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* National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan;
and
Ibaraki Branch of National Livestock Breeding Center, Fujigaya, Ibaraki 308-0112, Japan;
and
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan; and
and
Shirakawa Institute of Animal Genetics, Nishigo, Fukushima 961-8061, Japan
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Abstract |
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 Top Abstract IntroductionMaterials and MethodsResults and DiscussionImplicationsLiterature Cited |
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Key Words: Growth • Linkage Analysis • Meat Quality • Pigs • Quantitative Trait Loci
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Introduction |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionImplicationsLiterature Cited |
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first reported a cluster of loci affecting growth and fatness on Sus scrofa chromosome (SSC) 4 in wild boar and Large White pigs. A more detailed whole-genome scan of the same population identified more QTL (Knott et al., 1998). Marklund et al. (1999) confirmed the presence of QTL with major effects on growth and fatness on SSC 4 by backcrossing. We generated an F2 resource population from a cross between a Meishan female and a Duroc male in order to map loci affecting economically important traits. Duroc boars are extensively used in terminal crosses as sires for the production of pork meat with improved meat quality in Japan because the Duroc breed is characterized by high meat quality and large muscle mass. Meishan, characterized by large litter size, differ from commercial breeds in many respects, including genetic characters. These two breeds exhibit large differences not only in growth performance, carcass composition, and meat quality, but also in reproductive traits. Therefore, we selected Meishan and Duroc breeds as parents for a resource population to detect QTL affecting growth, carcass and reproductive traits in pig and to obtain information and tools for breeding programs, such as marker-assisted introgression. We report porcine QTL results for 48 traits, including carcass traits and meat quality.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionImplicationsLiterature Cited |
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Coat Color.
Coat color was recorded from six angled photographs taken of each animal, and scored as follows: Class 1 score = gray coat color; Class 2 score = brown coat color; Class 3 score = black; Class a score = spotting; Class b score = no spotting. Although coat color is a qualitative trait, we treated it as a quantitative trait for analysis.
Data Collection.
Pigs were weighed at birth and at 21, and 30 d of age. From these pigs, 292 were weighed at 60 d of age. Testicular weights were recorded from F2 males that were castrated at 2 mo of age. Among the castrated males, 165 were raised until they obtained a body weight of 90 kg. Average daily gain was calculated between 30-kg and 90-kg body weights. These males were slaughtered at a live weight of approximately 90 kg. At slaughter, these males were recorded for body weight, size, and length, including the circumference of the chest and cannon bone, the height at the withers, and the chest depth and width. Carcasses were scalded and dehaired, and chilled overnight. Then carcass measurements were recorded for weight; lengths I, II, and III; thickness; and vertebra number. Carcass lengths I, II, and III refer to the lengths from the first cervical to the pubic bone, from the first rib to the pubic bone, and from the first rib to last lumbar vertebra, respectively. Depth of backfat over the midline was recorded at the first rib (shoulder), the thinnest depth at ribs (back), and the first lumbar vertebra (loin) with a ruler. Depth of belly over the midline was recorded at the last rib (forebelly), at the diaphragm (middle belly), and at the last lumbar vertebra (hind belly). One side of the carcass was split between the 4th and 5th ribs, last rib, and the first lumbar vertebra (at the middle); the longissimus muscle was traced on acetate paper; and the area was determined using computerized morphometric planimetry. The remaining side was then weighed and cut into the major wholesale cuts. The weight of each wholesale cut was recorded. Intramuscular fat (IMF) content was measured as described by Gerbens et al. (1999). After minced meat was dried by heating to 102°C for 24 h in a drying oven, moisture was calculated from weights taken before and after drying and was expressed as a percentage. Objective measurements of meat color were taken with a color meter, model ZE 2000 (Nippon Denshoku Industries Co., Tokyo, Japan); L values measure light reflectance, a values represent the degree of redness, and b values represent the degree of yellowness. Cooking loss and shear force were measured as described by Hovenier et al. (1992).
