Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Experimental Design
2.2. Muscle Biopsy Sampling Procedure
2.3. Determination of Intramuscular Fat
2.4. Determination of Fat Melting Point
2.5. Determination of Fatty Acid Composition
2.6. Blood Collection and Genomic DNA Extraction
2.7. Primer Design
2.7.1. FASN, FABP4, and SCD Primers
2.7.2. Long-Range PCR
2.7.3. FASN Gene
2.7.4. FABP4 and SCD
2.8. PCR Clean-Up
2.9. Library Preparation, Quantification, Normalization, and Sequencing
2.10. Bioinformatics and Next Generation Sequencing Data Analysis
2.11. Statistical Analyses
3. Results
3.1. SCD, FASN, and FABP4 Gene SNP Variants and Genotypes
3.2. Correlations between SCD, FASN, and FABP4 Gene SNP, FMP, IMF, and Fatty Acids
3.3. Associations between SCD, FASN and FABP4 SNP, FMP, IMF, and Fatty Acids
3.4. Tukey-Adjusted Multiple Comparison Tests for Significant SNP, FMP, IMF, and Fatty Acids
4. Discussion
4.1. SCD Gene Polymorphism
4.2. FASN Gene Polymorphism
4.3. FABP Gene Polymorphism
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Sequence | Length (bp) | Ta (°C) | Fragment Length (bp) | |
---|---|---|---|---|---|
FASN 1 | Forward | CCTACTTTCCCATGCTCAGAGAA | 23 | 68 | 7890 |
Reverse | CTACGTTGCTGAGGAAGAACTCTA | 24 | 68 | ||
FASN 2 | Forward | ACCGTCTCTCCTTCTTCTTTGAC | 23 | 68 | 8798 |
Reverse | GAAGTTGAGGGAGGCGTAATAGAT | 24 | 68 | ||
FASN 3 | Forward | CTAGAGTTCTTCCTCAGCAACGTA | 24 | 68 | 9288 |
Reverse | GCCAGGGAGCTGTGAATAATACTA | 24 | 68 | ||
FABP4 | Forward | TTGTTGAATGGCTGGGCTTATAAC | 24 | 60 | 4107 |
Reverse | TAAGAAAATACTTCCTGGGGCACA | 24 | 60 | ||
SCD | Forward | CAAACTTAGGTCTGCAACTTTCGT | 24 | 65 | 11,545 |
Reverse | TTTCCCACTTCAACTCACCCTATT | 24 | 65 |
Lamb breed, generation, type of control and genotypes (major allele frequencies in brackets) Parental composites 1st (F1) and 2nd (F2) composites Positive (+) and negative (−) controls | ||||||
SNP Locus | TAW Parents (n = 147) | TAW F1 (n = 75) | TAW F2 (n = 75) | Poll Dorset (+n = 2) | Texel (+n = 2) | Rambouillet (−n = 2) |
g.23880613A>G | GG (0.82) | GG (0.93) | GG (0.73) | GG | GG | AA |
g.23881050T>C | CT (0.58) | CT (0.54) | CT (0.90) | CC | CC | TT |
g.23883280G>A | AG (0.53) | AG (0.71) | AG (0.60) | AA | AA | GG |
g.23885910C>A | AC (0.57) | AC (0.71) | AC (0.53) | CC | CC | CC |
g.23887165A>G | GA (0.69) | GG (0.82) | GG (0.70) | GG | GG | AA |
g.23888763C>T | TC (0.58) | TC (0.54) | CC (0.93) | CC | CC | CC |
g.23889346T>G | GT (0.68) | GG (0.82) | GG (0.70) | GG | GG | TT |
g.23890209T>C | CT (0.67) | CC (0.82) | CC (0.70) | CC | CC | TT |
Lamb breed, generation, type of control, and genotypes (major allele frequencies in brackets) Parental composite 1st (F1) and 2nd (F2) composites, Positive (+) and negative (−) controls | ||||||
SNP Locus | TAW Parents (n = 147) | TAW F1 (n = 75) | TAW F2 (n = 75) | Poll Dorset (+n = 2) | Texel (+n = 2) | Rambouillet (−n = 2) |
