Mol Biol Rep (2012) 39:4083–4090 DOI 10.1007/s11033-011-1190-7
Fatty acid composition of beef is associated with exonic nucleotide variants of the gene encoding FASN Dongyep Oh • Yoonseok Lee • Boomi La • Jungsou Yeo • Euiryong Chung • Younyoung Kim Chaeyoung Lee
•
Received: 18 June 2011 / Accepted: 11 July 2011 / Published online: 20 July 2011 Ó Springer Science+Business Media B.V. 2011
Abstract Genetic associations of fatty acid composition with exonic single nucleotide polymorphisms (SNPs) in the gene encoding fatty acid synthase (FASN) were examined using 513 Korean cattle. All five individual SNPs of g.12870 T[C, g.13126 T[C, g.15532 C[A, g.16907 T[C and g.17924 G[A were associated with a variety of fatty acid compositions and further with marbling score (P \ 0.05). Their genotypes of CC, TT, AA, TT, and GG were associated with increased monounsaturated fatty acids and with decreased saturated fatty acids (P \ 0.05). The genotypes at all the SNPs also increased marbling score (P \ 0.05). Further genetic associations with fatty acid composition suggested that homozygous genotype with the haplotype of ATG at g.15532, g.16907, and g.17924 in a linkage disequilibrium block increased monounsaturated fatty acids and marbling score (P \ 0.05). We concluded that the five exonic SNPs of
Electronic supplementary material The online version of this article (doi:10.1007/s11033-011-1190-7) contains supplementary material, which is available to authorized users. D. Oh B. La J. Yeo School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, South Korea Y. Lee Institute of Charmpoom Hanwoo, Gyeongsan, Gyeongbuk 712-210, South Korea E. Chung Division of Animal Science and Resources, Sangji University, Wonju, Gangwon 220-702, South Korea Y. Kim C. Lee (&) School of Systems Biomedical Science, Soongsil University, Seoul 156-743, South Korea e-mail:
[email protected]
g.12870, g.13126, g.15532, g.16907, and g.17924 in the FASN gene could change fatty acid contents. Their genotypes of CC, TT, AA, TT, and GG and haplotype of ATG at g.15532, g.16907, and g.17924 were recommended for genetic improvement of beef quality. Keywords Beef flavor Fatty acid composition Genetic association Unsaturated fatty acid
Introduction Fatty acid composition of beef has been a great concern to producers and consumers because of its significant roles in beef flavor and human health. For example, oleic acid has been known to contribute to beef flavor [1], and saturated fatty acids such as myristic acid and palmitic acid have been known to contribute to susceptibility to cardiovascular diseases [2]. Nevertheless, genetic architecture for the fatty acid composition is quite limitedly known. Recently, genetic associations of the fatty acid composition in beef cattle were identified with multiple nucleotide sequence variants in the gene encoding fatty acid synthase (FASN), a complex homodimeric enzyme regulating biosynthesis of long-chain fatty acids [3]. Five variants of g.17250–17251 AT Indel, g.16907 T[C, g.15532 C[A, g.15603 G[A, and g.17924 G[A turned out to be associated with the portion of myristic acid in adipose tissue of a beef cattle crossbred between Jersey and Limousin (P \ 0.05) [4]. Another crossbred produced from Japanese Black cattle and Limousin showed associations of fatty acid composition with g.16024 A[G and g.16039 T[C (P \ 0.05) [5]. Associations of g.17924 G[A and g.18663 T[C were identified with oleic acid of adipose tissue in Japanese Black cattle (P \ 0.05) [6]. These results suggested that allelic
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substitution of single nucleotide polymorphism (SNP) in the FASN gene would change beef flavor, and thus contribute to beef quality. This study aimed to conduct a genetic association analysis for the fatty acid composition of Korean cattle with FASN gene using exonic SNPs which can change nucleotide of mature mRNA.
