Assessment of genetic diversity of Wua-lan in Thailand

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Damrongsak Arlai
Theerapol Sirinarumitr
Janjira Phavaphutanon
Sudtisa Laopiem
Mananya Preyavitchayapugdee


Wua-lan (Khao-Lan) is one of the indigenous cattle (Bos indicus) in Thailand that needs immediately scientific data of animal breeding plans for this cattle management. Genetic characterization is the first step in the development of proper management strategies for preserving genetic diversity and preventing undesirable loss of alleles. Thus, in this study, we investigated genetic diversity and relationship of Wua-lan among different areas using 20 microsatellite markers. In this study, the analysis of autosomal DNA was performed on 76 Wua-lan which exhibited sufficient diversity across all the areas. The mean observed heterozygosity across all loci in this population was 0.484. Wua-lan had the allele size larger than both Thai native cattle (CSSM66 and TGLA153) and domestic cattle (BM6117 and CSSM66), but some allele size of domestic cattle (BM6445) was larger than Wua-lan. The genetic diversity was identified by expected heterozygosity (He), observed heterozygosity (Ho) and inbreeding coefficient (⨏) that was identified by areas as follows: Phetchaburi (0.546, 0.484 and 0.126), Ratchaburi (0.532, 0.478 and 0.134) andPrachuap Khiri Khan (0.508, 0.488 and 0.067), respectively. The Ho and He did not show differences between each area (∆He-Ho), the Wua-lan in Phetchaburi was the most different value, and Wua-lan in Prachuap Khiri Khan was the lowest difference value. The total of the observed heterozygosity and inbreeding coefficient (⨏) of Wua-lan in 3 areas were equal to 0.484 and 0.129. A broad variation of inbreeding coefficient (⨏) was found among all loci, ranging from -0.875 (CSSM66) in Phetchaburi to 0.894 (BM848) in Ratchaburi Province. The genetic differentiation of Wua-lan ranged from 0.930 (Rat-Pet pair) to 0.965 (Pra-Pet pair) that was genetically differentiated by a similar magnitude. The shortest of Nei’s genetic distances was observed between the Wua-lan from Ratchaburi (Rat) and Phetchaburi Province (Pet) (0.072) followed by Wua-lan from Prachuab Khiri Kahn (Pra) and Phetchaburi Province (Pet) (0.036). The Wua-lan from Prachuap Khiri Khan Province (Pra) was the most distant population, displaying the largest of Nei’s genetic distances (0.119) when compared with the Wua-lan from Phetchaburi Province (Pet). The bootstrap values among this breed ranged from 2.99 to 4.78. Thus, the low values in this study were caused by the high genetic similarity between areas of animal husbandry. This result of the change in interred clusters (∆K) values peaked at K=4, which exhibited a reliable grouping pattern. These points suggest a distant relationship between the populations of a single geographic area, with minimal appearance of shared genetic materials between the three areas. The finding in the current study point origins of Wua-lan in Phetchaburi, Ratchaburi, and Prachuap Khiri Khan and their close relationship has been supported, in this study that showed relatively more admixture within the west region of Thailand.

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Arlai, D., Sirinarumitr, T. ., Phavaphutanon, J., Laopiem, S., & Preyavitchayapugdee, M. (2022). Assessment of genetic diversity of Wua-lan in Thailand. Interdisciplinary Research Review, 17(1), 25–32. Retrieved from
Research Articles


P. Riethmuller, N. Chalermpao, Some issues associated with the livestock industries of the asia-pacific region (2002).


DLD, Yearly statistics report, Department of Livestock Development (2010).


R. Sharma, A. Kishore, M. Mukesh, S. Ahlawat, A. Maitra, A. K. Pandey, M. S. Tantia, Genetic diversity and relationship

of indian cattle inferred from microsatellite and mitochondrial dna markers 16 (2015) 73–84

G. Nyamushamba, C. Mapiye, O.Tada, T. E. Halimani, V. Muchenje, Conservation of indigenous cattle genetic resources in southern africa’s smallholder areas: turning threats into opportunities - a review, Asian-Australasian journal of animal sciences 30 (5) (2017) 603–621.

R. Charoensook, C. Knorr, B. Brenig, K. Gatphayak, Thai pigs and cattle production, genetic diversity of livestock and strategies for preserving animal genetic resources maejo, Int. J. Sci. Technol 7 (2013) 113–132.

FAO, The state of the world’s animal genetic resources for food and agriculture, Rome, p. 524, iSBN 978-92-5-105762-9.

