Frequency of Favorable Alleles for Meat Quality, Litter Size, Adaptation, and Growth Traits in Closed Nucleus Population of Philippine Native Swine (Sus philippensis var. markaduke)
DOI:
https://doi.org/10.52331/v31i25p50Keywords:
Allele, biomarker, genotype, homozygosity, markaduke, meat qualityAbstract
The Philippine native swine (PNS) are heritage domestic animal genetic resources for food security and geo-cultural uses. Among the PNS, the markaduke is known for the "best lechon" (roast whole pork) and comminuted pork products, moderate litter size (>8), and adaptability. Its genetic property needs assessment to develop a breeding program suited for optimum production system. A total of 67 heads (17 males & 50 females) from the 4.37+0.12 generations with inbreeding coefficient of 0.1493 +0.0167 was genotyped for meat quality using seven (7) biomarkers, three (3) biomarkers for litter size, two (2) biomarkers for adaptation, and one (1) for growth trait. The results of genotyping were tested in Hardy-Weinberg equilibrium and chi-square statistics. Of the seven biomarkers for meat quality, the RN, CTSD, and LEPR had genotypic frequency >50% in both sexes. Remarkably, the population expresses full presence of favorable allele for RN (100% rn, p<0.05). In terms of litter size, the most prominent allele was observed in PRLR at almost equal frequencies of 0.77 in both sexes (p<0.05). For adaptation trait, the N allele for halothane gene that command for stress tolerance was observed at frequencies or 0.97 (p>0.05). The favorable allele for growth, MYOG, was observed in heterozygote only at low frequencies of 0.08, 0.14, and 0.13 for males, females, and in combined data; respectively. These molecular findings show that the closed nucleus population of markaduke carries favorable genes necessary for genetic improvement.
References
1. Piper PJ, Campos FZ and Hung HC. 2009a. A study of the animal bone recovered from pits 9 and 10 at the site of Nagsabaran in Northern Luzon, Philippines. Hukay, 14:47-90, http://www.journals.upd.edu.ph/index.php/asp/article/view/4119.
2. Piper PJ, Hung HC, Campos FZ, Bellwood P, and Santiago R. 2009b. A 4000 year-old introduction of domestic pigs into the Philippine archipelago: implications for understanding routes of human migration through is-land Southeast Asia and Wallacea. Antiquity, 83:689-695, http://www.thefreelibrary.com/A+4000+year-old+introduction+of+
3. Cabanas AJC, de Guia APO, Vega RSA, Dimalibot JC. 2022. Occurrence and distribution of Philippine warty pig (Sus philippensis Nehring 1886) in Mt. Banahaw de Tayabas, Luzon Island, Philippines. Philippine Jour-nal of Science. 151 (5): 1605-1621, October 2022. https://philjournalsci.dost.gov.ph.
4. Banayo JB, Manese KLV, Salces AJ, Yamagata T. 2023a. Phylogeny and genetic diversity of Philippine native pigs (Sus scrofa) as revealed by mitochondrial DNA analysis. Biochem Genet 61, 1401–1417 (2023). https://doi.org/10.1007/s10528-022-10318-0
5. Banayo JB, Manese KLV, Furusho KO, Salces AJ, Yamagata T. 2023b. Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation. Ecology and Evolution. Volume13, Issue11. https://doi.org/10.1002/ece3.10618
6. Lingao JQ, Rofes J, Eusebio MS, Baretto G. 2024. This little piggy: Pig-human entanglement in the Philippines. International Journal of Historical Archaeology 29(1):40-71. https://DOI:10.1007/s10761-024-00754-6
7. Banayo JB, Manese KLV, Furusho KO, Kingan MS, Ayomen JP, Saliw-an MG, Nicholas KMG, Petipit KJS, Pag-bilao DP, Arellano VRE, Santiago RC, Caguicla FA, Monleon AM. Perlas GM, Ortego RPA, Singzon SB, Salces AJ, Yamagata T. 2024. Production objectives and trait preferences of smallholder farmers in the Philippines: Implications for designing breeding schemes utilizing indigenous swine genetics. Philipp Agric Scientist. 107(4):318-332. https://doi.org/10.62550/HDE8048024.