Materials and methods Animals and phenotypes A total of 513 Korean cattle (called Hanwoo in Korean) produced with 18 sires in Gyeongbuk, Korea was used in the current study. They were all steers slaughtered at 941 ± 72 days of age, and carcass phenotypes were measured 24 h after slaughter. First, carcass was dissected at the last rib and the first lumber vertebra according to Animal Product Grading System of Korea. Both sides of carcass were summed up as carcass weight with the average carcass weight of 427.25 kg. Back fat thickness and marbling score were measured or scored in the left carcass cut across the vertebra between the last thoracic vertebra and the first lumbar vertebra. The marbling degree was scored from 1 to 9 with the mean of 5.43 where a larger score meant more abundant intramuscular fat (Table 1, Supplementary Fig. 1). Table 1 Phenotypic mean and standard deviation (SD) of Korean cattle used in the current genetic association analysis
Trait
Total lipids were extracted from approximately 500 mg of longissimus muscle with chloroform/methanol (2/1, v/v) [7] and then methylated with sodium methylate [8]. They were filtered through a filter paper in a water bath (40°C). The filtrate was mixed with distilled water, from which a layer of methanol and water was removed. After removal of the chloroform and lipid layers using nitrogen gas, the sample was treated with BF3-methanol (14%) and then subjected to transmethylation at 65°C. Contents of fatty acids were analyzed using gas-chromatography (PerkinElmer, Inc., Waltham, MA, USA). They included myristic acid, palmitic acid, stearic acid, myristoleic acid, palmitoleic acid, oleic acid, linoleic acid, and linolenic acid. The compositions and their functions were used as phenotypes for genetic association analyses (Table 1). Genotypes Genomic DNA was extracted from longissimus muscle TM using a LaboPass Tissue Mini kit (Cosmo Genetech, Seoul, Korea). Exonic SNPs in FASN gene were selected based on the nucleotide sequence of the bovine FASN gene in GenBank (Accession no. AF285607). Genotypes at ten SNPs were preliminary analyzed. Primers for amplification and extension were designed for single-base extension [9] using forward, reverse, and extension primer sequences (Supplementary Table 1). Reactions of primer extension were
Description
Mean
SD
Fatty acid composition (%) C14:0
Myristic acid
3.63
0.65
C16:0
Palmitic acid
25.65
1.96
C18:0
Stearic acid
10.48
1.39
C14:1
Myristoleic acid
1.24
0.38
C16:1
Palmitoleic acid
6.61
0.97
C18:1
Oleic acid
44.30
2.66
C18:2n6
Linoleic acid
3.02
0.76
C18:3n3
Linolenic acid
0.35
0.20
SFA
Saturated fatty acid
40.60
2.86
MUFA
Monounsaturated fatty acid
53.50
2.96
Fatty acid index M/S3
MUFA/SFA
1.32
0.16
IC14
[C14:1/(C14:0 ? C14:1)] 9 100
25.37
6.37
IC16
[C16:1/(C16:0 ? C16:1)] 9 100
20.50
2.81
IC18
[C18:1/(C18:0 ? C18:1)] 9 100
80.86
2.43
427.25
43.28
13.22 5.43
5.13 1.93
Carcass trait
123
CW (kg)
Carcass weight
BFT (cm) MS
Backfat thickness Marbling score
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performed using SNaPshot ddNTP Primer Extension Kit (Applied Biosystems, Foster City, CA, USA). To purify reactions of primer extension, mixtures containing exonuclease 1 and shrimp alkaline phosphatase were added to the reaction mixtures. Samples were cultured at 37°C for 1 h and then inactivated at 72°C for 15 min. PCR products were mixed with Genescan 120 LIZ standard and HiDi formamide (Applied Biosystems), followed by denaturation at 95°C for 5 min. Electrophoresis was performed using an ABI PRISM 3130XL Genetic Analyzer. Then, electrophoresis products were assayed using GeneMapper v.4.0 software (Applied Biosystems).
