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ANIMAL GENETICS |
,2
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* National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan;
and
Tokachi Branch of National Livestock Breeding Center, Otofuke, Hokkaido 080-0572, Japan;
and
Ohu Branch of National Livestock Breeding Center, Shichinohe, Aomori 039-2567, Japan;
and
Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan;
and
# National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602,Japan; and
|| Shirakawa Institute of Animal Genetics, Nishigo, Fukushima 961-8061, Japan
| Abstract |
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Key Words: bovine F2 family meat quality quantitative trait loci
| INTRODUCTION |
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Since 1994, we have generated an F2 resource population derived from crosses between Japanese Black sires and Limousin dams to map loci affecting economically important traits. A unique characteristic of the Japanese Black breed is the high fat content in the meat (so-called highly marbled beef), which is an important criterion for beef quality in the present Japanese market. May et al. (1993)
described the difference in fatty acid compositions of the intramuscular fat of Wagyu crossbred and Angus steers, and Kuber et al. (2004)
reported that Wagyu steaks had lower Warner-Bratzler shear force values than did Limousin steaks (note that most cattle known as Wagyu are Japanese Black breeds). Given those findings, Japanese Black cattle may have other economically favorable traits, in addition to marbling, compared with other breeds. In contrast to Japanese Black cattle, Limousin cattle produce leaner meat and have a larger body size. We chose these 2 breeds, the phenotypes of which differ dramatically, to construct an experimental F2 resource family for bovine QTL analysis.
In this report, we describe QTL underlying the difference in growth, carcass, and meat quality traits between Japanese Black and Limousin cattle. We incorporated physicochemical property traits of the F2 beef, including the fatty acid composition of backfat, intermuscular fat, and LM i.m. fat. We also identified QTL for computer image analysis (CIA) traits.
| MATERIALS AND METHODS |
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Generation and Feeding of F2 Population
F2 Population.
An F2 resource population was generated at the Tokachi and Ohu branches of the National Livestock Breeding Center in Japan. The animals used as parents were 2 Japanese Black (JB) sires (JB-A and JB-B) and 2 Limousin (L) dams (L-A and L-B). The F1 animals were obtained by crossing JB-A with L-A (family A) and JB-B with L-B (family B). Family A consisted of 2 F1 males and 17 F1 females, and family B consisted of 2 F1 males and 15 F1 females. To avoid obtaining progeny homozygous for latent recessive hereditary disease loci that may be present in the 2 JB sires, F2 animals were obtained by crossing F1 males and their nonsibling F1 females (between family A and B) using embryo transfer techniques. Both F1 families were produced and raised at the Tokachi branch, and fertilized eggs were collected in a frozen state. The majority of the frozen eggs were then sent to the Ohu branch and used to produce F2 animals. We produced 37 F2 animals at the Tokachi branch from July 1999 to January 2000. The remaining 149 F2 animals were produced at the Ohu branch during 4 periods: October to December 1999 (18 cattle); April to June 2000 (44 cattle); January to March 2001 (52 cattle); and July to October 2001 (35 cattle). The recipient dams of the F2 population consisted of 6 breeds, and ages were distributed from 2 to 13 yr (Table 1
).
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Phenotype Measurements
Growth and Carcass Traits. The F2 animals were weighed at birth, 4 wk of age, and on the first and last day of the fattening period. Withers height (from the ground to the peak between shoulder blades), hip cross height (from the ground to the intersecting point of hip points line and the median line), body length (from lower edge of the scapula to the end of the ischial tuberosity), chest girth and width (close behind the fore foot), hip length (from the hip cross to back end of the ischial bone), hip point width (between the points of the hip), rump width, and pin bone (back end of the ischial bone) width were measured 1 d before slaughter. The F2 animals were slaughtered at the age of 24 mo (731.62 ± 5.01 d of age). At the meat plant, HCW of the F2 animals were obtained, and carcass quality was evaluated about 48 h after slaughter by certified graders belonging to the Japan Meat Grading Association (Tokyo, Japan). Graded traits were LM area, rib thickness (the length from the abdominal lining to the external side of latissimus dorsi at around the midpoint of entire rib bone of the cross section), backfat thickness (the length from the external side of latissimus dorsi to carcass surface on the vertical line from the lower end of iliocostalis to carcass surface), beef marbling standards (BMS; No. 1 to 12), beef color standards (No. 1 to 7), beef fat standards (No. 1 to 7), luster, firmness, and texture. All graded traits were measured at the sixth rib bone side of the cross section between the sixth and seventh rib bones.
