J. Anim. Sci. 2005. 83:2247-2254
© 2005 American Society of Animal Science
Two quantitative trait loci on Sus scrofa chromosomes 1 and 7 affecting the number of vertebrae1
S. Mikawa*,2,
T. Hayashi*,
M. Nii
,
S. Shimanuki
,
T. Morozumi and
T. Awata*
* Genome Research Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan;
and
Livestock Research Institute, Tokushima Agriculture, Forestry and Fisheries Technology Center, Anan, Tokushima 774-0047, Japan; and
and
STAFF Institute, Tsukuba, Ibaraki 305-0854, Japan
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Abstract
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The objective of the research was to identify QTL affecting the number of vertebrae in swine, one of the major determining factors of growth and body composition. Previously, we reported a QTL for the number of vertebrae located on SSC1qter (terminal band of the q arm of SSC 1) in an F2 family produced by crossing a Göttingen miniature male with two Meishan females. Eight other swine families were subsequently produced by crosses between different breeds of European, Asian, and miniature pigs. In these families, the QTL on SSC1qter for the number of vertebrae was detected. Unlike the Asian alleles, all European alleles in this study had the effect of increasing the number of vertebrae by 0.44 to 0.69 and acted additively without dominance. The Göttingen miniature sire, for which we previously reported a smaller additive effect, seemed to be heterozygous at the QTL. In the present study, another QTL was found for the number of vertebrae on SSC7. This QTL was not fixed in the European pigs used as parents in our experimental families, and some of the European alleles increased the number of vertebrae. A half-sib analysis confirmed that this QTL was segregating in a commercial Large White population. Analysis in an F2 family in which the parental pigs were fixed for alternative alleles revealed that the effects of the QTL on SSC1 and on SSC7 were additive and similar in size. The two QTL acted independently without epistatic effects and explained an increase of more than two vertebrae.
Key Words: Pigs • Quantitative Trait Loci • Swine • Vertebrae
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Introduction
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For many years, it has been known that the number of vertebrae in pigs varies. The number of cervical vertebrae is fixed at seven, as in other mammals, but the thoracic and lumbar vertebrae vary in number (King et al., 1960
). In the King et al. (1960) report, the number of thoracic vertebrae ranged from 14 to 16, and the number of lumbar ranged from five to seven, in commercial pigs. The number of vertebrae affects carcass length, and an increase of approximately 15 mm for each additional vertebra can be expected in a carcass approximately 800 mm long. Today, the total number of thoracic and lumbar vertebrae in European breeds ranges from 21 to 23. Wild boars, which are ancestors of pigs, have a uniform number of 19 thoracic and lumbar vertebrae. European breeds have been improved for years, as body size has been enlarged to increase meat production. We can assume that, in the process, the number of vertebrae has increased as well.
In our previous study, we reported a QTL analysis for various traits in an F2 family produced at the National Institute of Animal Industry (NIAI) of Japan (referred to here as the NIAI family) by crossing a Göttingen miniature (Porter, 2002) male and two Meishan females, and detected QTL for various traits (Wada et al., 2000). Among them, we detected a QTL on SSC1qter (terminal band of the q arm of SSC1), which affected the number of vertebrae. Interestingly, alleles of the Göttingen miniature sire had the effect of increasing the number of vertebrae, despite the smaller body size of this pig. For further investigation of QTL affecting economic traits, we produced eight other F2 families by crossing different breeds of Asian, European, and miniature pigs. In the present study, we used these families to detect novel QTL affecting the number of vertebrae, as well as that on SSC1qter, and analyzed the variation of these QTL in commercial pigs.