Statistical analysis Hardy–Weinberg equilibrium (HWE) was tested for each locus in the Korean cattle population by employing a Chisquare statistic. Associations of fatty acid composition and carcass traits with individual SNPs were analyzed using the following mixed model using SPSS v19.0 (SPSS Inc., Chicago, IL, USA). Yijk ¼ l þ Si þ Pj þ Gk þ b age þ eijk
where Yijkl is a phenotype, l is overall mean, Si is a random effect of sire i with an assumption of independent and identical Normal distribution, Pj is a fixed effect of calving place j (14 classes), Gk is a fixed effect of genotype k, b is a regression coefficient, age is a covariate for age in days at slaughter, eijk is a random residual assumed to have independent and identical Normal distribution. This genetic association model was applied to haplotype analysis as well as individual SNP analysis by replacing genotype effect with haplotype effect (Hk). The genotype and haplotype effects were estimated with variance components estimated based on restricted maximum likelihood. For haplotype analysis, pairwise linkage (r2) was estimated, and linkage disequilibrium blocks were identified by the 4-gamete rule using Haploviewer v4.2 [10]. Probability for phase was inferred for each individual using PHASE (http://depts.washington. edu/uwc4c/express-licenses/assets/phase/).
Results A preliminary analysis for genotype frequencies of ten candidate SNPs in exons of FASN gene showed five
Table 2 Genotype frequency distribution of exonic variants in FASN gene in Korean cattle SNP
Exon
Genotype
Ha
MAFb
HWEc
0.00
0.00
–
0.00
0.00
–
frequency (N) g.841 C[G g.10671 G[C
1 19
CC
CG
GG
1.000 (44)
0.000 (0)
0.000 (0)
GG
GC
CC
1.000 (44)
0.000 (0)
0.000 (0)
g.11319 G[A
21
GG
GA
AA
0.00
0.00
–
g.12870 T[C
23
1.000 (44) TT
0.000 (0) TC
0.000 (0) CC
0.48
0.41
0.429
0.386 (17)
0.409 (18)
0.205 (9)
CC
CT
TT
0.50
0.47
0.936
0.250 (11)
0.523 (23)
0.227 (10) 0.00
0.00
–
0.36
0.28
0.681
0.41
0.28
0.168
0.25
0.12
0.962
0.00
0.00
–
g.13126 T[C g.14284 C[T g.15532 C[A
24 28 34
CC
CT
TT
1.000 (44)
0.000 (0)
0.000 (0)
CC
CA
AA
0.591 (26)
0.341 (15)
0.068 (3)
TC
CC
g.16907 T[C
37
TT 0.614 (27)
0.205 (9)
0.182 (8)
g.17924 G[A
39
GG
GA
AA
0.727 (32)
0.250 (11)
0.023 (1)
TT
TC
CC
1.000 (44)
0.000 (0)
0.000 (0)
g.18663 T[C a
42
Heterozygosity
b
Minor allele frequency
c
P-value for testing Hardy–Weinberg equilibrium
123
123
TT
160
Genotype
N
25.86 ± 0.13b
25.80 ± 0.15b
10.58 ± 0.11
1.24 ± 0.03
C16:0
C18:0
C14:1
80.47 ± 0.20a
IC18
353
N
2.95 ± 0.04
0.37 ± 0.01
C18:3n3
43.87 ± 0.20b
6.60 ± 0.05
44.69 ± 0.14b
C16:1
C18:1
C18:2n6
6.67 ± 0.08
10.42 ± 0.07a 1.23 ± 0.02ab
C18:0 C14:1
b
0.32 ± 0.01
3.17 ± 0.06
ab
ab
10.45 ± 0.13a 1.30 ± 0.04b
25.83 ± 0.16