g.12316077T>G | GG (0.89) | GG (0.86) | GG (0.95) | GG | GG | TT |
g.12318491A>G | GG (0.89) | GG (0.86) | GG (0.95) | GG | GG | AA |
g.12320583T>C | CC (0.89) | CC (0.86) | CC (0.97) | CC | CC | TT |
g.12321671T>C | CC (0.89) | CC (0.86) | CC (0.97) | CC | CC | TT |
g.12323864A>G | GA (0.70) | GA (0.69) | GA (0.70) | GG | GG | AA |
g.12324288G>A | AG (0.69) | AG (0.68) | AG (0.69) | AA | AA | GG |
g.12326992T>C | CC (0.88) | CC (0.79) | CC (0.90) | CC | CC | TT |
g.12327084->CT | CT (0.50) | CT (0.50) | CT (0.50) | CT | CT | TT |
g.12328120T>C | CC (0.89) | CC (0.86) | CC (0.97) | CC | CC | TT |
Lamb breed, generation, type of control, and genotypes (major allele frequencies in brackets) Parental composites 1st (F1) and 2nd (F2) composites Positive (+) and negative (−) controls | ||||||
SNP Locus | TAW Parents (n = 147) | TAW F1 (n = 75) | TAW F2 (n = 75) | Poll Dorset (+n = 2) | Texel (+n = 2) | Rambouillet (−n = 2) |
g.62826961T>C | CT (0.61) | TT (0.64) | CT (0.60) | TT | TT | TT |
g.62826965C>G | GC (0.61) | GC (0.57) | GC (0.60) | GG | GG | CC |
g.62829478A>T | AT (0.55) | AT (0.61) | AT (0.53) | AA | AA | AA |
SNP effect (p-values) SCD FABP4 FASN | ||||||
Variable | Mean | SD | CV (%) | g.23881050T>C | g.62829478A>T | g.12323864A>G |
FMP (°C) | 33.65 | 2.74 | 8.14 | 0.2700 | 0.6115 | 0.0544 * |
IMF (%) | 4.43 | 1.31 | 29.58 | 0.0089 ** | 0.0539 * | 0.1915 |
Fatty acids (mg/100 g) | ||||||
ALA (C18:3n-3) | 163.03 | 192.27 | 117.94 | 0.7755 | 0.1419 | 0.0033 ** |
EPA (C20:5n-3) | 25.20 | 11.62 | 46.10 | 0.7683 | 0.1023 | 0.9810 |
DHA (C22:6n-3) | 8.43 | 4.16 | 49.27 | 0.0111 * | 0.2145 | 0.9480 |
DPA (C22:5n-3) | 23.85 | 13.70 | 57.44 | 0.0532 * | 0.3894 | 0.0927 |
EPA + DHA | 33.64 | 14.75 | 43.84 | 0.2036 | 0.4794 | 0.9915 |
EPA + DHA + DPA | 57.49 | 26.97 | 46.92 | 0.0728 | 0.8958 | 0.2004 |
MUFA | 3694.70 | 4099.08 | 110.94 | 0.6824 | 0.3949 | 0.0025 ** |
SFA | 4392.18 | 5238.81 | 119.28 | 0.4000 | 0.5472 | 0.0029 ** |
C18:2n-6 | 253.68 | 247.70 | 97.64 | 0.6781 | 0.0647 | 0.0138 * |
C14:0 | 287.92 | 437.58 | 151.98 | 0.0632 | 0.7354 | 0.1190 |
C16:0 | 2076.17 | 2419.46 | 116.53 | 0.5414 | 0.3751 | 0.0039 ** |
C18:0 | 1683.83 | 2065.71 | 122.68 | 0.3891 | 0.9125 | 0.0012 ** |
C18:1n-9 | 2901.10 | 3212.65 | 110.74 | 0.8555 | 0.3696 | 0.0023 ** |
Multiple Genotype Comparisons | ||||||
SNP Locus | Variable | Mean ± SE | Genotypes | Difference ± SE | p-Value | |
SCD g.23881050T>C | DHA (C22:6n-3) (mg/100 g) | |||||
CC | 7.00 ± 2.11 | CC vs. | CT | −0.639 ± 0.834 | 0.7247 | |
CT | 7.64 ± 2.09 | CC vs. | TT | −3.998 ± 1.334 | 0.0105 * | |
TT | 11.00 ± 2.34 | CT vs. | TT | −3.359 ± 1.235 | 0.0223 * | |
IMF (%) | ||||||
CC | 3.98 ± 0.312 | CC vs. | CT | −0.407 ± 0.323 | 0.4224 | |
CT | 4.39 ± 0.287 | CC vs. | TT | −1.446 ± 0.532 | 0.0222 * | |
TT | 5.43 ± 0.516 | CT vs. | TT | −1.038 ± 0.502 | 0.1041 | |
DPA (C22:5n-3) (mg/100 g) | ||||||