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Materials and Methods
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Swine Populations and Traits
The MG family was produced by crossing a Göttingen miniature male with two Meishan females. This MG family, consisting of the NIAI family, was used for the construction of a linkage map by Mikawa et al. (1999) and for the QTL analysis by Wada et al. (2000). Additional F2 animals were produced later. Eight novel three-generation families were produced by crossing a Landrace male with two Meishan females (ML), a Japanese wild boar with two Landrace females (LWb), a Large White male with a Jinhua female (JW), a Clawn miniature (Nakanishi, 1981; Kamimura et al., 1996) male with a Berkshire female (BC), a Large White male with a Meishan female (MW), a Meishan male with a Landrace female (LM), a Duroc male with five Jinhua females (JD), and a Japanese wild boar with three Large White females (WWb; Nii et al., 2005). The numbers of F1 and F2 individuals in each family are listed in Table 1. The JW and JD families were bred under specific-pathogen-free conditions, and the others were bred conventionally. All F2 animals were weaned at 28 d of age, and males were castrated. In the ML, JW, MW, LM, and JD families, F2 animals were slaughtered at approximately 70 kg of live weight. Those of the BC family were slaughtered at 80 kg, and those of the LWb family were slaughtered at 90 kg. In the MG family, male pigs were slaughtered at 91 d of age, and females were slaughtered after the first estrous cycle. After slaughter, the numbers of thoracic and lumbar vertebrae were scored.
QTL Analysis for the Number of Vertebrae
A QTL scan of the genome was performed for the number of vertebrae in each of the MG, ML, and LWb families. An interval mapping approach developed by Haley et al. (1994) was used. The model used assumed that the founder breeds were fixed for alternative alleles. The genome-wide significance threshold was calculated by a permutation test (Churchill and Doerge, 1994) with 5,000 repetitions. We used 293, 138, and 152 microsatellite markers in the USDA linkage map (Rohrer et al., 1996) for the MG, ML, and LWb families, respectively. In these analyses, map positions of the USDA linkage map were used. For each of the JW, BC, MW, LM, JD, and WWb families, the existence of QTL was investigated by analyzing, with interval mapping, each of SSC1 and SSC7, on which QTL for the number of vertebrae were detected in genome scanning in the MG, ML, or LWb families. The model used was the same as described previously. We used 11, 15, 16, 6, 8, and 21 markers on SSC1, and 8, 12, 8, 6, 9, and 9 markers on SSC7 in the JW, BC, MW, LM, JD, and WWb families, respectively. The USDA linkage map positions were used for the analyses. The chromosome-wide significance threshold was calculated by a permutation test (Churchill and Doerge, 1994) for each of SSC1 and SSC7, with 5,000 repetitions. We also estimated the genome-wide significance threshold from the chromosome-wide significance threshold following the method of de Koning et al. (1999):
The contributions (r) of SSC1 and SSC7 to the total length of autosomal chromosome were 0.0667 and 0.0726, respectively, calculated using the report of Rohrer et al. (1996). Genomewise P = 0.01 corresponds to SSC1 P = 6.7 x 10–4 and SSC7 P = 7.3 x 10–4. Genomewise P = 0.05 corresponds to SSC1 P = 3.4 x 10–3 and SSC7 P = 3.7 x 10–3.