25.44 ± 0.10
C16:0
a
5.76 ± 0.17b
12.58 ± 0.41
b
a
0.27 ± 0.03
3.27 ± 0.13
a
b
41.10 ± 0.48a
6.36 ± 0.20
11.51 ± 0.36b 1.08 ± 0.09a
27.69 ± 0.37
b
5.17 ± 0.15a
12.99 ± 0.38
425.13 ± 3.28
80.37 ± 0.19a
20.28 ± 0.22
24.45 ± 0.44
1.29 ± 0.01a
52.70 ± 0.23
a
41.22 ± 0.22
0.30 ± 0.01a
43.54 ± 0.20a 3.18 ± 0.06b
6.59 ± 0.07
1.23 ± 0.02
10.63 ± 0.11
25.92 ± 0.15b
3.77 ± 0.05b
163
CC
g.13126 T[C
4.13 ± 0.13b
25
CC
428.60 ± 3.50
81.45 ± 0.21b
20.79 ± 0.24
3.57 ± 0.03a
a
b
27.22 ± 0.62
1.39 ± 0.01b
b
54.77 ± 0.24
3.71 ± 0.05a
135
TC
a
39.73 ± 0.23
0.41 ± 0.01b
45.50 ± 0.20b 2.81 ± 0.06a
C14:0 a
TT
Genotype
Fatty acid composition (%)
g.16907 T[C
5.44 ± 0.12ab
SNP
13.67 ± 0.36
13.14 ± 0.40
5.13 ± 0.15a
BFT (cm)
MS
428.64 ± 3.12
424.21 ± 3.28
CW (kg)
Carcass trait
80.77 ± 0.15a
20.40 ± 0.23
24.69 ± 0.42 20.39 ± 0.19
24.73 ± 0.43
IC16
a
IC14
1.31 ± 0.01a
53.23 ± 0.19
1.29 ± 0.01a
a
52.81 ± 0.24
M/S3
Fatty acid index
MUFA
a
40.83 ± 0.18
a
41.04 ± 0.23
SFA
b
0.34 ± 0.01a
0.31 ± 0.01a
C18:3n3
b
44.04 ± 0.16a 3.05 ± 0.04b
6.60 ± 0.08
6.62 ± 0.06
6.60 ± 0.07
43.63 ± 0.22a 3.17 ± 0.06b
C16:1
C18:1 C18:2n6
1.29 ± 0.03
10.37 ± 0.13
25.15 ± 0.15a
3.44 ± 0.05a
136
CC
1.22 ± 0.02
10.48 ± 0.08
3.68 ± 0.04b
3.75 ± 0.05b
217
TC
C14:0
Fatty acid composition (%)
g.12870 T[C
SNP
b
a
a
0.37 ± 0.01
b
2.95 ± 0.04
a
44.69 ± 0.13b
6.59 ± 0.05
10.43 ± 0.07a 1.23 ± 0.02b
25.43 ± 0.10
3.57 ± 0.03a
358
GG
g.17924 G[A
5.40 ± 0.13ab
13.75 ± 0.37
428.61 ± 3.18
80.77 ± 0.15a
20.41 ± 0.19
24.82 ± 0.43
1.31 ± 0.01a
53.23 ± 0.19
a
40.83 ± 0.19
0.34 ± 0.01b
44.03 ± 0.17a 3.05 ± 0.04b
6.63 ± 0.07
1.23 ± 0.03
10.48 ± 0.09
25.85 ± 0.13b
3.67 ± 0.04b
209
CT
Table 3 Genotypic effects of exonic variants in FASN gene on fatty acid composition of intramuscular fat
a
b
a
0.31 ± 0.01
3.17 ± 0.05
ab
ab
43.84 ± 0.19b
6.67 ± 0.09
10.44 ± 0.13a 1.29 ± 0.04b
25.89 ± 0.16
3.72 ± 0.05a
134
GA
5.76 ± 0.17b
12.70 ± 0.41
427.67 ± 3.42
81.55 ± 0.20b
20.86 ± 0.23
27.26 ± 0.60
1.40 ± 0.01b
54.80 ± 0.24
b
39.55 ± 0.24
0.42 ± 0.02c
45.57 ± 0.21b 2.79 ± 0.06a
6.60 ± 0.07
1.28 ± 0.03
10.31 ± 0.12
25.05 ± 0.15a
3.42 ± 0.05a
141
TT
b
b
5.48 ± 0.11a
13.07 ± 0.30
428.23 ± 2.63
80.95 ± 0.13ab
20.52 ± 0.16
25.29 ± 0.36
1.33 ± 0.01a
53.53 ± 0.16
a
40.54 ± 0.16
0.35 ± 0.01a
44.37 ± 0.15b 3.03 ± 0.04b
6.61 ± 0.06
1.24 ± 0.02
10.44 ± 0.08
25.62 ± 0.11b
3.64 ± 0.04b
279
CA
0.28 ± 0.03a
3.34 ± 0.15b
40.68 ± 0.49a
6.34 ± 0.21
11.62 ± 0.38b 1.05 ± 0.09a
27.82 ± 0.42b
4.20 ± 0.13b
21
AA
5.10 ± 0.15a
13.78 ± 0.41
425.14 ± 3.27
80.44 ± 0.20a
20.37 ± 0.23
24.96 ± 0.52
1.29 ± 0.01a
52.84 ± 0.22
a
41.09 ± 0.22
0.32 ± 0.01a
43.62 ± 0.19a 3.15 ± 0.05b
6.63 ± 0.08
1.24 ± 0.03
10.61 ± 0.12
25.93 ± 0.15b
3.71 ± 0.05b
179
CC
g.15532 C[A
6.05 ± 0.22b