8. Sto. Domingo DAM. 2021. State College R&D Center launches its native pork processed products as African Swine Fever and COVID-19 Pandemic continue to cripple the Philippine swine industry. Agriculture Maga-zine. May 23, 2021. https://agriculture.com.ph/2021/05/23/state-college-rd-center-launches-its-native-pork-processed-products-as-african-swine-fever-and-covid-19-pandemic-continue-to-cripple-the-philippine-swine-industry/
9. Medenilla V. 2022. Markaduke: A native pig recognized as the best lechon in the Philippines. https://mb.com.ph/2022/05/14/markaduke-a-native-pig-recognized-as-the-best-lechon-in-the-philippines/
10. Larga-Loto JO., Perlas GM., Seño M., Lozano SJM., Monleon AM. 2021. Productivity of markaduke native pig at the farmers’ care during the pandemic. Asian Intellect Research and Education Journal. (June 2021) 19: 63-66 https://nebula.wsimg.com/b191ac0bd6d9dd8.
11. Perlas GM., Robles JR. 2022. Reproductive performance of markaduke in different parities. Philippine Journal of Veterinary & Animal Sciences. 48 (1). https://openurl.ebsco.com/EPDB%3Agcd%3A15%3A4449807/detailv2?bquery=IS%200115-2173%20AND%20VI%2048%20AND%20IP%201%20AND%20DT%202022&page=1&sid=ebsco:ocu:record.
12. Robles JR., Perlas GM. 2024. Optimizing carcass recovery in markaduke native pigs: insights from Marinduque State College nucleus farm. Ignatian International Journal for Multidisciplinary Research. 2(5): 467-478. https://hcommons.org/deposits/item/hc:65883/.
13. Davoli R., Braglia S. 2008. Molecular approaches in pig breeding to improve meat quality. Briefings in Func-tional Genomics and Proteomics. 6(4): 313-321. doi:10.1093/bfgp/elm036. https://academic.oup.com/bfg/article/6/4/313/206680.
14. Rohrer G.A., D.J. Nonneman, R.K. Miller, H. Zerby, S.J. Moeller. 2012. Association of single nucleotide poly-morphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs. Meat Science 92: 511–518. https://doi:10.1016/j.meatsci.2012.05.020.
15. Tabon GR, Medina NP, Uy–De Guia MRD, Mingala CN. 2022. ESR1 candidate marker gene associated with lit-ter size in the Philippine native pigs (Sus philippensis). Adv. Anim. Vet. Sci. 10(8):1747-1751. https://dx.doi.org/10.17582/journal.aavs/2022/10.8.1747.1751
16. Matias S, Gajeton M, Flores E. 2023. Genetic screening of halothane gene on selected Philippine native pig herds. bioRxiv. https://doi.org/10.1101/2023.07.07.548076
17. Hamilton DN, M. Ellis, K.D. Miller, F.K. McKeith, D.F. Parrett. 2000. The effect of the halothane and rendement napole genes on carcass and meat quality characteristics of pigs. Journal of Animal Science. 78:2862-2867. https://doi.org/10.2527/2000.78112862x.
18. Lundstrӧm K. and L. Andersson, 2001. The effect of the RN-allele on meat quality and how the gene was dis-covered. Proc. 54th Annual Reciprocal Meat Conference. 143-147. https://meatscience.org/docs/default-source/publications-resources/rmc/2001/the-effect-of-the-rn--allele-on-meat-quality-and-how-the-gene-was-discovered.pdf?sfvrsn=2
19. Miller K.D., M. Ellis, F.K. McKeith, B.S. Bidner, D.J. Meisinger. 2000. Frequency of rendement napole RN-allele in a population of American hampshire pigs. Journal of Animal Science. 78: 1811-1815. https://doi.org/10.2527/2000.7871811x
20. Russo V., Fontanesi L., Scotti E., Beretti F., Davoli R., Nanni Costa L., Virgili R., Buttazzoni L. 2008. Single nu-cleotide polymorphisms in several porcine cathepsin genes are associated with growth, carcass, and produc-tion traits in Italian Large White pigs. J. Anim. Sci. 2008. 86:3300–3314. https://doi:10.2527/jas.2008-0920.
21. Han X, Jiang T, Yang H, Zhang Q, Wang W, Fan B, Liu B. 2012. Investigation of four porcine candidate genes (H-FABP, MYOD1, UCP3 and MASTR) for meat quality traits in Large White pigs. Molecular Biology Reports. 39: 6599–6605 (07 February 2012). https://doi.org/10.1007/s11033-012-1490-6.
22. Galve A, Burgos C, Silió L, Varona L, Rodríguez C, Ovilo C, López-Buesa P. 2012. The effects of leptin receptor (LEPR) and melanocortin-4 receptor (MC4R) polymorphisms on fat content, fat distribution and fat composi-tion in a Duroc × Landrace/Large White cross. Livestock Science 145 (2012) 145–152. www.elsevier.com/locate/livsci.