Meat Quality Traits.
Physicochemical property traits of the F2 beef were measured. The rib roast blocks of the seventh to eighth rib bone were sampled in all F2 animals. The LM was excised from the block and minced for analysis of moisture, crude fat, and CP content as described by Okumura et al. (2007)
, where approximately 50 g of LM was excised and put in a plastic bag, and then incubated for 1 h in a constant-temperature bath at 70°C, and reweighed to calculate the cooking loss value. This incubated muscle was then cut thinly to yield pieces that were 1 cm x 1 cm x 5 cm cuboids) and used to measure the Warner-Bratzler shear force (Salter, Kent, UK). Meat color was measured as described by Sato et al. (2003)
. In addition, we determined the fatty acid content of 3 parts of the rib loin block: backfat (on M. trapezius), intermuscular fat (between M. rhomboideus and LM), and intramuscular fat (of LM). Fat extractions were done as described by Folch et al. (1957)
, and extracted fat was saponified with potassium hydrate-ethanol solution and methylesterified with boron trifluoride-methanol complex. Processed fat was analyzed by gas chromatography (6890A, Agilent Technologies Japan Ltd., Tokyo, Japan) under the following conditions: the temperature of the inlet was 150°C, the oven was warmed from 150 to 220°C, and the temperature of the detector sensor was 220°C. We used helium gas as a carrier, a capillary column (TC-70, 0.25 mm i.d. x 60 m, df (the phase thickness of the inside of the capillary column) = 0.25 µm; GL Science, Tokyo, Japan), and flame-ionization detector for detection.
Computer Image Analysis Traits.
Digital images of the carcass cross section were taken between the sixth and seventh ribs using photographic equipment developed by Kuchida et al. (2001a)
. This equipment comprised 2 parts: a dome with 570 white light-emitting diodes and a digital camera (2 megapixels, FinePix2900Z, Fuji Film, Tokyo, Japan) with a wide conversion lens (WL-FX29, Fuji Film). The distance between the camera and the surface of the carcass was fixed, and the lens was always parallel to the carcass cross section. As a result, area and length could be measured with high accuracy using the equipment. Obtained digital images were then analyzed using software developed by Kuchida et al. (2000)
. The total muscle area, lean area, and fat area of LM, M. trapezius, M. semispinalis, and M. semispinalis capitus were calculated by this software. Here, the total muscle area represents the internal area of the muscle outline form. Therefore, the lean and fat areas are summed to give total muscle area. The ratio of the length of minor and major axes of LM was also calculated.
Genotyping
We extracted DNA from blood using automatic extraction equipment (NA1000, Kurabo, Osaka, Japan), and the final DNA concentration was adjusted to 20 ng/µL. A genome screen was conducted with microsatellite markers (Kappes et al., 1997
; Ihara et al., 2004
). Polymerase chain reaction amplification was performed in a volume of 15 µL containing 20 ng of genomic DNA, 1.67 mM MgCl2, 6.25 pmol of each primer, 0.2 mM de-oxynucleotides, and 0.375 U of Taq DNA polymerase (ABgene, Epsom, UK). The annealing temperatures of each marker in thermocycling steps were optimized by referencing those recommended by Ihara et al. (2004)
. Amplifications were performed under the following conditions: 5 min at 94°C, 30 cycles of 30 s at 94°C, 30 s at annealing temperature, 30 s at 72°C, and a final extension of 7 min at 72°C. After PCR amplification, reaction products were fractionated on an ABI377 DNA sequencer (Applied Biosystems, Foster City, CA), and fragment analysis was performed with GeneScan and Genotyper software (Applied Biosystems).