12.40 ± 0.54
428.49 ± 4.77
81.53 ±0.27b
20.76 ± 0.33
26.78 ± 0.79
1.41 ± 0.02b
55.10 ± 0.39b
39.61 ± 0.38a
0.42 ± 0.03b
45.76 ± 0.35c 2.65 ± 0.10a
6.54 ± 0.10
1.26 ± 0.04
10.34 ± 0.15
25.07 ± 0.28a
3.43 ± 0.08a
65
AA
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5.53 ± 0.10
5.39 ± 0.17
a
4.20 ± 0.39
a
15.52 ± 1.14b
428.36 ± 10.36
18.71 ± 0.62 78.15 ± 0.59a
a
20.45 ± 1.30
1.15 ± 0.03a
50.11 ± 0.52
a
43.84 ± 0.56b
CC
b
5.53 ± 0.10
b
12.86 ± 0.26a
429.25 ± 2.33
20.62 ± 0.14 81.06 ± 0.12b
b
25.61 ± 0.31
1.35 ± 0.01b
53.87 ± 0.15
b
40.28 ± 0.15a
GG
g.17924 G[A
b
5.39 ± 0.17
b
13.74 ± 0.46a
423.30 ± 3.54
20.49 ± 0.24 80.78 ± 0.21b
b
25.62 ± 0.59
1.31 ± 0.01b
53.13 ± 0.23
b
40.90 ± 0.23a
GA
3.90 ± 0.40a
16.00 ± 1.32b
418.33 ± 9.65
18.61 ± 0.68a 77.82 ± 0.63a
19.78 ± 1.40a
1.13 ± 0.03a
49.68 ± 0.54a
44.10 ± 0.63b
AA
SFA Saturated fatty acid, MUFA Mono unsaturated fatty acid, M/S Mono unsaturated fatty acid/Saturated fatty acid, IC14 [C14:1/(C14:0 ? C14:1)] 9 100, IC16 [C16:1/ (C16:0 ? C16:1)] 9 100, IC18 [C18:1/(C18:0 ? C18:1)] 9 100, CW carcass weight, BFT backfat thickness, MS marbling score from 1 to 9 indicating that a larger score means more abundant intramuscular fat
Means with different superscripts in the same row within each SNP indicate statistical difference with P \ 0.05
MS
b
13.62 ± 0.46ab
b
425.10 ± 3.30
427.99 ± 2.36
12.90 ± 0.26a
20.52 ± 0.25 80.78 ± 0.21b
b
b
CW (kg)
20.62 ± 0.14 80.08 ± 0.12b
25.75 ± 0.59
1.31 ± 0.01b
BFT (cm)
Carcass trait
IC16 IC18
b
25.58 ± 0.32
IC14
b
1.35 ± 0.01b
M/S3
Fatty acid index
MUFA
53.16 ± 0.24
b
53.88 ± 0.15
40.84 ± 0.24a
40.28 ± 0.15a b
TT
Genotype
SFA
TC
g.16907 T[C
SNP
Table 3 continued
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monomorphic loci in Korean cattle (Table 2), and they were excluded in the following genetic association analysis. The other loci had their minor allele frequencies ranged from 0.12 to 0.47, and their genotypes were not deviated from the Hardy–Weinberg equilibrium (P [ 0.05, Table 2). The selected 5 SNPs were associated with a variety of fatty acid compositions (P \ 0.05, Table 3). Especially, g.16907 T[C and g.17924 G[A were associated with all the phenotypes of fatty acid compositions except for palmitoleic acid (C16:1). Their homozygous genotypes with minor alleles increased the portion of palmitic acid (C16:0, saturated fatty acid) and decreased the portion of oleic acid (C18:1, monounsaturated fatty acid). The five SNPs were also associated with marbling score, but not with carcass weight (P \ 0.05, Table 3). Backfat thickness was associated only with the SNPs of g.16907 T[C and g.17924 G[A. Individuals with their minor alleles had larger backfat thickness and smaller marbling