J. Dairy Sci. 2009. 92:4676-4682. doi:10.3168/jds.2008-1965
© 2009 American Dairy Science Association ®
Short communication: Genome-wide scan for bovine milk-fat composition. II. Quantitative trait loci for long-chain fatty acids
A. Schennink1,2,
W. M. Stoop2,
M. H. P. W. Visker,
J. J. van der Poel,
H. Bovenhuis and
J. A. M. van Arendonk
Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH Wageningen, the Netherlands
1 Corresponding author: aschennink{at}ucdavis.edu
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ABSTRACT
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We present the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in long-chain milk fatty acids. Milk-fat composition phenotypes were available on 1,905 Dutch Holstein-Friesian cows. A total of 849 cows and their 7 sires were genotyped for 1,341 single nucleotide polymorphisms across all Bos taurus autosomes (BTA). We detected significant QTL on BTA14, BTA15, and BTA16: for C18:1 cis-9, C18:1 cis-12, C18:2 cis-9,12, CLA cis-9,trans-11, C18:3 cis-9,12,15, the C18 index, the total index, total saturated fatty acids, total unsaturated fatty acids (UFA), and the ratio of saturated fatty acids:unsaturated fatty acids on BTA14; for C18:1 trans fatty acids on BTA15; and for the C18 and CLA indices on BTA16. The QTL explained 3 to 19% of the phenotypic variance. Suggestive QTL were found on 16 other chromosomes. The diacylglycerol acyltransferase 1 (DGAT1) K232A polymorphism on BTA14, which is known to influence fatty acid composition, most likely explains the QTL that was detected on BTA14.
Key Words: fatty acid • quantitative trait locus • dairy cow • diacylglycerol acyltransferase 1
Milk-fat is characterized by a high amount of saturated fatty acids (SFA), especially the medium-chain fatty acids (FA) C14:0 and C16:0, and by a low amount of (poly)unsaturated FA. Whereas the medium-chain FA C16:0 is commonly considered to have a negative effect on human health because of its cholesterol-raising properties, long-chain FA of 18 or more carbon atoms are considered to have neutral or positive effects (Mensink et al., 2003). Of the long-chain FA, special attention is paid to conjugated linoleic acids (CLA) because of their supposed role in the modulation of plasma lipid concentrations, and their anticarcinogenic and antiinflammatory effects, as shown in studies mostly performed in cell lines and animal models (Haug et al., 2007). Long-chain FA in the mammary gland are not synthesized de novo, but are derived from circulating plasma lipids (Harfoot and Hazlewood, 1997).
Genetic variation in bovine milk-fat composition has been shown in several recent studies (Soyeurt et al., 2007; Bobe et al., 2008; Stoop et al., 2008). Although estimated heritabilities for the individual FA vary between studies, all reveal substantial genetic variation between cows and suggest opportunities to improve composition of milk-fat by selective breeding. Studies have revealed several QTL affecting milk-fat percentage and milk-fat yield in several cattle populations (Khatkar et al., 2004). However, a genome-wide scan for QTL affecting milk-fat composition is lacking. Morris et al. (2007) performed QTL mapping for fat composition of milk and adipose tissue on a single chromosome, Bos taurus autosome (BTA) 19, and identified a QTL with significant effects on, among others, C18 FA. They identified fatty acid synthase (FASN) as a candidate gene. Association studies showed that mutations in candidate genes diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-coenzyme A desaturase 1 (SCD1) were also associated with milk-fat composition (Mele et al., 2007; Moioli et al., 2007; Schennink et al., 2007, 2008). Although these genes have shown major effects, a large proportion of the genetic variation in milk-fat composition still cannot be attributed to specific chromosomal regions or genes. The objective of this study was to present the results of the first genome-wide scan to map QTL contributing to the genetic variation in long-chain FA composition of bovine milk.
Milk-fat composition phenotypes were available on 1,905 Dutch Holstein-Friesian cows. For the genome scan, genotypes were available from 7 paternal half-sib families of 849 cows and 7 sires in total. The 849 were genotyped for 1,341 SNP across all autosomes. The QTL analyses were performed using an across-family regression on corrected phenotypes. A detailed description of animals, phenotypes, genotypes, and the QTL analysis is given in the companion paper (Stoop et al., 2009) on QTL for short- and medium-chain FA. In the present study, 21 traits were analyzed: milk-fat percentage; the individual FA C18:0, C18:1 cis-9, C18:1 cis-11, C18:1 cis-12, C18:1 trans-4–8, C18:1 trans-9, C18:1 trans-10, C18:1 trans-11, C18:2 cis-9,12, C18:2 cis-9,trans-11 (CLA), C18:3 cis-9,12,15, C19:0, and C20:0; the group C18:1 trans FA; the group SFA (C4:0 to C18:0 and C20:0); the group unsaturated FA (UFA: mono- and polyunsaturated C10 to C18); the ratio SFA:UFA; and the unsaturation indices for C18, CLA, and total FA. Means, standard deviations, and intraherd heritabilities of the traits, as calculated according to Stoop et al. (2008), are shown in Table 1.
