Detection of Polymorphisms in FASN, DGAT1, and PPARGC1A Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh
Abstract
:Simple Summary
Abstract
1. Introduction
2. Methods and Materials
2.1. Animals and Phenotypes
2.2. Blood Sampling and DNA Extraction
2.3. PCR Amplification
2.4. Sequencing and Polymorphism Detection
2.5. Statistical Analysis
3. Results
3.1. Descriptive Statistics of Milk Yield and Milk Composition Traits of Riverine Buffalo
3.2. Detection of the Polymorphisms
3.3. Population Genetic Information for the Identified SNPs in Three Candidate Genes
3.4. Association between the SNPs of FASN and DGAT1 Genes with Milk Traits
3.5. Association between SNP Genotypes of PPARGC1A Gene and Milk Traits
3.6. Association between Constructed Haplotypes of PPARGC1A Genes and Milk Traits
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trait | N | Minimum | Maximum | Mean ± SE | SD | CV% |
---|---|---|---|---|---|---|
DMY (liter) | 142 | 1.03 | 5.50 | 2.78 ± 0.06 | 0.721 | 25.92 |
Milk fat% | 116 | 3.69 | 11.24 | 8.34 ± 0.17 | 1.800 | 21.59 |
Protein% | 116 | 2.20 | 6.29 | 3.64 ± 0.06 | 0.687 | 18.86 |
SNF% | 116 | 6.45 | 12.63 | 9.41 ± 0.10 | 1.097 | 11.66 |
Primer Set | Primer Sequence (5′ to 3′) | Product Size (bp) | Identified SNP | SNP Location |
---|---|---|---|---|
FASNF1 FASNR1 | F: CCCACTCTGGTTCATCTGCTC R: CCTCCCACGAAGACCCTCA | 660 | g.7163G>A g.7271C>T | Intron 9 Exon 10 |
DGAT1F1 DGAT1R1 | F: GCTGTTCTGGCACCTGGCAC R: CACCCACCTGATGCACCACT | 300 | g.7809C>T | Exon 13 |
DGAT1F2 DGAT1R2 | F: AGGCTCACTCCCGTCCCAT R: GTGAGGCAAAGCAGTCCAAC | 230 | g.8525C>T | Exon 17 |
PPARGC1AF1 PPARGC1AR1 | F: AGTGGACACGAGGAAAGGAAG R: GGGTGGGTTTTGACAAGGTT | 724 | g.387642C>T g.387758A>G | Exon 8 |
PPARGC1AF2 PPARGC1AR2 | F: TGAACACATGCACCCCATCAT R: CGTGCCAGGAGTTTGGTTGT | 789 | g.409354A>G g.409452G>A | 3′ UTR |
Gene | SNP 1 | Genotype Frequency 2 | Allele Frequency | Heterozygosity | χ2 (p-Value) | ||||
---|---|---|---|---|---|---|---|---|---|
Ho | He | ||||||||
FASN | g.7163G>A | GG | GA | AA | G | A | 0.43 | 0.41 | 55.51 *** |
0.50 (72) | 0.43 (63) | 0.07 (10) | 0.71 | 0.29 | |||||
g.7271C>T | CC | CT | TT | C | T | 0.42 | 0.39 | 67.43 *** | |
0.52 (76) | 0.42 (61) | 0.06 (08) | 0.73 | 0.27 | |||||
DGAT1 | g.7809C>T | CC | CT | TT | C | T | 0.46 | 0.47 | 10.20 ** |
0.39 (32) | 0.46 (38) | 0.15 (12) | 0.62 | 0.38 | |||||
g.8525C>T | CC | CT | TT | C | T | 0.54 | 0.48 | 11.57 ** | |
0.32 (48) | 0.54 (80) | 0.14 (20) | 0.59 | 0.41 | |||||
PPARGC1A | g.387642C>T | CC | CT | TT | C | T | 0.17 | 0.15 | 228.00 *** |