score than those with their major alleles. Two blocks were produced based on the estimates of linkage disequilibrium between SNPs (Table 4, Supplementary Fig. 1). Block 1 included g.12870 T[C in exon 23 and g.13126 T[C in exon 24, and Block 2 included g.15532 C[A in exon 34, g.16907 T[C in exon 37, and g.17924 G[A in exon 39. Haplotypic associations of each block were found with fatty acid compositions (P \ 0.05, Table 5). The haplotypes were also associated with backfat thickness and marbling score (P \ 0.05), but not with carcass weight (P [ 0.05, Table 5) as shown in the single locus analysis.
Discussion The current study identified associations of 5 exonic SNPs in FASN gene with a variety of fatty acid compositions of Korean cattle. They were all further associated with marbling score. This implied that the SNPs might be critical genetic markers in improving beef quality. They were partitioned into Block 1 and Block 2 based on linkage disequilibrium. The genetic associations of fatty acid
composition with 2 individual SNPs in Block 1 (g.12870 T[C in exon 23 and g.13126 T[C in exon 24) were novel. On the other hand, the associations with the other three SNPs in Block 2 concurred with previous studies in which they were associated with proportions of specific fatty acids. The three SNPs in exons 34 (g.15532 C[A), 37 (g.16907 T[C), and 39 (g.17924 G[A) were all associated with myristic acid in a crossbred of Limousin and Jersey (P \ 0.05) [4]. The g.17924 was associated also with oleic acid in American Angus cattle (P \ 0.05) [6] and Korean cattle (P \ 0.05) [11]. Some of these SNPs might change their functions by producing missense codons. The g.13126 T[C in Block 1 changes an amino acid from tyrosine to histidine. The g.15532 C[A or g.17924 G[A in Block 2 changes an amino acid from leucine to isoleucine or from alanine to threonine. Although the other SNPs are synonymous, we could not rule out a possibility that they might change splicing regulatory sequences. Or such genetic associations might be spuriously produced with their linked loci within each block. Homozygous genotypes with C, T, A, T, and G allele at g.12870, g.13126, g.15532, g.16907, and g.17924 increased the proportion of oleic acid, the major content of monounsaturated fatty acids, and thus increased the proportion of monounsaturated fatty acids. Similarly, they decreased the proportion of palmitic acid, the major content of saturated fatty acids, and thus decreased the proportion of saturated fatty acids. This concurred with the study of Zhang et al. [6] where GG genotype of g.17924 increased oleic acid and reduced palmitic acid in American Angus (P \ 0.05). Furthermore, the current study