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
- Hoffman, L.C.; Cawthorn, D. Meat, Animal, Poultry And Fish Production and Management | Exotic and Other Species. In Encyclopedia of Meat Sciences; Dikeman, M., Devine, C., Eds.; Academic Press: Oxford, UK, 2014; pp. 190–198. [Google Scholar]
- Biswas, H.; Roy, B.C.; Dutta, P.K.; Hasan, M.M.; Parvin, S.; Choudhury, D.K.; Begum, N.; Talukder, M.H. Prevalence and risk factors of Toxocara vitulorum infection in buffalo calves in coastal, northeastern and northwestern regions of Bangladesh. Vet. Parasitol. Reg. Stud. Rep. 2021, 26, 100656. [Google Scholar] [CrossRef] [PubMed]
- Ashiagbor, A.A.; Ablateye, S.; Essel-Mensah, K.A. Agriculture growth in Ghana: A time-series analysis with autoregressive distributed lag approach. Cogent Food Agric. 2023, 9, 2244267. [Google Scholar] [CrossRef]
- Napolitano, F.; De Rosa, G.; Chay-Canul, A.; Alvarez-Macias, A.; Pereira, A.M.F.; Bragaglio, A.; Mora-Medina, P.; Rodriguez-Gonzalez, D.; Garcia-Herrera, R.; Hernandez-Avalos, I.; et al. The Challenge of Global Warming in Water Buffalo Farming: Physiological and Behavioral Aspects and Strategies to Face Heat Stress. Animals 2023, 13, 3103. [Google Scholar] [CrossRef]
- Vargas-Ramella, M.; Pateiro, M.; Maggiolino, A.; Faccia, M.; Franco, D.; De Palo, P.; Lorenzo, J.M. Buffalo Milk as a Source of Probiotic Functional Products. Microorganisms 2021, 9, 2303. [Google Scholar] [CrossRef]
- Hosseini, S.M.; Tingzhu, Y.; Pasandideh, M.; Liang, A.; Hua, G.; Farmanullah; Schreurs, N.M.; Raza, S.H.A.; Salzano, A.; Campanile, G.; et al. Genetic Association of PPARGC1A Gene Single Nucleotide Polymorphism with Milk Production Traits in Italian Mediterranean Buffalo. BioMed Res. Int. 2021, 2021, 3653157. [Google Scholar] [CrossRef]
- Michelizzi, V.N.; Dodson, M.V.; Pan, Z.; Amaral, M.E.; Michal, J.J.; McLean, D.J.; Womack, J.E.; Jiang, Z. Water buffalo genome science comes of age. Int. J. Biol. Sci. 2010, 6, 333–349. [Google Scholar] [CrossRef]
- Zhang, Y.; Colli, L.; Barker, J.S.F. Asian water buffalo: Domestication, history and genetics. Anim. Genet. 2020, 51, 177–191. [Google Scholar] [CrossRef] [PubMed]
- Manzoor, S.; Nadeem, A.; Maryam, J.; Hashmi, A.S.; Imran, M.; Babar, M.E. Osteopontin gene polymorphism association with milk traits and its expression analysis in milk of riverine buffalo. Trop. Anim. Health Prod. 2018, 50, 275–281. [Google Scholar] [CrossRef] [PubMed]
- Stobiecka, M.; Krol, J.; Brodziak, A. Antioxidant Activity of Milk and Dairy Products. Animals 2022, 12, 245. [Google Scholar] [CrossRef]
- Shingfield, K.J.; Bonnet, M.; Scollan, N.D. Recent developments in altering the fatty acid composition of ruminant-derived foods. Animal 2013, 7 (Suppl. 1), 132–162. [Google Scholar] [CrossRef]
- Haque, M.A.; Alam, M.Z.; Iqbal, A.; Lee, Y.M.; Dang, C.G.; Kim, J.J. Evaluation of accuracies of genomic predictions for body conformation traits in Korean Holstein. Anim. Biosci. 2024, 37, 555–566. [Google Scholar] [CrossRef] [PubMed]
- El-Komy, S.M.; Saleh, A.A.; Abdel-Hamid, T.M.; El-Magd, M.A. Association of GHR Polymorphisms with Milk Production in Buffaloes. Animals 2020, 10, 1203. [Google Scholar] [CrossRef]
- Gu, M.; Cosenza, G.; Iannaccone, M.; Macciotta, N.P.P.; Guo, Y.; Di Stasio, L.; Pauciullo, A. The single nucleotide polymorphism g.133A>C in the stearoyl CoA desaturase gene (SCD) promoter affects gene expression and quali-quantitative properties of river buffalo milk. J. Dairy Sci. 2019, 102, 442–451. [Google Scholar] [CrossRef] [PubMed]
