Limits...
Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs.

Cho IC, Yoo CK, Lee JB, Jung EJ, Han SH, Lee SS, Ko MS, Lim HT, Park HB - Genet. Sel. Evol. (2015)

Bottom Line: QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level.In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10(-55)).Our results confirm several previously reported QTL.

View Article: PubMed Central - PubMed

Affiliation: Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea. choic4753@korea.kr.

ABSTRACT

Background: We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis.

Results: We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10(-55)). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization.

Conclusions: Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs.

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Related in: MedlinePlus

QTL profiles for meat quality related traits on SSC12. The y-axis represents the F-value testing the hypothesis of a single QTL on a given position on the chromosome. The marker map with genetic distance between microsatellite (MS) markers in Kosambi cM is given on the x-axis. The thick horizontal line indicates the 1% genome-wide significant threshold and thin horizontal line indicates the 5% chromosome-wide significant threshold. Trait abbreviations are in Table 1. (A) QTL profile for CFAT. (B) QTL profiles for EMA (eye muscle are), ALLEMA (EMA area and spinalis dorsi muscle), MARB (marbling score in EMA), SHEAR (shear force), MOIST (moisture percentage), DRIPL (drip loss), CIE-a (meat color red/green), CIE-b (meat color yellow/blue), and CHROMA (meat color chroma).
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Fig1: QTL profiles for meat quality related traits on SSC12. The y-axis represents the F-value testing the hypothesis of a single QTL on a given position on the chromosome. The marker map with genetic distance between microsatellite (MS) markers in Kosambi cM is given on the x-axis. The thick horizontal line indicates the 1% genome-wide significant threshold and thin horizontal line indicates the 5% chromosome-wide significant threshold. Trait abbreviations are in Table 1. (A) QTL profile for CFAT. (B) QTL profiles for EMA (eye muscle are), ALLEMA (EMA area and spinalis dorsi muscle), MARB (marbling score in EMA), SHEAR (shear force), MOIST (moisture percentage), DRIPL (drip loss), CIE-a (meat color red/green), CIE-b (meat color yellow/blue), and CHROMA (meat color chroma).

Mentions: On SSC12, we identified a major additive QTL for CFAT (F-ratio = 278.0, nominal P-value = 5.5 × 10−55) (Figure 1A). This QTL was the most significant QTL detected in this study and explained 22.5% of the phenotypic variance. The allele of this QTL present in the KNP breed was found to be associated with higher phenotypic values of CFAT. A highly significant QTL for MARB was also identified in the same region, with an F-ratio of 68.3 (nominal P-value = 5.5 × 10−16) and accounting for 7.6% of the phenotypic variance. Previous studies reported that a cluster of genes on SSC12 that encode the myosin heavy chain (MYH) was associated with IMF [26,27]. However, the genetic map used in our study did not include MYH loci. Thus, further studies are necessary to investigate the effects of MYH loci on CFAT and MARB. An allele present in the KNP breed was associated with higher phenotypic values of MARB. Interestingly, this QTL region overlapped with those of EMA, ALLEMA, SHEAR, MOIST and DRIPL in this study. The same region also influenced backfat thickness between the 4th and 5th ribs [28].Figure 1


Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs.

Cho IC, Yoo CK, Lee JB, Jung EJ, Han SH, Lee SS, Ko MS, Lim HT, Park HB - Genet. Sel. Evol. (2015)

QTL profiles for meat quality related traits on SSC12. The y-axis represents the F-value testing the hypothesis of a single QTL on a given position on the chromosome. The marker map with genetic distance between microsatellite (MS) markers in Kosambi cM is given on the x-axis. The thick horizontal line indicates the 1% genome-wide significant threshold and thin horizontal line indicates the 5% chromosome-wide significant threshold. Trait abbreviations are in Table 1. (A) QTL profile for CFAT. (B) QTL profiles for EMA (eye muscle are), ALLEMA (EMA area and spinalis dorsi muscle), MARB (marbling score in EMA), SHEAR (shear force), MOIST (moisture percentage), DRIPL (drip loss), CIE-a (meat color red/green), CIE-b (meat color yellow/blue), and CHROMA (meat color chroma).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4336478&req=5

Fig1: QTL profiles for meat quality related traits on SSC12. The y-axis represents the F-value testing the hypothesis of a single QTL on a given position on the chromosome. The marker map with genetic distance between microsatellite (MS) markers in Kosambi cM is given on the x-axis. The thick horizontal line indicates the 1% genome-wide significant threshold and thin horizontal line indicates the 5% chromosome-wide significant threshold. Trait abbreviations are in Table 1. (A) QTL profile for CFAT. (B) QTL profiles for EMA (eye muscle are), ALLEMA (EMA area and spinalis dorsi muscle), MARB (marbling score in EMA), SHEAR (shear force), MOIST (moisture percentage), DRIPL (drip loss), CIE-a (meat color red/green), CIE-b (meat color yellow/blue), and CHROMA (meat color chroma).
Mentions: On SSC12, we identified a major additive QTL for CFAT (F-ratio = 278.0, nominal P-value = 5.5 × 10−55) (Figure 1A). This QTL was the most significant QTL detected in this study and explained 22.5% of the phenotypic variance. The allele of this QTL present in the KNP breed was found to be associated with higher phenotypic values of CFAT. A highly significant QTL for MARB was also identified in the same region, with an F-ratio of 68.3 (nominal P-value = 5.5 × 10−16) and accounting for 7.6% of the phenotypic variance. Previous studies reported that a cluster of genes on SSC12 that encode the myosin heavy chain (MYH) was associated with IMF [26,27]. However, the genetic map used in our study did not include MYH loci. Thus, further studies are necessary to investigate the effects of MYH loci on CFAT and MARB. An allele present in the KNP breed was associated with higher phenotypic values of MARB. Interestingly, this QTL region overlapped with those of EMA, ALLEMA, SHEAR, MOIST and DRIPL in this study. The same region also influenced backfat thickness between the 4th and 5th ribs [28].Figure 1

Bottom Line: QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level.In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10(-55)).Our results confirm several previously reported QTL.

View Article: PubMed Central - PubMed

Affiliation: Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea. choic4753@korea.kr.

ABSTRACT

Background: We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis.

Results: We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10(-55)). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization.

Conclusions: Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs.

Show MeSH
Related in: MedlinePlus