23. Ros-Freixedes R., Gol S., Pena RN., Tor M., Ibáñez-Escriche N., Dekkers JCM., Estany J. 2016. Genome-wide as-sociation study singles out SCD and LEPR as the two main loci influencing intramuscular fat content and fatty acid composition in Duroc pigs. PLOS ONE | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152496
24. Jeremiah LE. 2006. Marbling and pork tenderness. Pork Information Gateway. Factsheets Number PIG 12-04-01. https://porkgateway.org/resource/marbling-and-pork-tenderness/.
25. Muñoz G, Alcázar E, Fernández A, Barragán C, Carrasco A, de Pedro E, Silió L, Sánchez JL, Rodríguez MC. 2011. Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc × Iberian crossbred pigs. Meat Science 88 (2011) 169–173. https://digital.csic.es/handle/10261/82089
26. Balatsky VN, Bankovska IB, Saienko AM. 2016. Association between leptin receptor gene polymorphism and quality of both meat and backfat in large white pigs of Ukrainian breeding. Agricultural Science and Practice, 2016, Vol. 3, No. 2. https://agrisp.com/index.php/agrisp/article/view/79
27. Kuryl J., Kapelański W., Pierzchała M., Grajewska S., Bocian M. 2003. Preliminary observations on the effect of calpastatin gene (CAST) polymorphism on carcass traits in pigs. Animal Science Papers and Reports vol. 21 (2003) no. 2, 87-95. https://www.researchgate.net/publication/262602834_Preliminary_observations_on_the_effect_of_calpastatin_gene_CAST_polymorphism_on_carcass_traits_in_pigs
28. Xue W., Wang W., Jin B., Zhang X., Xu X. 2015. Association of the ADRB3, FABP3, LIPE, and LPL gene poly-morphisms with pig intramuscular fat content and fatty acid composition. Czech J. Anim. Sci., 60, 2015 (2): 60–66. https://www.researchgate.net/profile/Xue-Wenda/publication/276404773_Association_of_the_ADRB3_FABP3_LIPE_and_LPL_gene_polymorphisms_with_pig_intramuscular_fat_content_and_fatty_acid_composition/links/55632dfb08ae6f4dcc961cb1/Association-of-the-ADRB3-FABP3-LIPE-and-LPL-gene-polymorphisms-with-pig-intramuscular-fat-content-and-fatty-acid-composition.pdf
29. Davoli R., Braglia S. 2008. Molecular approaches in pig breeding to improve meat quality. Briefings in Func-tional Genomics and Proteomics. 6(4): 313-321. doi:10.1093/bfgp/elm036. https://academic.oup.com/bfg/article/6/4/313/206680.
30. Clark DL., Clark DI., Beever JE., Dilger AC. 2015. Increased prenatal IGF2 expression due to the porcine IGF2 in-tron3-G3072A mutation may be responsible for increased muscle mass. J. Anim. Sci. 2015.93:2546–2558. https://doi:10.2527/jas2014-8389.
31. Kolaøíková O, Putnová L, Urban T, Adámek J, Knoll A, Dvoøák J. 2003. Associations of the IGF2 gene with growth and meat efficiency in Large White pigs. J. Appl. Genet. 4(44), 2003, pp. 509-513. https://www.researchgate.net/publication/9008486_Associations_of_the_IGF2_gene_with_growth_and_meat_efficiency_in_Large_White_pigs
32. Vincent AL, Tuggle CK, Rothschild MF, Evans G, Short TH, Southwood OI, Plastow GS. 1998. The prolactin re-ceptor gene is associated with increased litter size in pigs. Proc 6th World Cong Genet Appl Livest Prod. 29. https://www.researchgate.net/publication/242389838_The_Prolactin_Receptor_Gene_is_Associated_with_Increased_Litter_Size_In_Pigs.
33. Sun YX, Zeng YQ, Tang H, Fan XZ, Chen QM, Li H, Qian Y, Song YP. 2009. Relationship of genetic polymor-phism of PRLR and RBP4 genes with litter size traits in pig. Vol. 31. Issue (1):63-68.doi:10.3724/SP.J.1005.2009.00063. http://www.chinagene.cn/CN/10.3724/SP.J.1005.2009.00063.