revealed that individuals with the same genotype above had large marbling scores at all the SNPs. These pleiotropic effects suggested a desirable selection strategy for beef cattle with the favorable genotypes of all the SNP. In this regard, Korean cattle are more qualified than other breeds. Especially, the G allele frequency at g.17924 was 0.83 in the Korean cattle, which was quite larger than that in American Angus (0.38) [6]. The genetic associations with fatty acid composition could be strengthened by employing haplotype analysis in this study. Especially, homozygous genotype with the
Table 4 Haplotype frequency distribution of exonic variants by linkage disequilibrium (LD) block of FASN gene in Korean cattle Block 1
g.12870 T[C
g.13126 T[C
Frequency
Block 2
g.15532 C[A
g.16907 T[C
g.17924 G[A
Frequency
Ht1
T
C
0.5053
ht1
C
T
G
0.4193
Ht2
C
T
0.4604
ht2
A
T
G
0.3968
Ht3
T
T
0.0177
ht3
C
C
A
0.1677
Ht4
C
C
0.0166
ht4
C
C
G
0.0122
ht5
C
T
A
0.0022
ht6
A
T
A
0.0018
123
ab
b
b
b
53.22 ± 0.19b 1.31 ± 0.01b a
ab
c
41.48 ± 0.21
52.43 ± 0.21a
a
MUFA
Fatty acid index M/S 1.27 ± 0.01a
a
SFA
80.19 ± 0.20a
IC18
5.05 ± 0.14
5.41 ± 0.13
ab
13.68 ± 0.37b
427.96 ± 3.21
80.77 ± 0.15b
20.43 ± 0.19
24.76 ± 0.44
40.83 ± 0.19
0.34 ± 0.01
a
a
b
5.87 ± 0.17
b
12.30 ± 0.40a
428.10 ± 3.52
81.67 ± 0.21c
21.00 ± 0.24
27.57 ± 0.62
b
1.41 ± 0.01c
55.12 ± 0.25c
39.35 ± 0.24
0.43 ± 0.02
c
2.73 ± 0.07a
45.83 ± 0.22c
6.62 ± 0.08
1.29 ± 0.03
10.28 ± 0.12
24.92 ± 0.16
a
5.21 ± 0.22
b
13.27 ± 0.57ab
427.06 ± 4.96
80.67 ± 0.25bc
20.64 ± 0.33
b
25.75 ± 0.73
b
1.32 ± 0.01b
53.27 ± 0.30b
40.66 ± 0.29
ab
0.33 ± 0.02
ab
3.09 ± 0.07bc
44.09 ± 0.25b
6.65 ± 0.11
1.26 ± 0.04
10.56 ± 0.14
a
25.55 ± 0.19
ab
3.59 ± 0.06ab a
ab
b
5.50 ± 0.12
bc
12.87 ± 0.35a
429.37 ± 3.18
81.08 ± 0.15bc
20.56 ± 0.18
25.12 ± 0.38
b
1.34 ± 0.01b
53.72 ± 0.19b
40.34 ± 0.18
0.37 ± 0.01
bc
2.98 ± 0.05ab
44.59 ± 0.18b
6.60 ± 0.06
1.21 ± 0.02
10.39 ± 0.09
25.50 ± 0.13
ab
3.61 ± 0.04ab
ht1*ht2 (N = 201)
5.34 ± 0.25
bc
13.66 ± 0.73ab
416.98 ± 4.78
81.02 ± 0.33bc
20.54 ± 0.35
b
25.46 ± 0.89
b
1.32 ± 0.02b
53.28 ± 0.35b
40.67 ± 0.35
ab
0.33 ± 0.02
ab
3.17 ± 0.09bc
43.94 ± 0.29b
6.68 ± 0.13
1.27 ± 0.05
10.32 ± 0.22
a
25.82 ± 0.25
ab
3.71 ± 0.08b
ht1*ht3 (N = 56)
a
a
b
6.05 ± 0.22
5.47 ± 0.24
bc
13.70 ± 0.63ab
428.62 ± 4.56
80.51 ± 0.29b
20.39 ± 0.36
b
25.69 ± 0.85
b
1.30 ± 0.02b
52.98 ± 0.34b
41.09 ± 0.33
b
0.30 ± 0.02
ab
3.18 ± 0.08bc
43.76 ± 0.28b
6.64 ± 0.11
1.31 ± 0.05
10.58 ± 0.16
a
25.91 ± 0.21
b
3.73 ± 0.07b
ht2*ht3 (N = 73)
3.90 ± 0.40a
16.00 ± 1.32b
418.33 ± 9.65
77.82 ± 0.63a
18.61 ± 0.67a
19.77 ± 1.40a
1.13 ± 0.03a
49.68 ± 0.54a
44.10 ± 0.63c
0.28 ± 0.03a
3.34 ± 0.15c
40.68 ± 0.49a
6.34 ± 0.21
1.05 ± 0.09
11.62 ± 0.38b
