Journal of Heredity Advance Access originally published online on September 19, 2006
Journal of Heredity 2006 97(5):535-537; doi:10.1093/jhered/esl026
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Brief Communications |
A Quantitative Trait Locus for Oleic Fatty Acid Content on Sus scrofa Chromosome 7
From the Ilsong Institute of Life Science, Hallym University, Anyang, Kyonggi-do 431-060, Korea
Address correspondence to C. Lee at the address above, or e-mail: clee{at}hallym.ac.kr.
A partial genome scan using microsatellite markers was conducted to detect quantitative trait loci (QTLs) for 10 fatty acid contents of backfat on 15 chromosomes in a porcine resource population. Two QTLs were discovered on Sus scrofa chromosome 4 (SSC4) and SSC7. The QTL on SSC4 was located between marker loci sw1336 and sw512, and this QTL was detected (P < 0.05) only for linoleic acid. Its position was in proximity of those mapped for linoleic acid content in previous studies. The QTL on SSC7 was mapped between markers swr1343 and sw2155, and it was significant (P < 0.05) only for oleic acid. A novelty of the QTL for oleic acid was suggested because the QTL was located far from any other QTLs previously mapped for fatness traits. The QTL on SSC7 explained 19% of phenotypic variation for oleic acid content. Further studies on fine mapping and positional comparative candidate gene analysis would be the next step toward better understanding of the genetic architecture of fatty acid contents.
The fatty acids have been concerned as important nutrients for health. Especially, they help to maintain the health of cell membranes, to improve nutrient use, and to establish and control cellular metabolism. In despite of the great concern, the genetic characterization of the metabolism for fatty acid contents has been limitedly known. Recently, a few attempts of quantitative trait locus (QTL) mapping for fatty acid contents have been made on porcine chromosomes [Sus scrofa chromosomes (SSCs)]. The first report on the QTL mapping related to the fatty acid metabolism was the study by Perez-Enciso et al. (2000) on SSC4 where ample evidence for a QTL influencing fat deposition had been shown and a QTL influencing linoleic and oleic fatty acid contents was detected in subcutaneous adipose tissue. Clop et al. (2003) mapped QTLs for the fatty acids on the whole autosomes and discovered significant QTLs located on SSC4 (linoleic acid), SSC8 (palmitic and palmitoleic acids), SSC10 (myristic acid), and SSC12 (linoleic acid). Also, Lee et al. (2003) studied QTL mapping for the fatty acid composition on SSC1, SSC13, and SSC18 to see pleiotropic effects of the QTLs that had already been identified also for fatness traits and found 2 QTLs in SSC1 (linoleic fatty acid) and SSC18 (myristic fatty acid).
The objective of this study was to search for QTLs contributing to fatty acid contents by a genome scan on the full porcine autosomes except for the chromosomes 1, 13, and 18 on which QTLs for fatty acid contents were previously studied with a priority by Lee et al. (2003). This study completed the full autosomal genome scan project for QTL mapping to characterize the effect on the metabolism of fatty acids.
 |
Materials and Methods |
|---|
 Top Materials and Methods Results and DiscussionReferences |
|---|
Resource Population and Trait Measurement
The population utilized in this QTL-mapping study included a total of 298 pigs with a pedigree consisting of 2 founders, 7 F1 animals, 185 intercross, and 104 backcross progeny (Lee et al. 2003). The resource population was initiated by mating a single Landrace boar with a single Yorkshire sow, followed by backcross, intercross, and sib matings. The phenotypes analyzed for QTL mapping were the percentages of 10 different fatty acid contents in porcine backfat. The fatty acid composition was measured from backfat samples by gas chromatography. The phenotypic means of F2 and backcross progeny in the population are presented in Table 1.
|
Microsatellite Analysis and Genotyping
Genomic DNAs were isolated following a conventional method of Sambrook et al. (1989). We used 233 microsatellite markers over the whole porcine genome in the polymerase chain reaction (PCR) amplification, of which 159 were polymorphic in the founder generation. These microsatellite markers gave a reasonable coverage of the porcine genome mostly at 5- to 15-cM intervals. The PCR analyses of the microsatellites were carried out as described in Lee et al. (2003).