Table 1 summarizes the data of 48 traits, including ADG, vertebra number, backfat thickness (BFT), and IMF. Because the 165 F2 males were produced in three independent groups and in different parities, possible phenotypic differences derived from groups and parities were corrected for using the mixed-model least squares, maximum-likelihood computer program described by Harvey (1977).
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Linkage Analysis
Linkage maps were constructed using CRI-MAP (Green et al., 1990) for 18 autosomes and the sex chromosome. The sex-averaged map was used for the whole-genome scan of QTL. The information content was calculated using the method described by Knott et al. (1998). When a given location belonged to a pseudoautosomal region of a sex chromosome, analyses were performed using the same method as for autosomes. For testing QTL in sex-specific regions of the sex chromosome, the analysis model was modified as described by Knott et al. (1998). We assumed that the Y chromosome contained no loci. A test statistic for detecting QTL and the threshold was constructed as for autosomes.
A QTL analysis for each trait was performed using the method developed by Haley et al. (1994). The statistical model in the method is based on a linear regression of phenotypes on the probabilities of QTL genotypes at a given location. We assumed that the grandparental breeds were fixed for alternative alleles at a QTL. Two alleles at a putative QTL at a given location were denoted by Q and q. Probabilities of QTL genotypes, denoted by Prob(QQ), Prob(Qq), and Prob(qq), were calculated from the observed genotypes of markers linked to the QTL. The calculation was described by Haley et al. (1994). In the analyses of real data, sex difference was taken into account.
There are three possible genotypes, QQ, Qq, and qq, for a QTL at the given location on an autosome. Let the effects of genotypes QQ, Qq, and qq be denoted by a, d, and -a. We assume that phenotypic value of a trait is written for the ith individual in F2 as follows:
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where µ is the mean; si is the indicator of the sex of individual i, which is equal to 1 or -1 for male or female, respectively; h is a sex effect; cai is the coefficient for the additive component for individual i at the given location that is calculated from the probability 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 a sum of squares,
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is minimized, where n is the number of individuals of F2. Denoting least squares estimators of µ, h, a, and d, by the terms 
, 
, â, and 
, the minimum sum of squares is obtained as
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Under the null model corresponding to no QTL, where a = d = 0 is assumed, the minimum sum of squares is denoted by S0. Significance detection of QTL is declared based on the ratio of S1 and S0. In this report, we used F-ratio, [(S0 - S1)/2]/[S1/(n - 2)], as a statistic for detecting QTL. Significance thresholds were obtained with 10,000 repeated permutation test cycles for each trait.
In chromosomal regions exceeding the suggestive and significance level on some QTL, P-values of the nearby markers were computed by SAS-GLM (SAS Inst. Inc., Cary, NC). When two parents have more than two marker alleles, an analysis of the individual marker genotypes will efficiently detect the associations of the different alleles in one or both breeds with specific traits. Phenotypic difference among genotypes of nearby markers was estimated with SAS-GLM. The number of marker genotypes was different depending on the genotypes of the parents. This analysis of variance supported results of QTL analysis and estimated within-breed allele effects rather than between-breed allele effects.
Linkage Map
We searched for informative microsatellites from the USDA-MARC linkage map (Rohrer et al., 1996) and selected 180 microsatellites at approximately 20-cM intervals in the whole pig genome. The 180 microsatellites were genotyped across parents, 28 F1, and 865 F2 animals. A sex-averaged linkage map was constructed with multipoint analysis. The order of the markers was the same as in the USDA-MARC linkage map (Rohrer et al., 1996). The average interval was 12.6 cM, and the total length was 2,263.6 cM, which was comparable to that of the USDA-MARC linkage map (Rohrer et al., 1996). Two large gaps existed between SW274 and SW72 on SSC 3 (34.6 cM) and SW949 and SW980 on SSC X (40.7 cM). The average information content was 0.80.
As this F2 population consisted of only full-sib families, each genotype was checked for segregation distortion. To confirm the presence of a lethal allele, we examined whether the segregation ratio at each marker fit with mendelian ratios 1:2:1, Duroc homozygous, heterozygous, and Meishan homozygous, respectively, by chi-squared test.