Linkage Analysis
Linkage maps for the 29 bovine autosomes were constructed by using CRI-MAP (Green et al., 1990
), and the constructed map was used for the whole-genome QTL scan. The information content of markers was calculated by the method described by Knott et al. (1998)
.
A QTL analysis for each trait was performed by the method developed by Haley et al. (1994)
. The statistical model is based on linear regression of phenotypes on the probabilities of QTL genotypes at a given location. We assumed that the grandparental breeds, Limousin and Japanese Black, were fixed for alternative alleles at a QTL. Two alleles at a putative QTL at a given location were denoted by Q and q. There are 3 possible genotypes, QQ, Qq, and qq, for a QTL at the given location on an autosome. The probabilities of the QTL genotypes [denoted as Prob(QQ), Prob(Qq), and Prob(qq)] were calculated from the observed genotypes of markers linked to the QTL. The calculation was done as described by Haley et al. (1994)
. In analyses of actual data, some fixed effects other than QTL effects including sex-associated differences, breeds, and ages of the recipient cows, seasons, and locations were taken into account.
Let the effects of genotypes QQ, Qq, and qq be denoted by a, d, and –a, respectively. We assumed that the phenotypic value of a trait is written for the ith individual in F2 as follows:

where bj is the jth element of the vector of fixed effects, which includes overall mean, sex effect, breeds of the recipients (6 breeds), ages of the recipients (10 levels), and combinations of seasons and locations (5 levels); xij is the (i,j)th element of the design matrix associating bj to yi; cai is the coefficient for the additive component for individual i at the given location that is calculated from the probabilities of QTL genotypes and equal to Prob(QQ) – Prob(qq); cdi is the coefficient for the dominance component for individual i at the given location, which is equal to Prob(Qq); and ei is the residual error. Model parameters µ, h, a, and d are estimated by a least squares method. That is, estimators of the parameters are obtained such that the sum of squares,

is minimized, where n is the number of individuals of F2. Denoting least squares estimators of bj, a, and d by the terms
j,
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Under the null model corresponding to no QTL, where a = d = 0 is assumed, the minimal sum of squares is denoted by S0. Detection of a significant QTL is declared based on the ratio involving S1 and S0. In this report, we used the F-ratio, [(S0 – S1)/2]/[S1/(n – 20)], as a statistic for detecting QTL, where it should be noted that degrees of freedom of 20 is assigned to the fixed effects. Significance thresholds were obtained by a permutation test with 1,000 repetitions for each trait.
Correlation coefficients among the 27 F2 phenotypes for which significant QTL were detected were calculated by PROC CORR (SAS Inst. Inc., Cary, NC).
| RESULTS AND DISCUSSION |
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The 76 traits measured are summarized in Table 2
. One trait of particular interest was the BMS number, because in the Japanese market, the value of a beef carcass is heavily dependent on this grading score. Although BMS numbers are categorized as 1 to 12 in Japanese grading systems, the highest number in our F2 population was 7. Furthermore, the distribution of the BMS numbers was extremely biased and was skewed toward lower scores (Figure 1
).
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Linkage Analysis and QTL Mapping
From the marker linkage analysis, 313 markers were mapped to 29 bovine autosomal chromosomes over 2,382 cM, and the average distance between markers was 8.4 cM. With this linkage map, we detected QTL on BTA2, 5, and 19 (Table 3
). We identified 9 QTL for 27 traits at the 5% genome-wide threshold level; QTL for 22 traits were significant at the 1% genome-wide level. Details of the significant QTL are presented in Figures 2
, 3
, and 4
. In the QTL analysis, we took into account the fact that our F2 population was produced at 2 different stations over different time periods. We also took into account the effects of recipient dams of the F2 population, including their breed and age, as they might have an effect on the performance of the offspring (Table 1
).