Evaluation of Heterozygosity of QTL on SSC1 of the Göttingen Miniature Sire in the MG Family
To scrutinize the heterozygosity of the QTL on SSC1 in the MG family, we inferred the inheritance of each homologous allele at the QTL in the Göttingen miniature sire to F1 and F2 individuals by using the micro-satellite marker SW705, for which the Göttingen miniature sire was heterozygous. Marker SW705 was at the peak position of the plotting of F-ratios, and all alleles of two Meishan grand dams were different from those of the Göttingen miniature sire. Whether the sire was homozygous or heterozygous at the QTL was determined by testing four hypotheses for QTL genotype—H0, H1, H2, and H3—wherein we assumed the genotypes of the Göttingen miniature sire to be q/q in H0, Q/Q in H1, Q/q in H2, and Q1/Q2 in H3. In contrast, we assumed the QTL genotype of the Meishan dam to be q/q in all hypotheses. In accordance with each of these hypotheses, we inferred the QTL genotype of each F2 individual from the genotype at SW705. We applied linear models assuming the additive allelic effect without dominance for a QTL at position SW705 to the number of vertebrae of F2 individuals corresponding to each of the hypotheses. Under H0, all individuals in the F2 had a genotype q/q at QTL. Under H1 and H2, three possible genotypes—Q/Q, Q/q, and q/q—existed in the F2, and their effects were assumed to be a, 0, and –a, respectively. Under H3, there were six QTL genotypes—Q1/Q1, Q2/Q2, Q1/Q2, Q1/q, Q2/q, and q/q—for which we assumed the genotypic effects to be 2a, 2b, a + b, a, b, and 0, respectively. We evaluated heterozygosity at the QTL for the Göttingen miniature sire on the basis of the comparisons of goodness-of-fit in models between H1 and H3. We measured this by log-likelihood ratio test statistics obtained from the maximum likelihood under each of the two hypotheses to be compared, assuming normal distributions for the number of vertebrae of F2 individuals with means corresponding to their QTL genotypes. If H3 (Q1/Q2) showed a better (P < 0.05) model fit than H1 (Q/Q), then we judged the sire to be heterozygous at the QTL. The significance level of log-likelihood ratio test statistic was determined by a permutation test of 10,000 repetitions.
Evaluation of Heterozygosity of QTL on SSC7 in Parental European Pigs in Experimental Families
We searched for heterozygous microsatellite markers around the QTL region in each parental European pig. To examine the heterozygosity of the QTL on SSC7, we used one of the heterozygous markers for each parental European pig to infer the inheritance of each of two homologous alleles by the F1 and F2 offspring. We determined whether each parental European pig was homozygous or heterozygous by the same statistical testing used to evaluate the heterozygosity of the QTL on SSC1 in the Göttingen miniature sire.
Half-Sib Analysis of Sires in a Large White Population on SSC7 for the Number of Vertebrae
We scored the number of vertebrae in 896 individuals produced from a Large White population. The population was derived from 10 sires and 65 dams as founder individuals and was bred in a closed population for seven generations (1987 to 1993) with 8 to 11 sires and 28 to 36 dams in the Livestock Research Institute of Tokushima prefecture in Japan. Using the microsatellite markers SW147 (90.1 cM in the USDA map), SW252 (99.4 cM), and S0115 (102.2 cM), which were located on SSC7 near the QTL for vertebral number, we genotyped the 896 progeny, as well as their 25 sires and 69 dams. Haplotypes consisting of these three microsatellite markers on each homologous chromosome of the sires were reconstructed by using genotype data of the sires, dams, and their progeny. Among 896 progeny, 786 derived from 12 sires and 24 dams were classified with certainty into two groups based on the haplotype (left or right) inherited. We compared the average number of vertebrae in two groups of progeny for each sire and used t-tests to evaluate the significance of the differences. Sires were considered to be heterozygous (Q/q) at the QTL when differences (P < 0.05) were detected. Moreover, to detect the sires homozygous for the QTL, we performed Z-tests following the manner of Nezer et al. (2003). The Q-to-q substitution effect was set at 0.43, which was derived from the value 0.43 ± 0.10 calculated from nine heterozygous sires. Sires were judged to be homozygous when Z < –2.
Interaction of Two QTL on SSC1 and SSC7 for Number of Vertebrae
By using the JD family, in which the grand sire and the five grand dams were fixed for the alternative alleles of the QTL on both SSC1 and SSC7, a two-dimensional search was carried out on SSC1 and SSC7 for testing hypotheses H0 (no epistasis exists) vs. H1 (epistasis exists). The numbers of microsatellite markers on SSC1 and SSC7 were eight and nine, respectively. A test statistic to detect epistasis was n x log (RSS0/RSS1), where RSS0 (RSS1) is RSS (residual sum of squares) under H0 (H1), and n is the sample size. A threshold for this statistic was determined by a permutation test with 1,000 repetitions.