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Results and Discussion |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionImplicationsLiterature Cited |
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Mapping of Coat Color Traits
The F2 animals exhibited coat colors of black (n = 373), brown (n = 383), and gray (n = 109). Several brown and gray pigs had black spotting (spotting, n = 289; no spotting, n = 576). The regions associated with coat color were mapped on SSC 1 (107.7 cM) at an F-ratio of 28.2 and SSC 6 (1 cM) at an F-ratio of 122.0. The spotting region was also mapped on SSC 6 (2 cM) with an F ratio of 111.7. The locus on SSC 1 was not previously reported. On SSC 6, the genotypes of marker S0035 at the coat color and the spotting loci were tightly linked to black and brown coat color and spotting. Because the melanocortin-1 receptor (MC1R) gene was mapped on the SSC 6 telomeric region (Mariani et al., 1996) and the mutations were associated with pig coat color and spotting (Kijas et al., 1998, 2001), partial MC1R was amplified by PCR using genomic DNA from F1 and F2 pigs, and sequenced. We confirmed a previous report that Duroc and Meishan pigs are homozygous for MC1R*4 and heterozygous for MC1R*2/3 (Kijas et al., 1998), respectively, suggesting that the MC1R gene is responsible for coat color and spotting on SSC 6.
QTL Mapping Results
The QTL mapping results are summarized in Table 2. We identified 38 QTL for 28 traits at the 5% genomewise level. Of the 38 QTL, 24 QTL for 17 traits were significant at the 1% genomewise level. The significant QTL are presented in Figures 1 through 7 in detail. Some of the detected QTL replicated previous findings.
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) and SSC X (Figure 7
). Our results show that males with Meishan alleles at each QTL had larger testicular weight than males with Duroc alleles. The onset of sperm production occurs at a much younger age (56 to 84 d) in Meishans than in conventional boars (120 to 180 d; Lunstra et al., 1997). Ford et al. (2001) have reported mapping a QTL for 220-d testicular size on SSC X using a Meishan x White composite crossbred population. Boars with Meishan alleles at SSC X QTL had smaller testicles than boars with White composite alleles. Therefore, our results for testicular weight at 2 mo of age support the Lunstra et al. (1997) report and are not inconsistent with the result of Ford et al. (2001). The androgen receptor (AR) gene was mapped to the same region of SSC X (Seifert et al., 1999), and testicular weight in AR-knockout mice was 80% smaller than wild type mice (Yeh et al., 2002). The location of the QTL on SSC X corresponds to human chromosome Xp11.23-21 and the distal end of mouse chromosome Xp, where mouse Ihtw1 (Interspecific hybrid testis weight 1), one of the loci responsible for testicular weight, was mapped (Elliott et al., 2001). Although the two genes were located near the testicular weight QTL, there could be additional genes affecting testicular weight on SSC X.
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) and QTL for 30-d weight and ADG (from 30 to 90 kg) on SSC 6 (Figure 3). A potential QTL for ADG was detected on SSC 4, and almost the same region was previously characterized as a QTL affecting growth rates between weaning and 70 kg (Knott et al., 1998) and between weaning and 35 to 56 kg (Paszek et al., 1999). Growth-related QTL other than on SSC 4 that were reported previously, however, were not detected in the present study. On SSC 4, large overdominance effects detected in this study may be due to two QTL linked in repulsion or the negative effect of homozygotes at this QTL. The unique effect at this QTL in our family will provide good information on the role of genes responsible for growth traits. The overdominance effect at this QTL needs to be investigated further. Understanding this QTL based on molecular genetics may aid our understanding of the heterosis effect.
