hwan Choi; Hak Kyo Lee; Seong Heum Yeon; Boh Suk Yang; Hee Seol Kang; Seong Koo Hong; Dajeong Lim; Cedric Gondro; Young Min Cho; Chang Gwon Dang; Aditi Sharma; Gul Won Jang; Kyung Tai Lee; Duhak Yoon

doi:10.1371/journal.pone.0074677

Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

Seung Hwan Lee, Bong Hwan Choi, Hak Kyo Lee, Seong Heum Yeon, Boh Suk Yang, Hee Seol Kang, Seong Koo Hong, Dajeong Lim, Cedric Gondro, Young Min Cho, Chang Gwon Dang, Aditi Sharma, Gul Won Jang, Kyung Tai Lee, Duhak Yoon

School of Environmental & Rural Science

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Abstract

This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10ˉ⁶) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was 'BTB-01280026' (P = 4.02×10ˉ¹¹), located in the 25Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were 'Hapmap27934-BTC-065223' (P = 4.04×10ˉ¹¹) in 25.2 Mb, 'BTB-01143580' (P = 6.35×10ˉ¹¹) in 24.3 Mb, 'Hapmap30932-BTC-011225' (P = 5.92×10ˉ¹⁰) in 24.8 Mb, 'Hapmap27112-BTC-063342' (P = 5.18×10ˉ⁹) in 25.4 Mb, and 'Hapmap24414-BTC-073009' (P = 7.38×10ˉ⁸) in 25.4 Mb, all on BTA 14. One SNP ('BTB-01143580'; P = 6.35×10ˉ¹¹) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP ('BTB-01280026'; P = 4.02×10ˉ¹¹) had 16.96 kg of allele substitution effect, and the second most significant SNP ('Hapmap27934-BTC-065223'; P = 4.04×10ˉ¹¹) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

Original language	English
Article number	e74677
Pages (from-to)	1-9
Journal	PLoS One
Volume	8
Issue number	10
DOIs	https://doi.org/10.1371/journal.pone.0074677
Publication status	Published - 2013

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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Lee, S. H., Choi, B. H., Lee, H. K., Yeon, S. H., Yang, B. S., Kang, H. S., Hong, S. K., Lim, D., Gondro, C., Cho, Y. M., Dang, C. G., Sharma, A., Jang, G. W., Lee, K. T., & Yoon, D. (2013). Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle). PLoS One, 8(10), 1-9. Article e74677. https://doi.org/10.1371/journal.pone.0074677

@article{3bb10e14500941179e82b46bca221987,

title = "Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)",

abstract = "This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10ˉ⁶) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was 'BTB-01280026' (P = 4.02×10ˉ¹¹), located in the 25Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were 'Hapmap27934-BTC-065223' (P = 4.04×10ˉ¹¹) in 25.2 Mb, 'BTB-01143580' (P = 6.35×10ˉ¹¹) in 24.3 Mb, 'Hapmap30932-BTC-011225' (P = 5.92×10ˉ¹⁰) in 24.8 Mb, 'Hapmap27112-BTC-063342' (P = 5.18×10ˉ⁹) in 25.4 Mb, and 'Hapmap24414-BTC-073009' (P = 7.38×10ˉ⁸) in 25.4 Mb, all on BTA 14. One SNP ('BTB-01143580'; P = 6.35×10ˉ¹¹) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73\% to 10.55\% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP ('BTB-01280026'; P = 4.02×10ˉ¹¹) had 16.96 kg of allele substitution effect, and the second most significant SNP ('Hapmap27934-BTC-065223'; P = 4.04×10ˉ¹¹) had 18.06 kg of effect on carcass weight, which correspond to 44\% and 47\%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.",

keywords = "Quantitative Genetics (incl Disease and Trait Mapping Genetics)",

author = "Lee, \{Seung Hwan\} and Choi, \{Bong Hwan\} and Lee, \{Hak Kyo\} and Yeon, \{Seong Heum\} and Yang, \{Boh Suk\} and Kang, \{Hee Seol\} and Hong, \{Seong Koo\} and Dajeong Lim and Cedric Gondro and Cho, \{Young Min\} and Dang, \{Chang Gwon\} and Aditi Sharma and Jang, \{Gul Won\} and Lee, \{Kyung Tai\} and Duhak Yoon",

year = "2013",

doi = "10.1371/journal.pone.0074677",

language = "English",

volume = "8",

pages = "1--9",

journal = "PLoS One",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "10",

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TY - JOUR

T1 - Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

AU - Lee, Seung Hwan

AU - Choi, Bong Hwan

AU - Lee, Hak Kyo

AU - Yeon, Seong Heum

AU - Yang, Boh Suk

AU - Kang, Hee Seol

AU - Hong, Seong Koo

AU - Lim, Dajeong

AU - Gondro, Cedric

AU - Cho, Young Min

AU - Dang, Chang Gwon

AU - Sharma, Aditi

AU - Jang, Gul Won

AU - Lee, Kyung Tai

AU - Yoon, Duhak

PY - 2013

Y1 - 2013

N2 - This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10ˉ⁶) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was 'BTB-01280026' (P = 4.02×10ˉ¹¹), located in the 25Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were 'Hapmap27934-BTC-065223' (P = 4.04×10ˉ¹¹) in 25.2 Mb, 'BTB-01143580' (P = 6.35×10ˉ¹¹) in 24.3 Mb, 'Hapmap30932-BTC-011225' (P = 5.92×10ˉ¹⁰) in 24.8 Mb, 'Hapmap27112-BTC-063342' (P = 5.18×10ˉ⁹) in 25.4 Mb, and 'Hapmap24414-BTC-073009' (P = 7.38×10ˉ⁸) in 25.4 Mb, all on BTA 14. One SNP ('BTB-01143580'; P = 6.35×10ˉ¹¹) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP ('BTB-01280026'; P = 4.02×10ˉ¹¹) had 16.96 kg of allele substitution effect, and the second most significant SNP ('Hapmap27934-BTC-065223'; P = 4.04×10ˉ¹¹) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

AB - This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10ˉ⁶) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was 'BTB-01280026' (P = 4.02×10ˉ¹¹), located in the 25Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were 'Hapmap27934-BTC-065223' (P = 4.04×10ˉ¹¹) in 25.2 Mb, 'BTB-01143580' (P = 6.35×10ˉ¹¹) in 24.3 Mb, 'Hapmap30932-BTC-011225' (P = 5.92×10ˉ¹⁰) in 24.8 Mb, 'Hapmap27112-BTC-063342' (P = 5.18×10ˉ⁹) in 25.4 Mb, and 'Hapmap24414-BTC-073009' (P = 7.38×10ˉ⁸) in 25.4 Mb, all on BTA 14. One SNP ('BTB-01143580'; P = 6.35×10ˉ¹¹) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP ('BTB-01280026'; P = 4.02×10ˉ¹¹) had 16.96 kg of allele substitution effect, and the second most significant SNP ('Hapmap27934-BTC-065223'; P = 4.04×10ˉ¹¹) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

KW - Quantitative Genetics (incl Disease and Trait Mapping Genetics)

UR - https://www.scopus.com/pages/publications/84885072169

U2 - 10.1371/journal.pone.0074677

DO - 10.1371/journal.pone.0074677

M3 - Article

SN - 1932-6203

VL - 8

SP - 1

EP - 9

JO - PLoS One

JF - PLoS One

IS - 10

M1 - e74677

ER -

Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

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