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Table 1. Mean, phenotypic standard deviation ( P) and intraherd heritability (h2) and standard error (subscript) of all traits included in the analysis, measured on 1,905 cows
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Quantitative trait loci for long-chain milk FA were identified on several chromosomes and are summarized in Table 2. There was significant statistical evidence (Pgenome 
0.05) for QTL on BTA14, BTA15, and BTA16. Figure 1a to 1d gives graphical presentations of QTL. Suggestive QTL (Pchromosome 0.05) were found on 16 other chromosomes. Allele substitution effects for the significant QTL on BTA14, BTA15, and BTA16 are shown in Table 3. The identification of QTL for long-chain FA strongly supports the hypothesis of a genetic component that influences variation for these FA, as for the short- to medium-chain FA, which was already posed by the low to moderate heritabilities. Long-chain FA are not de novo synthesized by the cow herself, but are derived from circulating plasma lipids and originate from the diet, from microbial FA synthesis in the rumen, and from endogenous lipids. Therefore, the most obvious candidate genes for long-chain FA proportions would be those involved in the uptake, desaturation, esterification, biohydrogenation, and elongation of long-chain FA. Results of significant QTL are discussed per chromosome.
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Table 2. Location and characteristics of suggestive and significant QTL affecting long-chain fatty acids, unsaturation indices, and fat percentage
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Figure 1. Quantitative trait locus mapping across families for long-chain fatty acids on a) Bos taurus autosome (BTA) 14, b) BTA14 (phenotypes precorrected for the diacylglycerol acyltransferase 1 (DGAT1) K232A and stearoyl-coenzyme A desaturase 1 (SCD1) A293V genotypes), c) BTA15, and d) BTA16. Triangles on the x-axis represent the location of the markers. The dotted black line presents the genome-wise significance threshold. Although this threshold is slightly different for each trait, only the line of the trait with the lowest genome-wise significance threshold for each chromosome is shown. For b), all shown QTL are suggestive.
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Table 3. Allele substitution effects and standard errors (in subscript) within 7 paternal half-sib families for QTL on BTA14, BTA15, and BTA16, and approximate phenotypic variation explained by the QTL
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On BTA14, a QTL for fat percentage was found at the centromeric end of the chromosome. At the same position, significant evidence for QTL was detected for C18:1 cis-9, C18:1 cis-12, C18:2 cis-9,12, CLA cis-9,trans-11, C18:3 cis-9,12,15, the C18 index, the total index, SFA, UFA, and the ratio SFA:UFA (Table 2, Figure 1a). Families 1, 2, 3, 4, and 7 segregated for the QTL for fat percentage, C18:1 cis-9, and C18:3 cis-9,12,15 on BTA14 (Table 3). These families, but not necessarily all 5, also contributed to the QTL for the other traits. Families 5 and 6 did not segregate for any of the QTL on BTA14. The difference in fat percentage between the 2 daughter groups inheriting alternative sire alleles was 0.53, 0.69, 0.70, 0.68, and 0.93 in families 1, 2, 3, 4, and 7, respectively. The difference in C18:1 cis-9 between the 2 daughter groups was 1.10, 0.60, 1.37, 1.18, and 1.83% (wt/wt) in families 1, 2, 3, 4, and 7, respectively. This QTL explained 19% of the phenotypic variance for fat percentage, and 10% for C18:1 cis-9. For the other traits, this QTL explained 4 to 7% of the phenotypic variance. At the centromeric end of BTA14, QTL for several short- and medium-chain FA were detected as well (see Stoop et al., 2009). The centromeric region of BTA14 has been studied in detail in previous research on fat percentage (Farnir et al., 2002; Grisart et al., 2002; Winter et al., 2002) that revealed the role of DGAT1, which is mapped to BTA14 at 0 cM. The QTL at 0 cM was most likely caused by, or was very closely linked to, the DGAT1 K232A mutation, which was shown to affect milk-fat composition in this material (Schennink et al., 2007). The sires from segregating families 1, 2, 3, 4, and 7 were all heterozygous KA