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and 4. At the same regions on SSC 1, we detected QTL for loin length and loin area (Figure 1). Rohrer and Keele (1998a) and Wada et al. (2000) reported QTL for carcass length and vertebra number on the corresponding region of SSC 1, suggesting that a vertebra number QTL could be important for carcass length. A potential QTL was mapped on SSC 6 for carcass length (Table 2) and probably replicated the carcass length QTL on SSC 6 (P-value < 0.01) reported by Paszek et al. (2001). We confirmed the presence of a BFT QTL reported previously on SSC 7 (Rohrer and Keele, 1998a; de Koning et al., 1999; Wada et al., 2000; Malek et al., 2001b) and on SSC X (Knott et al., 1998; Rohrer and Keele, 1998a). Near the BFT QTL on SSC 7, we located a significant QTL for carcass yield and loin muscle area.
For meat quality, we located a significant QTL for IMF on SSC 7, where a potential QTL for muscle moisture was detected (Figure 5). In addition, we located both IMF and muscle moisture QTL at the same regions of SSC 9 (near SW983) and SSC 13 (near S0289; Figure 6). On the SSC 9 QTL, the F-ratios were 10.75 for IMF and 5.18 for muscle moisture. On the SSC 13 QTL, F-ratios were 6.20 for IMF and 11.04 for muscle moisture. Paszek et al. (2001) mapped both QTL on the same region of SSC 6. Whether IMF is directly associated with muscle moisture is not known. Uncoupling proteins 2 and 3 (UCP2 and UCP3), which are mitochondrial membrane transporters involved in thermogenesis, were mapped to SSC 9p21-p24 (Werner et al., 1999). Because UCP2 is associated with hyperinsulinemia and obesity in mouse and human (Fleury et al., 1997), UCP2 and UCP3 might affect lipid metabolism related to porcine IMF phenotypes.
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. The genomewise suggestive (P < 0.10) QTL for circumference of cannon bone had the highest P-value based on analysis of allele sizes. This QTL was mapped at 56.2 cM on SSC 7 with an F-ratio of 8.5, and the P-value of the nearby marker SW1856 was 9.51 x 10-17 (Table 3). Most of F2 animals that inherited allele 1 from Meishan had larger circumferences of cannon bone. The Meishan population may have genes that affect the circumference of the cannon bone near this marker.
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; Paszek et al., 1999; Rohrer and Keele, 1998a,b; Jeon et al., 1999; Wada et al., 2000), we detected more QTL at the 1% genomewise level in this study than previously reported. First, our F2 resource family had a simple structure, with a single boar and sow as founding parents. Second, we genotyped 180 microsatellite markers across 865 F2 offspring, resulting in a high information content of 0.80 in the pig linkage map. These two factors facilitate performing a reliable linkage analysis. Finally, we analyzed a comprehensive set of pig traits, including performance, growth, body size, and carcass and meat quality (Table 1).
Our results identified the presence of several previously identified QTL, such as for testicular weight on SSC X (Ford et al., 2001), growth on SSC 4 (Knott et al., 1998; Paszek et al., 1999), vertebra number on SSC 1 (Wada et al., 2000), and BFT on SSC 7 (Rohrer and Keele, 1998a; de Koning et al., 1999; Wada et al., 2000; Malek et al., 2001b) and on SSC X (Knott et al., 1998; Rohrer and Keele, 1998a). On the other hand, we detected IMF QTL on SSC 7, SSC 9, and possibly SSC 13, although IMF and marbling have also been mapped on SSC 1 (Malek et al., 2001a) and SSC 2, SSC 4, and SSC 5 (de Koning et al., 1999).
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Implications |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionImplicationsLiterature Cited |
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Footnotes |
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3 Present address: Ibaraki Prefectural Livestock Research Center, Yasato, Ibaraki, 315-0132, Japan.
1 Correspondence: Odakura (phone: 81-248-25-6165; fax: 81-248-25-3990; E-mail: s0sato{at}nlbc.go.jp).
Received for publication February 27, 2003. Accepted for publication August 20, 2003.
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Literature Cited |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionImplicationsLiterature Cited |
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= loin muscle area 4th to 5th rib, 
= loin length, and x = vertebra number.
= backfat thickness and * = testicular weight.
= 30-d weight and + = ADG.
= IMF %, — = moisture%, and bold line = carcass yield.