34. Yurina A, Skovorodin E, Dolmatova I. Evaluation of reproductive traits and ovarian and uterine morphology of sows with different genotypes for the estrogen receptor, prolactin receptor, and follicle-stimulating hormone subunit beta genes. Can J Vet Res. 2021 Jul;85(3):186-192. PMID: 34248262; PMCID: PMC8243814. https://pmc.ncbi.nlm.nih.gov/articles/PMC8243814/pdf/cjvr_03_186.pdf
35. Trenhaile MD, Petersen JL, Kachman SD, Johnson RK, Ciobanu DC. 2016. Long-term selection for litter size in swine results in shifts in allelic frequency in regions involved in reproductive processes. Animal Genet-ics/Volume 47, Issue 5/ pp. 534-542. doi:10.1111/age.12448. https://onlinelibrary.wiley.com/doi/10.1111/age.12448.
36. Rothschild M, Jacobson C, Vaske D, Tuggle C, Wang L, Short T, Eckardt G, Sasaki S, Vincent A, McLaren D, Southwood O, van der Steen H, Mileham A, Plastow G. The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):201-5. https://pubmed.ncbi.nlm.nih.gov/8552604/
37. Vega RSA, Castillo MRC, Barrientos NNB, Llanes-Autriz MM, Wook Cho B, de la Viña CB, and Villa NO. 2018. Leptin (T3469C) and Estrogen Receptor (T1665G) gene polymorphisms and their associations to backfat thick-ness and reproductive traits of large white pigs (Sus scrofa L.). Philippine Journal of Science 147 (2): 293-300, June 2018 ISSN 0031 – 7683. https://philjournalsci.dost.gov.ph/wp-content/uploads/2025/07/leptin_T3469C_and_estrogen_receptor.pdf.
38. Lin HC, Liu GF, Wang AG, Kong LJ, Wang XF, Fu JL. 2008. Effect of polymorphism in the leukemia inhibitory factor gene on litter size in large white pigs (Abstract). Molecular Biology Reports. https://link.springer.com/article/10.1007/s11033-008-9387-0
39. Ding Y, Ding C, Wu X, Wu C, Qian L, Li D, Zhang W, Wang Y, Yang M, Ding J, Zhang X, Gao Y, Yin Z. 2018. Porcine LIF gene polymorphisms and their association with litter size traits in four pig breeds. Can. J. Anim. Sci. 100: 85–92. https://cdnsciencepub.com/doi/10.1139/cjas-2018-0228
40. Silveira A.C.P., P.F.A. Freitas, A.S.M. Cesar, R.C. Antunes, E.C. Guimarāes, D.F.A. Batista, L.C. Torido. 2011. In-fluence of the halothane gene (HAL) on pork quality in two commercial crossbreeds. Genetics and Molecular Research. 10 (3): 1479-1489. https://geneticsmr.com/wp-content/uploads/2024/04/gmr925.pdf
41. Stupka R, Citek J, Sprysl M, Okrouhla M, Brzobohaty L. 2012. The impact of MYOG, MYF6 and MYOD1 genes on meat quality traits in crossbred pigs. African Journal of Biotechnology Vol. 11(88), pp. 15405-15409, 1 No-vember, 2012. http://www.academicjournals.org/AJB.
42. Cho I-C., Park H-B, Ahn JS, Han S-H, Lee J-B, Lim H-T, Yoo C-K, Jung E-J, Kim D-H, Sun W-S, Ramayo-Caldas Y, Kim S-G, Kang Y-J, Lee J-W. 2019. A functional regulatory variant of MYH3 influences muscle fiber-type com-position and intramuscular fat content in pigs. PLOS Genetics. Available at https://doi.org/10.1371/journal.pgen.1008279.
43. Zhao T, Tian T, Yu H, Cao C, Zhang Z, He Z, Ma Z, Cai R, Li F, Pang W. 2024. Identification of porcine fast/slow myogenic exosomes and their regulatory effects on lipid accumulation in intramuscular adipocytes. Journal of Animal Science and Biotechnology. 73 (2024). Available at https://jasbsci.biomedcentral.com/articles/10.1186/s40104-024-01029-0.
44. Rohrer G.A., D.J. Nonneman, R.K. Miller, H. Zerby, S.J. Moeller. 2012. Association of single nucleotide poly-morphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs. Meat Science 92: 511–518. https://doi:10.1016/j.meatsci.2012.05.020.
Downloads
Published
Issue
Section
Categories
License
Copyright (c) 2026 Arnolfo Monleon
This work is licensed under a Creative Commons Attribution 4.0 International License.
