Kwon, Anam
(Animal Genomics and Bioinformatics Division, National Institute of Animal Science)
,
Srikanth, Krishnamoorthy
(Animal Genomics and Bioinformatics Division, National Institute of Animal Science)
,
Lee, Eunjin
(Animal Genomics and Bioinformatics Division, National Institute of Animal Science)
,
Kim, Seonkwan
(Animal Genomics and Bioinformatics Division, National Institute of Animal Science)
,
Chung, Hoyoung
(Animal Genomics and Bioinformatics Division, National Institute of Animal Science)
Background: Our previous study had identified the SNP (g.81966377T > C) and indel (g.81966364D > I) located in the promoter of APM1 to have a significant effect on marbling in Hanwoo. APM1 encodes an adipocytokine called adiponectin, which plays a significant role in lipogenesis. The aim of this stu...
Background: Our previous study had identified the SNP (g.81966377T > C) and indel (g.81966364D > I) located in the promoter of APM1 to have a significant effect on marbling in Hanwoo. APM1 encodes an adipocytokine called adiponectin, which plays a significant role in lipogenesis. The aim of this study was to verify and validate the effect of the SNP and indel on marbling and other carcass traits in a large, representative, countrywide population of Hanwoo cattle. The carcass traits measured were marbling (MAR), backfat thickness (BFT), loin eye area (LEA), and carcass weight (CAW). Results: Primers were designed to amplify 346 bp of the genomic segment that contained the targeted SNP (g.81966377) and the indel (g.81966364). After data curation, the genotypes of 8,378 individuals identified using direct sequencing analysis estimated frequencies for C (0.686) and T (0.314) respectively showing genotype frequencies for CC (0.470), CT (0.430) and TT (0.098). The genotypes were significantly associated with MAR, BFT and LEA. The indel had significant effect on marbling (P < .0001) with strong additive genetic effects. The allele frequencies was estimated at (DEL, 0.864) and insertion (INS, 0.136) presenting genotypes of D/D (75.63 %), D/I (21.44 %), and I/I (2.92 %). Significant departure from Hardy-Weinberg equilibrium was not detected for both the SNP and the indel. Conclusion: The SNP genotypes showed significant association with MAR, BFT and LEA with strong additive genetic effects, while the indel was significantly associated with MAR. The results confirmed that the variants can be used as a genetic marker for improving marbling in Hanwoo.
Background: Our previous study had identified the SNP (g.81966377T > C) and indel (g.81966364D > I) located in the promoter of APM1 to have a significant effect on marbling in Hanwoo. APM1 encodes an adipocytokine called adiponectin, which plays a significant role in lipogenesis. The aim of this study was to verify and validate the effect of the SNP and indel on marbling and other carcass traits in a large, representative, countrywide population of Hanwoo cattle. The carcass traits measured were marbling (MAR), backfat thickness (BFT), loin eye area (LEA), and carcass weight (CAW). Results: Primers were designed to amplify 346 bp of the genomic segment that contained the targeted SNP (g.81966377) and the indel (g.81966364). After data curation, the genotypes of 8,378 individuals identified using direct sequencing analysis estimated frequencies for C (0.686) and T (0.314) respectively showing genotype frequencies for CC (0.470), CT (0.430) and TT (0.098). The genotypes were significantly associated with MAR, BFT and LEA. The indel had significant effect on marbling (P < .0001) with strong additive genetic effects. The allele frequencies was estimated at (DEL, 0.864) and insertion (INS, 0.136) presenting genotypes of D/D (75.63 %), D/I (21.44 %), and I/I (2.92 %). Significant departure from Hardy-Weinberg equilibrium was not detected for both the SNP and the indel. Conclusion: The SNP genotypes showed significant association with MAR, BFT and LEA with strong additive genetic effects, while the indel was significantly associated with MAR. The results confirmed that the variants can be used as a genetic marker for improving marbling in Hanwoo.
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문제 정의
The aim of this study was to verify the genetic effect of the SNP g.81966377T > C and an indel (g.81966364D > I) located in the promoter of AMP1 on carcass traits in a nationwide randomly sampled Hanwoo cattle.
제안 방법
The bovine APM1 gene sequence (GenBank: JQ7755868) was retrieved from the Genbank database to design PCR primers using DNA select program of the DNAstar package (Version 6.0). The forward and reverse sequences are CAGCTCGGTACTCATGGGGACAAG and GTGGGAG CTGATGGTGGTAACTGG, respectively.
대상 데이터
The samples were collected over a period of 3 years from 2013 to 2015. The data collected were (MAR, ranging from 1 (for poor) to 9 (highest quality)), loin eye area (LEA, cm2) and backfat thickness (BFT, cm). The average slaughter age of the animals was 31.
The primers were designed to amplify a 346 bp of the APM1 promoter region which included the targeted SNP (g.81966377T > C) and indel (g.81966364D > I) that was previously identified [2, 6, 8, 12].
The samples were collected from the longissimus thoracis muscle between the 12th and 13th rib and stored immediately at -70 °C until use.
The samples were collected from the longissimus thoracis muscle between the 12th and 13th rib and stored immediately at -70 °C until use. The samples were collected over a period of 3 years from 2013 to 2015. The data collected were (MAR, ranging from 1 (for poor) to 9 (highest quality)), loin eye area (LEA, cm2) and backfat thickness (BFT, cm).
데이터처리
The statistical analyses were performed using the Statistical Analysis System [14]. Analysis of Variance (ANOVA) based on general linear model (GLM) was performed to check the genotype effects on carcass traits. The statistical model used was as follows,
이론/모형
The statistical analyses were performed using the Statistical Analysis System [14]. Analysis of Variance (ANOVA) based on general linear model (GLM) was performed to check the genotype effects on carcass traits.
성능/효과
The genotypes of the indel was strongly associated with MAR (P < 0.0001) with significant additive effect, while no significant association with BFT, LEA and CAW was detected (Table 2).
However in order for using this SNP as a standardized genetic marker the effect of this variant on carcass traits has to be verified and validated on a large sample set that is representative of the entire Hanwoo population. Unlike our previous study which had used samples from a specific region, in this study samples were collected from KAPE located throughout the country, in all 8,378 samples were genotyped and their association with meat quality traits were analyzed. Significant additive effects were identified for MAR, BFT and LEA.
참고문헌 (19)
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