Recently, the development of “next-generation” sequencing technologies make it possible to use stored pig genetic information and high-density SNP analysis, which enable pig QTL to be discovered within a 1 or 2 Mb confidence interval.
The Korean native pig (KNP) has a black coat color and a capa...
Recently, the development of “next-generation” sequencing technologies make it possible to use stored pig genetic information and high-density SNP analysis, which enable pig QTL to be discovered within a 1 or 2 Mb confidence interval.
The Korean native pig (KNP) has a black coat color and a capacity to produce tender meat which is high in muscular fat, but low in cholesterol; and has more unsaturated fat than saturated fat. However, it also has a low birth weight, slow growth, small litter size and a small adult body size. The genetic factors for better marbling and pork quality of KNP is largely unknown and the amount of molecular genetics information is relatively insufficient.
Therefore, these studies consist of three chapters, which are i) QTL analysis for meat quality using Illumina Porcine SNP 60K Bead chip between Korean Native pig (KNP) and Yorkshire (YS), ii) GWAS to detect SNPs and candidate genes regarding meat quality traits for KNP⨯YS cross breeding population, iii) identifying variation in porcine FASN gene, determining if the variation is genetic factors that affect meat quality and fatty acid composition, and evaluation in different breeds.
i) attempted to generate a linkage map using Illumina Porcine 60K SNP Beadchip genotypes of the F2 offspring from Korean native pig (KNP) crossed with Yorkshire (YS) pig, and to identify quantitative trait loci (QTL) using the line-cross model.
Among the genotype information of the 62,136 SNPs obtained from the high-density SNP analysis, 45,308 SNPs were used to select informative markers with allelic frequencies >0.7 between the KNP (n=16) and YS (n=8) F0 animals. Of the selected SNP markers, a final set of 500 SNPs with polymorphic in formation contents (PIC) values of >0.300 in the F2 groups(n=252) was used for detection of thirty meat quality-related QTL on chromosomes at the 5% significance level and 10 QTL at the 1% significance level.
The QTL for crude protein were detected on SSC 2, 3, 6, 9 and 12; for intramuscular fat and marbling on SSC 2, 8, 12, 14 and 18; meat color measurements on SSC 1, 3, 4, 5, 6, 10, 11, 12, 16 and 18; water content related measurements in pork were detected on SSC 4, 6, 7, 10, 12 and 14. Additional QTL of pork quality traits such as texture, tenderness and pH were detected on SSC 6, 12, 13 and 16. The most important chromosomal region of superior pork quality in KNP compared to YS was identified on SSC 12.
Our results demonstrated that QTL linkage map of the F2 design in the pig breed can be generated with a selected data set of high density SNP genotypes. The QTL regions detected in this study will provide useful information for identifying genetic factors related to better pork quality in KNP.
ii) Pork quality is an economically important trait and one of the main selection criteria for breeding in the pork industry. In this genome-wide association study (GWAS), 344 pigs from a Korean native pig⨯Yorkshire cross population were genotyped using the Illumina Porcine SNP 9K BeadChip, and phenotyped for crude protein (C-pro), intramuscular fat (IMF), marbling score (MAR) meat color score (Color), lightness (CIE-L) redness (CIE-a), yellowness (CIE-b), palmitic (C16:0), Palmitoleic (C16:1), stearic (C18:0), oleic (C18:1), and linoleic acid (C18:2) in the longissimus muscle.
Association tests between each trait and the SNPs were performed via the single-locus mixed linear model GWAS (EMMAX) approach. From the NCBI porcine database, SNP annotation was implemented using Sus scrofa Build 10.2.
A total of 269 SNPs was detected; 5, 35, 34, 18, 13, 41, 16, 3, 8, 16, 16 and 7 SNPs for Crude Protein, Intramuscular Fat, Marbling Score, Color Score, Lightness, Redness, Yellowness, Palmitic acid, Palmitoleic acid, Stearic acid, Oleic acid and Linoleic acid respectively (PT (silent) in exon 4 and c.6545A>C (Asn→His) in exon 39. The frequency of the two SNPs was analyzed by PCR-RFLP in seven pig breeds and their associations with meat quality traits and fatty acid composition were studied.
In the KNP⨯YS F2 population, the two SNPs were significantly associated with the level of monounsaturated fatty acids (MUFAs) including palmitoleic (C16:1) and oleic acid (C18:1) (PC was associated with intramuscular fat (IMF) content in the two pig populations. Haplotype and linkage disequilibrium (LD) studies in five pig breeds revealed three major haplotypes: CA, TC, and CC. With respect to meat quality, the CA haplotype was significantly associated with IMF in the KNP⨯YS F2 and KNP⨯LR F2 populations. The CA and TC haplotypes were also significantly associated with C16:1 and C18:1 in the KNP⨯YS F2 population; in the pigs with one or two copies of CA had a relatively high C18:1 content, whereas those with TC had a relatively low C18:1 content. As pigs with CA had high C18:1, C16:1, and IMF contents, it was consistent that the frequency of CA was higher in KNP (0.990) and Berkshire (0.716) than in Duroc (0.500), Landrace (0.398), and Yorkshire (0.476).