- Li, J.; Liu, S.; Li, Z.; Zhang, S.; Hua, G.; Salzano, A.; Campanile, G.; Gasparrini, B.; Liang, A.; Yang, L. DGAT1 polymorphism in Riverine buffalo, Swamp buffalo and crossbred buffalo. J. Dairy Res. 2018, 85, 412–415. [Google Scholar] [CrossRef] [PubMed]
- Cosenza, G.; Iannaccone, M.; Auzino, B.; Macciotta, N.P.P.; Kovitvadhi, A.; Nicolae, I.; Pauciullo, A. Remarkable genetic diversity detected at river buffalo prolactin receptor (PRLR) gene and association studies with milk fatty acid composition. Anim. Genet. 2018, 49, 159–168. [Google Scholar] [CrossRef] [PubMed]
- Ye, T.; Deng, T.; Hosseini, S.M.; Raza, S.H.A.; Du, C.; Chen, C.; Zhang, X.; Hu, X.; Yang, L. Association analysis between FASN genotype and milk traits in Mediterranean buffalo and its expression among different buffalo tissues. Trop. Anim. Health Prod. 2021, 53, 366. [Google Scholar] [CrossRef] [PubMed]
- Isik, R.; Ozkan Unal, E.; Soysal, M.I. Polymorphism detection of DGAT1 and Lep genes in Anatolian water buffalo (Bubalus bubalis) populations in Turkey. Arch. Anim. Breed. 2022, 65, 1–9. [Google Scholar] [CrossRef] [PubMed]
- Khan, M.Z.; Ma, Y.; Ma, J.; ** Error. Front. Genet. 2017, 8, 167. [Google Scholar] [CrossRef] [PubMed]
- Lin, Y.; Sun, H.; Shaukat, A.; Deng, T.; Abdel-Shafy, H.; Che, Z.; Zhou, Y.; Hu, C.; Li, H.; Wu, Q.; et al. Novel Insight Into the Role of ACSL1 Gene in Milk Production Traits in Buffalo. Front. Genet. 2022, 13, 896910. [Google Scholar] [CrossRef] [PubMed]
- Kumar, M.; Vohra, V.; Ratwan, P.; Chakravarty, A.K. Snp Identification in Thioesterase Domain of Fatty Acid Synthase Gene in Murrah Buffaloes. J. Anim. Plant Sci. 2016, 26, 1828–1832. [Google Scholar]
- Pecka-Kielb, E.; Kowalewska-Luczak, I.; Czerniawska-Piatkowska, E.; Kroliczewska, B. FASN, SCD1 and ANXA9 gene polymorphism as genetic predictors of the fatty acid profile of sheep milk. Sci. Rep. 2021, 11, 23761. [Google Scholar] [CrossRef] [PubMed]
- Abdel-Hamid, M.; Huang, L.; Huang, Z.; Romeih, E.; Yang, P.; Zeng, Q.; Li, L. Effect of Buffalo Breed on the Detailed Milk Composition in Guangxi, China. Foods 2023, 12, 1603. [Google Scholar] [CrossRef]
- Cardoso, D.F.; de Souza, G.F.; Aspilcueta-Borquis, R.R.; Araujo Neto, F.R.; de Camargo, G.M.; Hurtado-Lugo, N.A.; Scalez, D.C.; de Freitas, A.C.; Albuquerque, L.G.; Tonhati, H. Short communication: Variable number of tandem repeat polymorphisms in DGAT1 gene of buffaloes (Bubalus bubalis) is associated with milk constituents. J. Dairy Sci. 2015, 98, 3492–3495. [Google Scholar] [CrossRef]
- Qiu, L.; Fan, X.; Zhang, Y.; Teng, X.; Miao, Y. Molecular characterization, tissue expression and polymorphisms of buffalo PPARGC1A gene. Arch. Anim. Breed 2020, 63, 249–259. [Google Scholar] [CrossRef] [PubMed]
- Sihag, S.; Rushdi, H.E.; Kumar, A.; Jangra, A.; Hassanane, M.S.; Abdel-Shafy, H.; Chhokar, V. Polymorphic Variants Analysis in (PPARGC1A) Gene of Indian and Egyptian Buffaloes. Indian J. Anim. Res. 2023, 57, 1474–1479. [Google Scholar] [CrossRef]
- Kowalewska-Łuczak, I.; Kulig, H.; Kmieć, M. Associations between the bovine PPARGC1A gene and milk production traits. Czech J. Anim. Sci. 2010, 55, 195–199. [Google Scholar] [CrossRef]
- Cobanoğlu, O.; Ardicli, S. Effects of Bovine PPARGC1A and LTF Gene Variants on Milk Yield and Composition Traits in Holstein-Friesian and Jersey Cows. J. Agric. Food Environ. Sci. 2022, 76, 9–20. [Google Scholar] [CrossRef]
- Liu, J.; Wang, Z.; Li, J.; Li, H.; Yang, L. Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo. BMC Genet. 2020, 21, 26. [Google Scholar] [CrossRef]
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 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
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