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In contrast, the QTL for RFA to LM, M. semispinalis, M. semispinalis capitus, and M. trapezius area were detected at 4.7 cM on BTA2 (Figure 2
, panel E), as was the QTL for BMS number (Figure 2
, panel A). Furthermore, QTL for crude fat content of LM and the C16:1 content of intramuscular fat were detected at 5.7 and 0 cM, respectively, on BTA2 (Figure 2
, panel B). In all these cases, animals that inherited the Japanese Black alleles had greater values. Kuchida et al. (2000
; 2001b
) described significant relationships between crude fat content and RFA (r = 0.98), and between RFA and BMS number (r = 0.93), respectively. They suggested that crude fat content and RFA are useful data for evaluating marbling objectively. This suggestion is consistent with the results of our study.
All of our F2 animals showed BMS numbers of 2 to 5, except for one animal that had a 6 and one that had a 7 (Figure 1
). This indicates the lower intramuscular fat content of the F2 population than of purebred Japanese Black cattle. In fact, Okumura et al. (2007)
noted that the crude fat content (%) of Japanese Black cattle slaughtered at 24 mo of age (identical to the age at slaughter for our F2 population) was 37.0 ± 4.4, whereas that in our F2 population was 17.7 ± 5.9 (Table 2
). Summarizing these results, we suggest that the Limousin alleles, which produced larger lean and muscle area, had a more extreme effect than those of the Japanese Black alleles, which produced beef with greater BMS, RFA, crude fat, and C16:1 content. Using a population that inherited the muscle hypertrophy locus, Casas et al. (1998)
detected a QTL for ribeye area, marbling, and fat thickness. Their results were similar to ours not only in the type of phenotypes affected, but also in the QTL regions reported; the multiple QTL were in the same chromosomal region. Furthermore, using a Wagyu x Limousin crossbred F2 population, Alexander et al. (2007a)
detected a QTL for LM area in the centromeric region of BTA2.
Recently, Sellick et al. (2007)
reported the effect of the F94L mutation of the myostatin gene. They treated this gene as a positional candidate of the QTL for meat percentage, eye muscle area, and silverside (meat block composed of M. gluteobiceps and M. semitendinosus) percentage detected in the 0 to 15 cM region of BTA2. They analyzed a population derived from a Jersey x Limousin cross and explained that the F94L mutation of the myostatin gene originated from the Limousin breed and significantly increased these traits. Their results seem applicable to our findings. Myostatin is one of the strong candidate genes for QTL of BTA2 detected in our F2 population.
Interestingly, a QTL for C18:2 content of LM was detected at 2 cM on BTA2 (Figure 2
, panel B). Animals that inherited the Limousin alleles had greater content of C18:2. This fatty acid is a constituent of CLA, which has recently been studied for its favorable effect on human health, especially for reducing human cancer cell growth (De La Torre et al., 2006
). The C18:2 fatty acid in beef cannot be synthesized in the bovine body, but originates from feedstuffs. Therefore, it seems strange that the genetic effect was observed on this trait. On the other hand, several studies have reported the difference in C18:2 content between muscle and adipose of cattle (Hristov et al., 2005
; Noci et al., 2005
). According to these studies, C18:2 is more abundant in muscle than in adipose. In our F2 population, animals that inherited the Limousin allele had leaner meat, as described above. Furthermore, there was a weak but positive correlation between C18:2 content and both CP content and LM lean area (r = 0.11 and 0.12, respectively). Conversely, there was a negative correlation between C18:2 and both crude fat content and RFA to LM area (r = –0.12 and –0.13, respectively). These results may relate to the fact that the QTL for C18:2 content was detected at the centromeric end of BTA2.