for the DGAT1 mutation, whereas sire 5 was homozygous KK, and sire 6 was homozygous AA. To validate that this QTL on BTA14 was caused by DGAT1, the combined DGAT1 K232A and SCD1 A293V genotypes were included as an additional fixed effect in the model in a second analysis. This correction resulted in the disappearance of the QTL effect on the centromeric region of BTA14 on all traits reported above (Table 2), indicating that the DGAT1 genotype was indeed responsible for this QTL effect. In the above-mentioned association study by Schennink et al. (2007, 2008), the DGAT1 232A allele was shown to be associated with more C18:1 cis-9 and more CLA cis-9,trans-11, which is in agreement with findings in the present study. The allele substitution effect for C18:1 cis-9 on BTA14 ranged between 0.60 and 1.83 for the different segregating sires. The allele substitution effect in the association study was 1.11 (calculated from contrasts between KK and KA, and KK and AA genotypes for the C18 unsaturated FA, which predominantly consists of C18:1 cis-9). Allele substitution effects for CLA cis-9,trans-11, the C18 index, the total index, and the ratio SFA:UFA are also in line with the genotype contrasts reported in the association study. Moreover, allele substitution effects showed that a lower fat percentage was correlated with more C18:1 cis-9, more CLA cis-9,trans-11, a higher C18 index, a higher total index, and a lower ratio SFA:UFA, which confirms effects of the DGAT1 232A allele in the association study.
Furthermore, a suggestive QTL at approximately 50 cM became clear for the C18:1 trans FA as a group, and for the individual FA C18:1 trans-4–8, C18:1 trans-9, C18:1 trans-10, C18:1 cis-11, and C19:0 (Figure 1b). This position also showed suggestive QTL for C10:1, C12:1, and C14:1 FA after the DGAT1/SCD1 correction (see companion paper by Stoop et al., 2009) and suggests the presence of another QTL for milk-fat composition on BTA14.
On BTA15, a QTL for the group of C18:1 trans FA was found at position 80 cM. This QTL region also affected the individual C18:1 trans FA C18:1 trans-4–8, C18:1 trans-9, and C18:1 trans-10, which, although not significant genome-wise, were suggestive (Table 2). The shape of the confidence interval and approximate position correspond to the observed similar shape of the QTL profile across families for the group of C18:1 trans FA (Figure 1c). Families 1 and 2 contributed to the QTL (Table 3), and the difference between the daughter groups in the fraction of the C18:1 trans group FA was 0.19 and 0.08% (wt/wt), respectively. The QTL explained 4% of the phenotypic variance of C18:1 trans FA. Precorrection for DGAT1/SCD1 slightly lowered the test statistic, because of which the genome-wise P-value did not exceed the 5% significance level (P = 0.08). In the rumen, dietary unsaturated FA are metabolized by ruminal microbes and, via intermediates, are reduced to C18:0 as a final end product in a process called biohydrogenation. The final reduction to C18:0, with C18:1 trans FA as common intermediates, is considered to be the rate-limiting step. When this metabolism is incomplete, C18:1 trans FA will accumulate. Among the C18:1 trans intermediates, the trans-11 isomer is the main one, but other isomers are also produced (Harfoot and Hazlewood, 1997; Shingfield et al., 2003; Loor et al., 2005). The rumen microbial population consists of, among others, several genetically very diverse bacteria, which metabolize FA by several possible routes (Edwards et al., 2004). Some kinds of C18:1 trans isomers that are produced have been reported to be specific to particular bacterial populations. We hypothesize that between-animal variation in rumen bacterial populations and the biohydrogenating activity of ruminal fluid, or both might partly be explained by genetic differences between cows (Wasowska et al., 2006; Paillard et al., 2007). The QTL on BTA15 may harbor a gene that is involved in differences in ruminal populations or ruminal activity, and thereby influence C18:1 trans FA. The route that long-chain FA undergo, from intake or adipose tissue release to triacylglycerol formation in the udder and secretion into the milk, is complex and involves many processes (e.g., lipolysis, transport, esterification), which can be influenced by different genes and affect C18:1 trans FA.