0.83 (120) | 0.17 (24) | 0.00 (00) | 0.92 | 0.08 | |||||
g.387758A>G | AA | AG | GG | A | G | 0.52 | 0.47 | 19.26 *** | |
0.37 (53) | 0.52 (75) | 0.11 (16) | 0.63 | 0.37 | |||||
g.409354A>G | AA | AG | GG | A | G | 0.41 | 0.40 | 51.00 *** | |
0.52 (61) | 0.42 (49) | 0.07 (08) | 0.72 | 0.28 | |||||
g.409452G>A | GG | GA | AA | G | A | 0.21 | 0.18 | 161.25 *** | |
0.79 (95) | 0.21 (25) | 0.00 (00) | 0.90 | 0.10 |
Gene and SNP | Genotype | DMY (Liter) | Fat% | Protein% | SNF% |
---|---|---|---|---|---|
FASN g.7163G>A | GG | 2.92 ± 0.08 (69) | 8.57 ± 0.25 a (58) | 3.74 ± 0.09 (58) | 9.48 ± 0.14 (58) |
GA | 2.73 ± 0.11 (61) | 7.88 ± 0.25 b (47) | 4.53 ± 0.75 (47) | 9.48 ± 0.15 (47) | |
AA | 2.95 ± 0.12 (10) | 8.80 ± 0.59 a (10) | 3.65 ± 0.38 (10) | 8.93 ± 0.42 (10) | |
p value | 0.2198 | 0.0452 | 0.8260 | 0.2900 | |
FASN g.7271C>T | CC | 2.91 ± 0.07 (73) | 8.50 ± 0.24 ab (62) | 3.74 ± 0.09 (62) | 9.74 ± 0.12 a (56) |
CT | 2.75 ± 0.12 (59) | 7.84 ± 0.27 b (45) | 4.57 ± 0.78 (45) | 9.47 ± 0.15 ab (45) | |
TT | 2.99 ± 0.21 (8) | 9.44 ± 0.45 a (8) | 3.67 ± 0.48 (8) | 8.63 ± 0.47 b (8) | |
p value | 0.2671 | 0.0099 | 0.8270 | 0.0069 | |
DGAT1 g.7809C>T | CC | 2.90 ± 0.14 (35) | 8.41 ± 0.38 (27) | 3.80 ± 0.13 (27) | 9.56 ± 0.20 (27) |
CT | 2.70 ± 0.12 (29) | 8.41 ± 0.37 (22) | 3.96 ± 0.29 (22) | 9.38 ± 0.14 (22) | |
TT | 3.01 ± 0.3 (10) | 8.58 ± 0.64 (9) | 3.70 ± 0.22 (9) | 9.62 ± 0.31 (9) | |
p value | 0.4133 | 0.9540 | 0.6785 | 0.6810 | |
DGAT1 g.8525C>T | CC | 2.78 ± 0.10 (46) | 8.37 ± 0.25 (39) | 3.46 ± 0.09 b (39) | 9.22 ± 0.17 (39) |
CT | 2.78 ± 0.08 (78) | 8.23 ± 0.24 (64) | 3.75 ± 0.09 a (62) | 9.45 ± 0.14 (64) | |
TT | 2.77 ± 0.18 (18) | 8.75 ± 0.58 (13) | 3.86 ± 0.20 a (13) | 9.97 ± 0.34 (13) | |
p value | 0.9980 | 0.5220 | 0.0056 | 0.2255 |
SNP | Genotype | DMY (Liter) | Fat% | Protein% | SNF% |
---|---|---|---|---|---|
g.387642C>T | CC | 2.90 ± 0.07 (117) | 8.52 ± 0.17 a (94) | 3.75 ± 0.10 (97) | 9.37 ± 0.11 (97) |
CT | 2.66 ± 0.16 (21) | 7.81 ± 0.36 b (19) | 3.79 ± 0.16 (19) | 9.55 ± 0.23 (19) | |
p value | 0.1390 | 0.0434 | 0.7940 | 0.4830 | |
g.387758A>G | AA | 2.84 ± 0.12 (51) | 8.26 ± 0.31 (42) | 3.49 ± 0.08 b (42) | 9.50 ± 0.17 ab (42) |
AG | 2.81 ± 0.09 (71) | 8.37 ± 0.21 (59) | 3.82 ± 0.14 ab (59) | 9.18 ± 0.13 b (59) | |
GG | 3.15 ± 0.17 (16) | 8.06 ± 0.51 (15) | 4.26 ± 0.25 a (15) | 9.96 ± 0.33 a (15) | |
p value | 0.1660 | 0.7563 | 0.0010 | 0.0185 | |
g.409354A>G | AA | 2.79 ± 0.09 (57) | 8.42 ± 0.26 (52) | 3.56 ± 0.08 b (51) | 9.46 ± 0.14 ab (51) |
AG | 2.97 ± 0.10 (49) | 8.44 ± 0.24 (41) | 3.87 ± 0.19 b (41) | 9.00 ± 0.16 b (41) | |