CC | 17.9 ± 6.81 | CC vs. | CT | −1.56 ± 2.65 | 0.8270 | |
CT | 19.4 ± 6.74 | CC vs. | TT | −9.19 ± 4.25 | 0.0850 | |
TT | 27.1 ± 3.26 | CT vs. | TT | −7.63 ± 3.93 | 0.0356 * | |
FASN g.12323864A>G | FMP (°C) | |||||
GG | 34.2 ± 0.4 | GG vs. | GA | 0.81 ± 0.64 | 0.4201 | |
GA | 33.4 ± 0.3 | GG vs. | AA | 2.98 ± 1.61 | 0.0536 * | |
AA | 31.5 ± 1.5 | GA vs. | AA | 2.16 ± 1.60 | 0.3685 | |
ALA (C18:3n-3) (mg/100 g) | ||||||
GG | 188.7 ± 67.6 | GG vs. | GA | 114.7 ± 39.9 | 0.0149 * | |
GA | 74.0 ± 66.7 | GG vs. | AA | 147.2 ± 100.1 | 0.3115 | |
AA | 41.5 ± 113.7 | GA vs. | AA | 32.6 ± 99.8 | 0.9430 | |
MUFA (mg/100 g) | ||||||
GG | 4524 ± 1384 | GG vs. | GA | 2617 ± 867 | 0.0099 ** | |
GA | 1907 ± 1361 | GG vs. | AA | 3089 ± 2175 | 0.3363 | |
AA | 1436 ± 2415 | GA vs. | AA | 472 ± 2168 | 0.9742 | |
SFA (mg/100 g) | ||||||
GG | 5479 ± 1715 | GG vs. | GA | 3270 ± 1121 | 0.0132 * | |
GA | 2208 ± 1684 | GG vs. | AA | 4162 ± 2812 | 0.3068 | |
AA | 1317 ± 3086 | GA vs. | AA | 892 ± 2803 | 0.9458 | |
C18:2n-6 (mg/100 g) | ||||||
GG | 281 ± 84.8 | GG vs. | GA | 142.5 ± 52.2 | 0.0216 * | |
GA | 139 ± 83.4 | GG vs. | AA | 105.8 ± 130.8 | 0.6988 | |
AA | 175 ± 146.4 | GA vs. | AA | −36.7 ± 130.4 | 0.9573 | |
C16:0 (mg/100 g) | ||||||
GG | 2539 ± 800 | GG vs. | GA | 1475 ± 518 | 0.0158 * | |
GA | 1063 ± 786 | GG vs. | AA | 1826 ± 1298 | 0.3433 | |
AA | 713 ± 1429 | GA vs. | AA | 350 ± 1294 | 0.9604 | |
C18:0 (mg/100 g) | ||||||
GG | 2227 ± 658 | GG vs. | GA | 1419 ± 441 | 0.0056 ** | |
GA | 809 ± 646 | GG vs. | AA | 1711 ± 1106 | 0.2756 | |
AA | 516 ± 1205 | GA vs. | AA | 292 ± 1102 | 0.9620 | |
C18:1n-9 (mg/100 g) | ||||||
GG | 3589 ± 1078 | GG vs. | GA | 2103 ± 679 | 0.0080 ** | |
GA | 1486 ± 1060 | GG vs. | AA | 2353 ± 1704 | 0.3566 | |
AA | 1236 ± 1892 | GA vs. | AA | 250 ± 1698 | 0.9882 | |
FABP4 g.62829478A>T | IMF (%) | |||||
A | 4.57 ± 0.39 | A vs. | AA | 0.07 ± 0.344 | 0.0556 | |
AA | 3.92 ± 0.39 |
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Pewan, S.B.; Otto, J.R.; Huerlimann, R.; Budd, A.M.; Mwangi, F.W.; Edmunds, R.C.; Holman, B.W.B.; Henry, M.L.E.; Kinobe, R.T.; Adegboye, O.A.; et al. Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb. Foods 2021, 10, 2288. https://doi.org/10.3390/foods10102288
Pewan SB, Otto JR, Huerlimann R, Budd AM, Mwangi FW, Edmunds RC, Holman BWB, Henry MLE, Kinobe RT, Adegboye OA, et al. Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb. Foods. 2021; 10(10):2288. https://doi.org/10.3390/foods10102288
Chicago/Turabian StylePewan, Shedrach Benjamin, John Roger Otto, Roger Huerlimann, Alyssa Maree Budd, Felista Waithira Mwangi, Richard Crawford Edmunds, Benjamin William Behrens Holman, Michelle Lauren Elizabeth Henry, Robert Tumwesigye Kinobe, Oyelola Abdulwasiu Adegboye, and et al. 2021. "Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb" Foods 10, no. 10: 2288. https://doi.org/10.3390/foods10102288