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Results
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Genome Scanning of QTL for the Number of Vertebrae
We performed genome scanning of QTL for the number of vertebrae in each of three swine families (MG, ML, and LWb). In all three families, a QTL was detected in a region around SW705 on SSC1qter (Figure 1a; Table 2). In the ML and LWb families, another QTL for the number of vertebrae was detected in a region around SW252 on SSC7 (Figure 1b; Table 3). To examine the existence of the QTL in the other six families, interval mapping analyses on SSC1 and SSC7 were performed.
QTL on SSC1 for the Number of Vertebrae
In the other six families (JW, BC, MW, LM, JD, and WWb), QTL also were detected in a region of SSC1qter (Table 2
). In all families, the alleles from the European breed pigs had a significant additive effect, but no significant dominance effect, increasing the number of vertebrae. In the MG family, the estimated additive effect of the alleles from the Göttingen miniature sire was lower (at 0.32) than those from other European breed pigs, at 0.44 to 0.69 (Table 2). The proportion of phenotypic variance in number of vertebrae explained by the QTL also was less in the MG family (12.3%) than in other families (26.0 to 42.6%).
Heterozygosity of QTL on SSC1 of the Göttingen Miniature Sire in the MG Family
The Göttingen miniature sire had a smaller estimated effect at the QTL than those detected in other families. It is possible that we underestimated the allelic effect of the QTL for the sire when the sire was assumed to be homozygous at the QTL in the interval mapping analysis. Therefore, we investigated the heterozygosity of the QTL of the Göttingen miniature sire using the microsatellite marker SW705 (Table 4). Hypothesis testing revealed that all models of H1 (Q/Q), H2 (Q/q), and H3 (Q1/Q2) gave better (P < 0.01) model fits than did model H0 (q/q). When models of H1 (Q/Q) and H3 (Q1/Q2) were compared, Model H3 (Q1/Q2) gave a better (P < 0.01) model fit than did Model H1 (Q/Q). Therefore, we judged the QTL to be heterozygous in the Göttingen miniature sire. Heterozygosity of this QTL was not detected either for the Meishan pigs in this family or for the other European pigs used as grand sires or grand dams in other families (data not shown).
QTL on SSC7 for the Number of Vertebrae
By genome scanning, we detected another QTL for the number of vertebrae in a region around microsatellite marker SW252 on SSC7 in the ML (1% genome-wide) and LWb (5% genome-wide) families but not in the MG family. In the ML family, estimates of additive effects of the QTL on SSC1 and on SSC7 in the Landrace sire were similar at 0.59 and 0.68, respectively (Tables 2 and 3). Conversely, in the LWb family, the additive effect of the QTL on SSC7 in the Landrace dams was estimated to be 0.28, which was less than one-half that on SSC1 (0.63). In both families, significant dominance effects were not observed. In the analysis of SSC7 with interval mapping, significant effects also were detected around the same region on SSC7 in the JW (5% genome-wide) family and in the BC, MW, and JD families (1% genome-wide), whereas no significant effects were detected in the LM and WWb families (Table 3) or in the MG family.
Heterozygosity of QTL on SSC7 of European Parental Pigs in Experimental Families
As a reason for not detecting the significant effects on SSC7 in some families, we considered that the allele that increases the number of vertebrae was not fixed in the European parental pigs in the experimental families. Therefore, heterozygosity of the QTL of the European parental pigs was examined in the same way that we tested the QTL on SSC1 of the Göttingen miniature sire in the MG family. In the LWb family, two Landrace female pigs (L1 and L2) had been used as grand dams. Analysis with microsatellite marker SW252 suggested that one Landrace grand dam (L1) was heterozygous at the QTL on SSC7 (Table 5). One allele had the effect of increasing the number of vertebrae by 0.64, an amount similar to that detected in the ML family (0.68). For the other Landrace grand dam (L2), significant effects of the QTL were not detected in any models. In the other families, we also analyzed the variation in the QTL on SSC7 in the European parental pigs, using heterozygous microsatellite markers near the QTL (Table 5). As a result, it was judged that the Large White male pig in the JW family, the Landrace female in the LM family, and one (W1) of the Large White females in the WWb family were heterozygous for the QTL on SSC7. In the ML, BC, MW, and JD families, the QTL on SSC7 was judged to be homozygous in the European parental pigs, and all European alleles had significant effects in increasing the number of vertebrae. For the Göttingen miniature male pig in the MG family and two (W2 and W3) of the Large White females in the WWb family, significant effects of the QTL were not detected on SSC7 in any models.