There are several reports on candidate gene analysis of BMS and subcutaneous fat depth (SFD) traits using similar Wagyu x Limousin F2 populations. Jiang et al. (2005)
detected genetic variation in the mitochondrial transcription factor A (TFAM) gene and determined its significant effect on both BMS and SFD. Michal et al. (2006)
analyzed the bovine fatty acid binding protein 4 (FABP4) gene as a candidate, and found a significant relationship between detected SNP and these 2 traits. Wibowo et al. (2007)
reported a significant effect of mutations detected in the corticotrophin-releasing hormone (CRH) gene on BMS and SFD. The first TFAM gene is located on BTA28, and the latter 2 genes (FABP4 and CRH) are both located on BTA14. We detected no significant (or suggestive) QTL for BMS or backfat thickness on those chromosomes. One possible explanation for this observation was the difference in parental individuals between those 2 F2 populations. In our F2 population, the mutations detected in these 3 genes might be fixed in the 2 breeds. In addition, the difference in the measuring procedure of BMS and SFD between the United States and Japan might have caused the different results.
We detected a QTL for withers height at 80.3 cM on BTA5 (Figure 3
). Animals that inherited the Limousin alleles were taller than those that inherited the Japanese Black alleles. Quantitative trait loci for birth weight were detected in this region (Casas et al., 2003
; Kim et al., 2003
) by use of a Bos indicus x Bos taurus crossbred family. Mizoshita et al. (2004)
detected a QTL for carcass yield on BTA5 in a half-sib population of purebred Japanese Black cattle, but the position was different from our QTL. Li et al. (2004)
detected a QTL for preweaning ADG and ADG on feed in the 73.5- to 77.6-cM region on BTA5 using a crossbred population developed from several bovine breeds. Those investigators considered IGF-I to be a positional candidate and included information regarding IGF-I polymorphisms in their analysis. Although we measured 14 growth-associated traits in total, including birth weight and ADG during the fattening period, the genome-wise significant QTL was detected only for withers height.
On BTA19, we detected QTL for fatty acid composition (Figure 4
, panels A to C). In addition, QTL for C14:0 content were detected at 62.3 cM for backfat (Figure 4
, panel A); QTL for C14:0 and C14:1 content were detected at 62.3 and 71.0 cM for intermuscular fat (Figure 4
, panel B) and at 62.3 and 41.1 cM for intramuscular fat (Figure 4
, panel C). For each of these 3 loci, animals that inherited the Limousin alleles showed increased C14:0 and C14:1 content. We also detected QTL for C16:0 and C18:1 content and the ratio of total unsaturated fatty acid content to total SFA content of intramuscular fat at 62.3 cM on BTA 19 (Figure 4
, panel C). Individuals that inherited the Japanese Black allele at this QTL demonstrated reduced C16:0 content, but increased C18:1 content and the ratio of total unsaturated fatty acid content to total SFA content. The degree of fatty acid composition in the intramuscular fat is an important factor for the eating quality of beef. Generally, the melting points of unsaturated fatty acids are less than those of SFAs, so beef with more unsaturated fatty acid in the intramuscular fat has superior eating quality and good texture. In addition, Mandell et al. (1998)
suggested that C18:1 content has a favorable effect on beef flavor. In contrast, Fernandez and West (2005)
stated that C12:0, C14:0, and C16:0 are considered to be associated with hypercholesterolemia, because they increase the concentration of low-density lipoprotein in human plasma, and Bláha et al. (2000)
suggested that SFA concentrations and coronary atherosclerosis are related. Considering these points, we suggest that our findings here may facilitate the production of beef that is both pleasant to eat and healthier for human consumption. Furthermore, Viitala et al. (2003)
detected a QTL for milk fat percentage at 67 cM on BTA19. Subsequently, Roy et al. (2006)
studied the bovine fatty acid synthase (FASN) gene as a candidate gene for the QTL and found various SNP that had significant effects on milk fat percentage. Morris et al. (2007)