GG | 3.06 ± 0.33 (8) | 7.49 ± 0.87 (7) | 4.64 ± 0.32 a (7) | 10.26 ± 0.44 a (7) | |
p value | 0.2821 | 0.2920 | 0.0004 | 0.0023 | |
g.409452G>A | GG | 2.98 ± 0.07 a (94) | 8.54 ± 0.20 a (82) | 3.89 ± 0.11 a (82) | 9.40 ± 0.12 (82) |
GA | 2.54 ± 0.15 b (22) | 7.64 ± 0.27 b (18) | 3.30 ± 0.11 b (18) | 9.14 ± 0.25 (18) | |
p value | 0.0009 | 0.0311 | 0.0031 | 0.3383 |
Haplotype | Observed Frequency | DMY (Liter) | Fat% | Protein% | SNF% |
---|---|---|---|---|---|
Hap1: CAAG | 0.26 | 2.89 ± 0.08 ab (93) | 8.57 ± 0.18 a (75) | 3.68 ± 0.08 ab (76) | 9.22 ± 0.12 (79) |
Hap2: CAGG | 0.12 | 2.96 ± 0.11 ab (43) | 8.63 ± 0.24 a (34) | 3.77 ± 0.13 ab (34) | 9.02 ± 0.16 (35) |
Hap3: CGAG | 0.18 | 2.91 ± 0.09 ab (63) | 8.51 ± 0.21 a (51) | 3.78 ± 0.11 ab (51) | 9.15 ± 0.14 (52) |
Hap4: CGGG | 0.16 | 3.01 ± 0.10 a (58) | 8.55 ± 0.21 a (47) | 3.91 ± 0.12 a (48) | 9.26 ± 0.16 (49) |
Hap5: CAGA | 0.02 | 2.40 ± 0.28 bc (8) | 8.08 ± 0.55 ab (5) | 3.21 ± 0.21 b (5) | 9.01 ± 0.36 (5) |
Hap6: CAAA | 0.06 | 2.47 ± 0.67 bc (19) | 7.80 ± 0.30 ab (15) | 3.38 ± 0.10 b (14) | 9.17 ± 0.26 (15) |
Hap7: CGAA | 0.05 | 2.46 ± 0.15 bc (17) | 7.41 ± 0.32 ab (14) | 3.34 ± 0.11 b (14) | 9.16 ± 0.21 (14) |
Hap8: TGAG | 0.06 | 2.84 ± 0.14 abc (21) | 7.97 ± 0.33 ab (19) | 3.80 ± 0.19 ab (19) | 9.36 ± 0.26 (19) |
Hap9: TAAG | 0.04 | 2.65 ± 0.25 abc (11) | 7.95 ± 0.49 ab (9) | 3.91 ± 0.29 ab (9) | 9.48 ± 0.32 (9) |
Hap10: TGAA | 0.03 | 2.30 ± 0.22 bc (9) | 6.91 ± 0.31 b (9) | 3.60 ± 0.07 ab (9) | 9.59 ± 0.19 (9) |
Hap11: TAAA | 0.02 | 2.01 ± 0.15 c (7) | 7.13 ± 0.37 ab (7) | 3.62 ± 0.08 ab (7) | 9.60 ± 0.25 (7) |
Level of Significance | *** | *** | *** | NS |
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Mou, M.A.; Deb, G.K.; Hridoy, M.F.A.; Alam, M.A.; Barai, H.R.; Haque, M.A.; Bhuiyan, M.S.A. Detection of Polymorphisms in FASN, DGAT1, and PPARGC1A Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh. Animals 2024, 14, 1945. https://doi.org/10.3390/ani14131945
Mou MA, Deb GK, Hridoy MFA, Alam MA, Barai HR, Haque MA, Bhuiyan MSA. Detection of Polymorphisms in FASN, DGAT1, and PPARGC1A Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh. Animals. 2024; 14(13):1945. https://doi.org/10.3390/ani14131945
Chicago/Turabian StyleMou, Monira Akter, Gautam Kumar Deb, Md. Forhad Ahmed Hridoy, Md. Ashadul Alam, Hasi Rani Barai, Md Azizul Haque, and Mohammad Shamsul Alam Bhuiyan. 2024. "Detection of Polymorphisms in FASN, DGAT1, and PPARGC1A Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh" Animals 14, no. 13: 1945. https://doi.org/10.3390/ani14131945