Our results indicate that variations in c.265C>T and c.6545A>C in pig FASN can be used to select animals with better fatty acid composition and meat quality, and that KNP is a useful breed for identifying genetic factors affecting meat quality and fatty acid composition and for the production of high quality pork.
Recently, the development of “next-generation” sequencing technologies make it possible to use stored pig genetic information and high-density SNP analysis, which enable pig QTL to be discovered within a 1 or 2 Mb confidence interval.
The Korean native pig (KNP) has a black coat color and a capacity to produce tender meat which is high in muscular fat, but low in cholesterol; and has more unsaturated fat than saturated fat. However, it also has a low birth weight, slow growth, small litter size and a small adult body size. The genetic factors for better marbling and pork quality of KNP is largely unknown and the amount of molecular genetics information is relatively insufficient.
Therefore, these studies consist of three chapters, which are i) QTL analysis for meat quality using Illumina Porcine SNP 60K Bead chip between Korean Native pig (KNP) and Yorkshire (YS), ii) GWAS to detect SNPs and candidate genes regarding meat quality traits for KNP⨯YS cross breeding population, iii) identifying variation in porcine FASN gene, determining if the variation is genetic factors that affect meat quality and fatty acid composition, and evaluation in different breeds.
i) attempted to generate a linkage map using Illumina Porcine 60K SNP Beadchip genotypes of the F2 offspring from Korean native pig (KNP) crossed with Yorkshire (YS) pig, and to identify quantitative trait loci (QTL) using the line-cross model.
Among the genotype information of the 62,136 SNPs obtained from the high-density SNP analysis, 45,308 SNPs were used to select informative markers with allelic frequencies >0.7 between the KNP (n=16) and YS (n=8) F0 animals. Of the selected SNP markers, a final set of 500 SNPs with polymorphic in formation contents (PIC) values of >0.300 in the F2 groups(n=252) was used for detection of thirty meat quality-related QTL on chromosomes at the 5% significance level and 10 QTL at the 1% significance level.
The QTL for crude protein were detected on SSC 2, 3, 6, 9 and 12; for intramuscular fat and marbling on SSC 2, 8, 12, 14 and 18; meat color measurements on SSC 1, 3, 4, 5, 6, 10, 11, 12, 16 and 18; water content related measurements in pork were detected on SSC 4, 6, 7, 10, 12 and 14. Additional QTL of pork quality traits such as texture, tenderness and pH were detected on SSC 6, 12, 13 and 16. The most important chromosomal region of superior pork quality in KNP compared to YS was identified on SSC 12.
Our results demonstrated that QTL linkage map of the F2 design in the pig breed can be generated with a selected data set of high density SNP genotypes. The QTL regions detected in this study will provide useful information for identifying genetic factors related to better pork quality in KNP.
ii) Pork quality is an economically important trait and one of the main selection criteria for breeding in the pork industry. In this genome-wide association study (GWAS), 344 pigs from a Korean native pig⨯Yorkshire cross population were genotyped using the Illumina Porcine SNP 9K BeadChip, and phenotyped for crude protein (C-pro), intramuscular fat (IMF), marbling score (MAR) meat color score (Color), lightness (CIE-L) redness (CIE-a), yellowness (CIE-b), palmitic (C16:0), Palmitoleic (C16:1), stearic (C18:0), oleic (C18:1), and linoleic acid (C18:2) in the longissimus muscle.
Association tests between each trait and the SNPs were performed via the single-locus mixed linear model GWAS (EMMAX) approach. From the NCBI porcine database, SNP annotation was implemented using Sus scrofa Build 10.2.
A total of 269 SNPs was detected; 5, 35, 34, 18, 13, 41, 16, 3, 8, 16, 16 and 7 SNPs for Crude Protein, Intramuscular Fat, Marbling Score, Color Score, Lightness, Redness, Yellowness, Palmitic acid, Palmitoleic acid, Stearic acid, Oleic acid and Linoleic acid respectively (PT (silent) in exon 4 and c.6545A>C (Asn→His) in exon 39. The frequency of the two SNPs was analyzed by PCR-RFLP in seven pig breeds and their associations with meat quality traits and fatty acid composition were studied.
In the KNP⨯YS F2 population, the two SNPs were significantly associated with the level of monounsaturated fatty acids (MUFAs) including palmitoleic (C16:1) and oleic acid (C18:1) (PC was associated with intramuscular fat (IMF) content in the two pig populations. Haplotype and linkage disequilibrium (LD) studies in five pig breeds revealed three major haplotypes: CA, TC, and CC. With respect to meat quality, the CA haplotype was significantly associated with IMF in the KNP⨯YS F2 and KNP⨯LR F2 populations. The CA and TC haplotypes were also significantly associated with C16:1 and C18:1 in the KNP⨯YS F2 population; in the pigs with one or two copies of CA had a relatively high C18:1 content, whereas those with TC had a relatively low C18:1 content. As pigs with CA had high C18:1, C16:1, and IMF contents, it was consistent that the frequency of CA was higher in KNP (0.990) and Berkshire (0.716) than in Duroc (0.500), Landrace (0.398), and Yorkshire (0.476).
Our results indicate that variations in c.265C>T and c.6545A>C in pig FASN can be used to select animals with better fatty acid composition and meat quality, and that KNP is a useful breed for identifying genetic factors affecting meat quality and fatty acid composition and for the production of high quality pork.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.