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Table 5. Evaluation of heterozygosity of QTL on SSC7 for the number of vertebrae of the European parent pigs in experimental families
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Variation in QTL on SSC7 in a Commercial Large White Population
In European pigs such as Landrace, Large White, and Duroc, the number of vertebrae are not fixed and may vary from 21 to 23. Indeed, when we scored the number of vertebrae in a total of 896 progeny derived from 25 sires in a Large White population, 303 pigs (33.8%) had 21 thoracic and lumbar vertebrae, 569 (63.5%) had 22 such vertebrae, and 24 pigs (2.7%) had 23; the average total number of thoracic and lumbar vertebrae was 21.69. To investigate whether this variation in the number of vertebrae was due to variation in the QTL on SSC7, we performed a half-sib analysis using the microsatellite markers SW147, SW252, and S0115, located on SSC7 near the QTL (Table 6). As a result of analysis using 786 progeny derived from 12 sires, which were classified with certainty into two groups based on the haplotype, nine sires seemed to be heterozygous for the QTL. One sire seemed to be homozygous, and it was not clear whether the others were homozygous. We performed the same analysis for the QTL on SSC1, but variation in the QTL was not detected (data not shown).
Interaction of Two QTL on SSC1 and SSC7 for Number of Vertebrae
In the JD family, which was the largest family in this study, the grand sire and the five grand dams were fixed for the alternative alleles of the QTL on both SSC1 and SSC7. Using this family, we analyzed the interaction between the two QTL. A two-dimensional search was performed on SSC1 and SSC7 to test the hypotheses H0 (no epistasis present) vs. H1 (epistasis present). No significant epistatic interaction between the two QTL was observed (data not shown). The average number of vertebrae of F2 progeny belonging to nine categories, as classified by the genotypes of the two QTL, showed clearly that the two QTL had an additive effect and acted independently without interaction (Figure 2). Substitution of four Asian alleles with four European alleles in the two QTL explained the increase in the number of vertebrae by an average of more than two.
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Figure 2. Average number of vertebrae in F2 progeny in each category as classified by the genotypes of the two QTL on SSC1 and SSC7. In accordance with the genotypes of the two QTL, 528 F2 progeny in the JD (Jinhua x Duroc) family were classified into nine categories. Standard deviations are shown by vertical lines. The letters (a, b, c, or d) indicate mean separation; average number of vertebrae of F2 progeny in categories that do not have a common letter differ (P < 0.05).
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Discussion
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In a previous study, we identified a QTL on SSC1 qter that affected the number of vertebrae in a three-generation family derived from a cross between Meishan and Göttingen miniature pigs. In the present study, we found that the Göttingen miniature sire was heterozygous in the QTL on SSC1 based on the comparison between goodness of model fitting for H1 (Q/Q) and H3 (Q1/Q2). Moreover, the likelihood ratio of Model H2 (Q/q) to Model H3 (Q1/Q2) can be calculated as 2.5 from Table 4, considering the difference between log-likelihood ratio test statistics of H2 vs. H0 (50.8) and H3 vs. H0 (53.3), which is not significant. Therefore, it was inferred that the genotype of the sire is Q/q. We speculate that the allele that had this effect was derived from a European breed and that the other was derived from Asian breeds as part of the process of breeding Göttingen miniature pigs, which were constructed by using European and Asian breeds (Porter, 2002). When the QTL genotype of the sire was assumed to be heterozygous (Q/q), the proportion of phenotypic variance in number of vertebrae explained by the QTL was calculated as 24.2%. In the experimental families in this study, all of the alleles of European breeds at the QTL on SSC1 had the effect of increasing the number of vertebrae, and Model H3 (Q1/Q2) did not give a significantly better model fit than did Model H1 (Q/Q; data not shown). Although we analyzed only a limited number of samples, it is possible that the allele increasing the number of vertebrae at the QTL on SSC1 has already spread widely in commercial pigs.