Statistical Analysis
The linkage maps of frame markers were constructed using CRIMAP (Green et al. 1990). The sex-averaged map was used for the full genome scan. Parents with two or more double recombinants between adjacent marker loci with an interval less than 15 cM were reexamined, and marker genotypes inconsistent with the pedigree were also reexamined. Unidentifiable marker genotypes were considered as unknown. The individuals with genotypes inconsistent with the pedigree information at two or more marker loci were all removed.
The QTL mapping with F2 and backcross progeny was analyzed by the method described in Lee (2005). The method was devised to estimate marker genotype means by a mixed model approach and then to estimate the QTL effects by a weighted least square analysis based on the conditional frequencies of QTL given marker genotypes. The marker genotype means were estimated based on a mixed model framework with restricted maximum likelihood estimation of variance components using SAS Release 9.1 (SAS Institute Inc., Cary, NC). The analytical model included age as a covariate, sex as a fixed effect, and full-sib litter and marker genotype as random effects. The full-sib litter effect reflected not only common environmental effects but also possible genetic effects accumulated by mating histories. A genomewise significance threshold was empirically obtained by the permutation test of Churchill and Doerge (1994). The 10 000 replicates were generated to obtain the threshold value at a significance level of 0.05.
|
Results and Discussion |
|---|
|
TopMaterials and MethodsResults and DiscussionReferences |
|---|
Linkage Map
The order of the markers in the linkage maps estimated in this study was in agreement with USDA-MARC linkage map database (http://www.marc.usda.gov/genome/swine). In the linkage analysis, 159 polymorphic microsatellite markers were assigned into 15 linkage groups with the total length of 1888.1 cM (Table 2).
|
QTL Detection
We discovered 2 QTLs located on SSC4 and SSC7 for fatty acid contents in this pig population (Figure 1). Furthermore, we found a suggestive QTL [logarithm of the odds (LOD) score = 4.8] near SW957 on SSC12 for palmitoleic and palmitic fatty acids (data not shown). This suggestive QTL was located close to the region where Clop et al. (2003) identified a QTL for palmitoleic and palmitic acids on SSC12.
|
= 0.05.QTL on SSC4
The QTL discovered on SSC4 was significant (P < 0.05) only for linoleic fatty acid content (Figure 1a), which concurred with the results of Perez-Enciso et al. (2000) and Clop et al. (2003). This QTL did not have a significant impact on the other fatty acids (P > 0.05). The QTL for linoleic acid was mapped between the marker loci sw1089 and sw512, and its peak position was at 68 cM. The region was located in the proximity of those mapped in the previous studies, and the 95% confidence intervals of the linkage positions estimated in the current and previous studies were all overlapped. The QTLs by Clop et al. (2003) and Perez-Enciso et al. (2000) mapped to position 79 and 75 cM, respectively. This QTL on SSC4 warrants further research and might be of great importance in genetic improvement of pigs.
This linoleic acid QTL explained 11% of phenotypic variance in this pig family. When we considered this QTL on SSC4 simultaneously with the QTL on SSC1 previously found in our laboratory (Lee et al. 2003), 40% of the phenotypic variance of the linoleic acid content could be explained by these 2 QTLs.
The QTL identified by Perez-Enciso et al. (2000) was also significant for growth traits as well as fatness traits (P < 0.05). The pleiotropic effects of this QTL were plausible because linoleic acid is an important fatty acid for growth. Especially, linoleic fatty acid is an essential component for cellular membranes and a precursor of prostaglandins and thromboxanes. The influence of the QTL on growth and fatness might contribute to the phenotypic correlation of these traits observed in the field data. Furthermore, understanding pleiotropic effects of a QTL might indicate a metabolic pathway and would provide valuable insights into the selection of positional candidate genes.
The QTL for linoleic acid detected by Perez-Enciso et al. (2000) had also a significant impact on oleic fatty acid content (P < 0.05). On the other hand, the QTL for oleic fatty acid content was not detected on SSC4 in the current study (P > 0.05). However, the maximum LOD score (3.8) estimated for oleic acid in this study was in proximity of the region where Perez-Enciso et al. (2000) identified a QTL. This QTL was suspected to contribute a negative correlation between the 2 fatty acid contents. A negative correlation was reported between fat deposition and linoleic fatty acid content (Nurnberg et al. 1998), suggesting that fat animals had low linoleic acid. On the other hand, there is a tendency of high oleic content in fat animals because the oleic acid is the main storage component.