27.82 ± 0.42c
4.20 ± 0.13c
ht3*ht3 (N = 21)
SFA Saturated fatty acid, MUFA Mono unsaturated fatty acid, M/S Mono unsaturated fatty acid/Saturated fatty acid, IC14 [C14:1/(C14:0 ? C14:1)] 9 100, IC16 [C16:1/ (C16:0 ? C16:1)] 9 100, IC18 [C18:1/(C18:0 ? C18:1)] 9 100, CW carcass weight, BFT backfat thickness, MS marbling score from 1 to 9 indicating that a larger score means more abundant intramuscular fat
c
12.40 ± 0.54a
428.49 ± 4.76
81.53 ± 0.27c
20.76 ± 0.32
26.78 ± 0.79
b
1.40 ± 0.02c
55.70 ± 0.39c
39.60 ± 0.37
0.42 ± 0.02
c
2.64 ± 0.10a
46.16 ± 0.32c
6.54 ± 0.10
1.26 ± 0.04
10.34 ± 0.15
25.06 ± 0.27
a
3.43 ± 0.07a
ht2*ht2 (N = 65)
Means with different superscripts in the same row within each linkage disequilibrium block indicate statistical difference with P \ 0.05
MS
13.12 ± 0.40ab
a
424.33 ± 3.34
CW (kg)
BFT (cm)
Carcass trait
20.19 ± 0.23
24.21 ± 0.42
IC16
IC14
C18:3n3
0.28 ± 0.01
3.05 ± 0.04b
3.25 ± 0.05c
a
6.59 ± 0.08
43.27 ± 0.19a
C16:1
C18:1
C18:2n6
6.63 ± 0.06 44.02 ± 0.17b
1.22 ± 0.02
C14:1
1.22 ± 0.03
10.68 ± 0.11
10.48 ± 0.09
25.84 ± 0.14
b
b
26.04 ± 0.14
3.68 ± 0.04b
3.81 ± 0.05b
C18:0
C16:0
C14:0
3.39 ± 0.05a
ht1*ht1 (N = 84)
Ht2/Ht2 (N = 135)
Ht1/Ht1 (N = 153)
Ht1/Ht2 (N = 205)
LD Block 2
LD Block 1
Fatty acid composition (%)
Trait
Table 5 Haplotypic effects within each linkage disequilibrium (LD) block in FASN gene on fatty acid composition of intramuscular fat
Mol Biol Rep (2012) 39:4083–4090 4089
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4090
haplotype of ATG at g.15532, g.16907, and g.17924 in Block 2 was recommended for genetic improvement of beef quality by increasing unsaturated fatty acids and intramuscular marbling degree. Simultaneous use of multiple markers would accelerate genetic improvement by such haplotypic effects here or by epistatic effects as shown in the study of Ryu et al. [12] where marbling score was influenced by epistasis among genes in a pathway of fat and energy metabolism. In conclusion, Korean cattle with the individual genotype of CC, TT, AA, TT, or GG at the exonic SNP of g.12870, g.13126, g.15532, g.16907, or g.17924 in the FASN gene had a larger proportion of monounsaturated fatty acids and a smaller proportion of saturated fatty acids. The genotypes also increased marbling scores. These genotypes of the individual SNPs and their haplotypes might be remarkable genetic markers for improving beef quality, which is one of the most important goals to the Korean beef cattle industry [13]. Acknowledgments This work was supported by a grant from NextGeneration BioGreen 21 Program, Rural Development Administration, Republic of Korea (Grant No. PJ008135).
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