The presence of a QTL on BTA15 for C18:1 trans-4–8, C18:1 trans-9, and C18:1 trans-10, but not for C18:1 trans-11, might be explained by the actions of the SCD1 enzyme in the mammary gland. Positional isomers of C18:1 trans, with double bonds at positions other than 8, 9, and 10, can be converted by SCD1, as shown by studies in rat liver microsomal systems (Mahfouz et al., 1980; Pollard et al., 1980). Because C18:1 trans-11 can be converted to C18:2 cis-9,trans-11 by SCD1, and thus involves different metabolism and maybe also different transport, no QTL for C18:1 trans-11 on BTA15 could possibly be detected.
On BTA16, QTL for the C18 and CLA indices were found at positions 45 and 52 cM, within the same confidence interval (Table 2, Figure 1d). A suggestive QTL within the same interval was also found for C18:0 and C20:0. Families 1, 3, and 4 were segregating for the QTL for the C18 index; for the CLA index, only families 1 and 3 segregated significantly (Table 3). The QTL explained 3% of the phenotypic variance of both the C18 index and the CLA index. An index reflects a ratio between a saturated FA and its cis-9 monounsaturated counterpart, which is influenced by (among others) SCD1 conversion. About 40% of the C18:0 taken up by the mammary gland is converted to C18:1 cis-9, and about 26% of C18:1 trans-11 is converted to CLA cis-9,trans-11 (Chilliard et al., 2000; Mosley et al., 2006). Although a significant association was previously shown between the SCD1 A293V genotype, located on BTA26, and the C18 and CLA indices (Schennink et al., 2008), significant or suggestive linkage could not be detected for these indices on BTA26. This would suggest that QTL for these indices were below detection. The QTL on BTA16 might harbor a gene involved in the complex regulation of SCD1; however, no obvious candidate genes are known on BTA16.
Furthermore, removal of the effects of DGAT1 and SCD1 genotypes resulted in 2 new significant linkage positions. On BTA1, a QTL at 129 cM for the C18 index was detected. Suggestive QTL within the same confidence interval on BTA1 were found for C18:0, C19:0, C20:0, and the CLA index. On BTA13, a QTL for C19:0 was found at 78 cM.
Quantitative trait locus mapping for milk-fat composition has been reported only by Morris et al. (2007), who restricted their study to BTA19 and identified FASN as a candidate gene. Although Morris et al. (2007) detected a QTL for C18 FA on BTA19, and found an association between SNP in FASN and C18:0 and C18:1 cis-9 in milk, these findings could not be confirmed in this study. Different production circumstances might explain this: a pasture-based system in New Zealand compared with an indoor winter period in the Netherlands.
This is the first genome-wide scan for milk-fat composition, which makes comparison with the literature impossible. However, (partial) genome scans to detect QTL for carcass-fat composition have been performed in beef cattle, pigs, and sheep (Clop et al., 2003; Karamichou et al., 2006; Alexander et al., 2007; Sanchez et al., 2007; Abe et al., 2008). Alexander et al. (2007) analyzed fat composition of the longissimus muscle of Wagyu x Limousin cattle and found significant QTL on BTA2 (among others, for monounsaturated FA, SFA, CLA, and the ratio of C18:1 to C18:0) and BTA7 (for monounsaturated FA). Abe et al. (2008) mapped QTL for fat composition of the longissimus muscle of Japanese Black x Limousin cattle and detected QTL on BTA2 (among others, for C18:2) and on BTA19 (among others, for C18:1).
The study described in this and the accompanying paper (Stoop et al., 2009) is the first, to our knowledge, to present results of a genome-wide scan for milk-fat composition, and is an important step in the unraveling of regulation of lipogenesis of FA. Quantitative trait loci were detected for short- and medium-chain FA (see accompanying paper by Stoop et al., 2009) and for long-chain FA (this paper), where only BTA14 was involved in both groups of FA. This finding indicates that short- and medium-chain FA, on the one hand, and long-chain FA, on the other hand, undergo distinct processes of synthesis and metabolism.
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ACKNOWLEDGMENTS
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This study is part of the Milk Genomics Initiative, funded by Wageningen University, the Dutch Dairy Association (NZO, Zoetermeer, the Netherlands), CRV (Arnhem, the Netherlands), and the Dutch Technology Foundation STW (Utrecht, the Netherlands). The authors thank the owners of the herds for their help in collecting the data, and Jeroen M. L. Heck and Hein J. F. van Valenberg for fruitful discussions.
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FOOTNOTES
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2 Contributed equally to this paper. 
Received for publication December 11, 2008.
Accepted for publication April 27, 2009.
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