QTL on SSC7
The QTL identified on chromosome 7 was significant (P < 0.05) only for oleic fatty acid content but not (P > 0.05) for the other fatty acid contents (Figure 1b). This QTL mapped near sw1354, and the QTL peak was at position 26 cM. The QTL explained 19% of phenotypic variance for oleic fatty acid content in this pig family.
Some QTLs have been discovered for porcine fatness on SSC7. Rohrer and Keele (1998) found QTLs for last rib backfat, last lumbar backfat, and average backfat (P < 0.05) and their positions were 62, 40, and 58 cM, respectively. Two QTLs were detected for subcutaneous fat thickness and intramuscular fat portion by Sato et al. (2003), and their positions were 56 and 113 cM. The positions of the QTLs for backfat estimated by Demeure et al. (2005) were 55 and 63 cM for average backfat; 62, 63, and 83 cM for rump backfat; and 62, 64, and 87 cM for back backfat. The discrepancies between the location estimates of the QTLs for oleic acid in the current study and for fatness traits in the former studies were not negligible, which might suggest a novelty of the QTL discovered in this study.
|
Acknowledgments |
|---|
We thank Prof Leif Andersson and 2 anonymous reviewers for their valuable comments on the previous version of this article. This study was supported by the Korea Research Foundation Grant (KRF-2005-202-F00032).
|
Footnotes |
|---|
Corresponding Editor: Leif Andersson
Received January 30, 2006
Accepted July 17, 2006
|
References |
|---|
|
TopMaterials and MethodsResults and DiscussionReferences |
|---|
-
Churchill GA and Doerge RW. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971.[Abstract]
Clop A, Ovilo C, Perez-Enciso M, Cercos A, Tomas A, Fernandez A, Coll A, Folch JM, Barragan C, Diaz I, et al. (2003) Detection of QTL affecting fatty acid composition in the pig. Mamm Genome 14:650–656.[CrossRef][Web of Science][Medline]
Demeure O, Sanchez MP, Riquet J, Iannuccelli N, Demars J, Feve K, Kernaleguen L, Gogue J, Billon Y, Caritez JC, et al. (2005) Exclusion of the swine leukocyte antigens as candidate region and reduction of the position interval for the Sus scrofa chromosome 7 QTL affecting growth and fatness. J Anim Sci 83:1979–1987.
Green P, Falls K, Crooks S. (1990) Documentation for CRIMAP. Version 2.4. (Washington University School of Medicine, St Louis, MO).
Lee C. (2005) Selection bias in quantitative trait loci mapping. J Hered 96:363–367.
Lee C, Chung Y, Kim JH. (2003) Quantitative trait loci mapping for fatty acid contents in the backfat on porcine chromosomes 1, 13, and 18. Mol Cells 28:62–67.
Nurnberg K, Wegner J, Ender K. (1998) Factors influencing fat composition in muscle and adipose tissue of farm animals. Livest Prod Sci 56:145–156.[CrossRef]
Perez-Enciso M, Clop A, Noguera JL, Ovilo C, Coll A, Folch JM, Babot D, Estany J, Oliver MA, Diaz I, et al. (2000) A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross. J Anim Sci 78:2525–2531.
Rohrer GA and Keele JW. (1998) Identification of quantitative trait loci affecting carcass composition in swine: I. Fat deposition traits. J Anim Sci 76:2247–2254.
Sambrook J, Fritish EF, Maniatis T. (1989) Molecular cloning. (Harbor Laboratory Press, Cold Spring Harbor, NY).
Sato S, Oyamada Y, Atsuji K, Nade T, Sato S, Kobayashi E, Mitsuhashi T, Nirasawa K, Komatsuda A, Saito Y, et al. (2003) Quantitative trait loci analysis for growth and carcass traits in a Meishan x Duroc F2 resource population. J Anim Sci 81:2938–2949.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Uemoto, S. Sato, C. Ohnishi, S. Terai, A. Komatsuda, and E. Kobayashi The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan x Duroc crossbred population J Anim Sci, November 1, 2009; 87(11): 3470 - 3476. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||