detected QTL for fatty acid composition in both adipose tissue and milk fat in the 60 to 80 cM region on BTA19; the locations of those QTL overlap those that we detected. Morris et al. (2007)
also analyzed FASN as a candidate gene for this QTL and found that the SNP haplotype had a significant effect on fatty acid composition; FASN may also be a strong candidate gene for controlling fatty acid composition in our F2 family. On the other hand, Alexander et al. (2007b)
analyzed the fatty acid composition of the LM of their Wagyu x Limousin F2 population, and carried out QTL mapping on this trait, but did not detect significant QTL on BTA19. A possible reason for this result is the difference in parental individuals of the 2 Wagyu x Limousin reference populations. Whereas their F2 population originated from 8 Wagyu bulls and 108 Limousin females, our family was constructed from only 2 Japanese Black sires and 2 Limousin females. Our 2 Japanese Black sires were considered excellent individuals in 1995, so several favorable genes (for meat qualities) might be fixed in the 2 sires. It could be said that the structure of our F2 population was more suitable for detecting effective QTL. Interestingly, Alexander et al. (2007b)
detected significant QTL for fatty acid composition on the centromeric region of BTA2, where we also detected the QTL on C16:1 and C18:2. The latent factor with effects on beef fatty acid composition may also be located in this region.
We observed several pairs of traits that showed highly positive or negative correlations among the 27 QTL-detected traits in this study. For example, BMS number had a strong positive relationship with RFA and LM muscle area (r = 0.85), but also showed a negative correlation with CP content (r = –0.78). Notably, QTL of those 3 traits were located at the same position, 4.7 cM on BTA2. This suggests that markers targeted for one trait may improve performance of the other trait. The opposite result might occur for other trait combinations. We may have to pay attention to this matter when consideration is given to marker-assisted selection.
Overall, the findings we report here provide fundamental information on the transmission of bovine quantitative traits. Because the QTL we detected may represent only breed-associated differences between Japanese Black and Limousin cattle, we need to confirm these QTL effects in a purebred Japanese Black population to obtain information useful in breeding Wagyu cattle.
| Footnotes |
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3 Current address: Agriculture, Forestry and Fisheries Research Council, Ministry of Agriculture, Forestry and Fisheries, Kasumigaseki, Tokyo 100-8950, Japan. ![]()
4 Current address: Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan. ![]()
5 Current address: Tokachi Branch of National Livestock Breeding Center, Otofuke, Hokkaido 080-0572, Japan. ![]()
6 Current address: Kinki Regional Agricultural Administration Office, Ministry of Agriculture, Forestry and Fisheries, Kamigyo, Kyoto 602-8054, Japan. ![]()
7 Current address: National Institute of Livestock and Grassland Sciences, Tsukuba, Ibaraki 305-0901, Japan. ![]()
1 Corresponding author: t0abe{at}nlbc.go.jp
Received for publication October 23, 2007. Accepted for publication June 27, 2008.
| LITERATURE CITED |
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, M. Brátová, P. Vyroubal, and Z. Zadák. 2000. Bioanalysis of PUFA metabolism and lipid peroxidation in coronary atherosclerosis. J. Pharm. Biomed. Anal. 22:563–572.[CrossRef][Medline]This article has been cited by other articles:
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A. Schennink, W. M. Stoop, M. H. P. W. Visker, J. J. van der Poel, H. Bovenhuis, and J. A. M. van Arendonk Short communication: Genome-wide scan for bovine milk-fat composition. II. Quantitative trait loci for long-chain fatty acids J Dairy Sci, September 1, 2009; 92(9): 4676 - 4682. [Abstract] [Full Text] [PDF] |
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L. J. Alexander, L. A. Kuehn, T. P. L. Smith, L. K. Matukumalli, B. Mote, J. E. Koltes, J. Reecy, T. W. Geary, D. C. Rule, and M. D. MacNeil A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F2 population J Anim Sci, May 1, 2009; 87(5): 1576 - 1581. [Abstract] [Full Text] [PDF] |
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