On SSC7 we also detected another QTL for the number of vertebrae; this QTL was located at a similar position to that reported by Sato et al. (2003). In this study, we attempted to evaluate the heterozygosity of the QTL on SSC7 for the Göttingen miniature and 11 European pigs used as parents of F2 experimental families and found that four European parent pigs, one each of the LWb, JW, LM, and WWb families, were heterozygous (Q1/Q2; Table 5) in the QTL. When models of H2 (Q/q) and H3 (Q1/Q2) were compared for the four European parent pigs, log-likelihood ratio test statistics of H2 vs. H3 ([H3 vs. H0] – [H2 vs. H0]) were calculated to be 0.4, 0.5, 0.2, and 0.6 for L1 of the LWb family, W of JW, L of LM, and W1 of WWb, respectively, and not significant. Thus, it was inferred that genotypes of the QTL for the four pigs were Q/q and that some of the European alleles at this QTL had the effect of increasing the number of vertebrae. The variation of this QTL on SSC7 also was detected in a Large White population. Although a limited number of samples were analyzed, it is possible that the allele that increases the number of vertebrae was only recently introduced into European breeds, spreading throughout the breeds along with breeding for increased body length, and is not yet fixed. For this reason, the QTL on SSC7 is valuable in the breeding of commercial pigs. A possible reason for the variation in the QTL on SSC7 in commercial pig breeds is that an unknown locus affecting productivity or meat quality is linked to the QTL and prevents fixation of the allele that increases the number of vertebrae. Many QTL have been identified on SSC7. Among them, QTL for backfat thickness and growth rate are located 30 cM away from the QTL for number of vertebrae, and Asian (Meishan) alleles have been reported to make the backfat thinner and growth faster (Rohrer and Keele, 1998; de Koning et al., 1999; Rohrer, 2000; Bidanel et al., 2001). In Asian pigs used for breeding, Asian alleles at QTL for backfat thickness and growth rate would have been selected for. At the same time, Asian alleles at QTL for the number of vertebrae, which would not have had the effect of increasing the number of vertebrae, might have been reintroduced unexpectedly.
In the present study, two QTL were detected on SSC1 and SSC7 that affect the number of vertebrae associated with body length. At the QTL on SSC7, variation was found within commercial pig breeds. This information should be useful in breeding programs, such as those that use marker-assisted selection.
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Footnotes
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1 This work was supported by the DNA Marker Project of the Ministry of Agriculture, Forestry, and Fisheries of Japan and by a Grant-in-Aid from the Japan Racing Association. 
2 Correspondence: Ikenodai 2 (phone: 81-29-838-8627; fax: 81-29-838-8627; e-mail: mikawa{at}affrc.go.jp).
Received for publication November 3, 2004.
Accepted for publication June 16, 2005.
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Top
Abstract
Introduction
= ML (Meishan x Landrace), ^ = LWb (Landrace x Japanese wild boar), and 
= MG (Meishan x Göttingen miniature) families. Triangles (
;
) on the x-axis indicate the positions of microsatellite markers. Uppermost triangles represent the ML family. Triangles positioned in the middle row represent the LWb family, and lowermost triangles represent the MG family. On SSC1, the positions of microsatellite marker SW705 are indicated by closed triangles. On SSC7, the positions of microsatellite markers SW147, SW252, and S0115 are indicated by closed triangles, from left to right.