C. Laosutthipong, P. Chuawongboon, Genetic relationship of maternal lineages in phetchaburi native cattle, International

Journal of Agricultural Technology 14 (7) (2018) 1379–1390.

I. A. Arif, H. A. Khan, Molecular markers for biodiversity analysis of wildlife animals: a brief review, Animal Biodiversity and Conservation 32 (1) (2009) 9–17.

S. Phandee, J. Phavaphutanon, K. Sirinarumitr, S. Laopiem, T. Sirinarumitr, Study of genetic variation of captive asiatic

golden cat (pardofelis temminckii) in thailand using domestic cat (felis catus) microsatellite markers, Thai J Vet Med 46 (1) (2016) 127–133.

M. A. Menotti-Raymond, S. J. O’Brien, Evolutionary conservation of ten microsatellite loci in four species of felidae, The

J. of Hered 86 (4) (1995) 319–322.

M. Culver, M. A. Menotti-Raymond, S. J. O’Brien, Pattern of size homoplasy at 10 microsatellite loci in pumas (pumaconcolor), Mol. Biol. Evol 18 (6) (2001) 1151–1156.

S. J. O’Brien, M. A. Menotti-Raymond, W. J. Murphy, N. Yuhki, The feline genome project, Anuu. Rev. Genet 36 (2002) 657–686.

F. Pereira, A. Amorim, B. Asch, title, in: M. de la Guardia, A. Gonzalvez (Eds.), In food protected designation of origin: methodologies and applications. Comprehensive Analytical Chemistry, Vol. 60, 2013, Ch. 8-Genetic and DNA-Based Techniques, pp. 195–220.

J. Sambrook, D. W. Russel, Molecular cloning, a laboratory manual 3rd Edition, Vol. 1, Cold Spring Harbor Laboratory

Press, New York, 2001, pp. 643.

D. Arlai, T. Sirnarumitr, J. Phavaphutanon, S. Laopiem, M. Preyavitchayapugdee, Effectiveness of microsatellite

primers for whua-lan cattle, in: The 9th NPRU National Academic Conference Nakhon Pathom Rajabhat University, 2017, pp. 2017–2025, 28th – 29th September 2017.

R. G. Mateescu, Z. Zhang, K. Tsai, J. Phavaphutanon, N. I. Burton-Wurster, G. Lust, R. Quaas, K. Murphy, G. M. Acland,

R. J. Todhunter, Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genomewide screening for hip dysplasia in a crossbreed pedigree, J Hered 96 (2005) 847–853.

FAO, Molecular genetic characterization of animal genetic resources, in: FAO Animal Production and Health Guidelines,

no. 9, Rome, Italy.

M. Nei, Genetic distance between populations, Am. Nat 106 (1972) 192–283.

D. Botstein, R. L. White, M. Skolnick, R. W. Davis, Construction of genetic linkage map in man using restriction fragment

length polymorphisms, Am J Hum Genet 32 (1980) 314–331.

H. C. Hines, J. P. Zikakis, G. F. Haenlein, Linkage relationships among loci of polymorphisms in blood and milk of cattle, J. Dairy Sci 64 (1) (1981) 71–76.

J. K. Pritchard, M. Stephens, P. Donnelly, Inference of population structure using multilocus genotype data, Genetics 155

(2000) 945–959.

D. Falush, M. Stephens, J. K. Pritchard, Inference of population structure using multilocus genotype data: linked loci and

correlated allele frequencies, Genetics 164 (2003) 1567–1587.

D. Falush, M. Stephens, J. K. Pritchard, nference of population structure using multilocus genotype data dominant markers and null alleles, Mol. Ecol. Notes 7 (2007) 574–578.

S. Mekchay, S. Chomdej, K. Nganvongpanit, Research project: Analysis of genetic diversity of northern thai native beef cattle by microsatellite and mitochondrial markers, Tech. rep., Department of Animal and Aquatic Science, Chiang Mai University, Thailand, the Thailand Research Fund: TRF RDG5020005 (2008).

M. Duangjinda, Y. Phasuk, Research project: Study of genetic diversity and genetic classification of thai native beef cattle using microsatellite and mitochondrial data, Tech. rep., Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Thailand, the Thailand Research Fund: TRF RDG4920055 (2008).

M. D. Bishop, S. D. Kappes, J. Keele, R. T. Stone, S. L. F. Sunden, G. A. Hawkins, S. S. Toldo, R. Fries, M. D. Grosz, J. Yoo, C. W. Beattie, A genetic linkage map for cattle, Genetics 13 (1994) 619–639.

H. Shahsavarani, G. Rahimi-Mianji, Analysis of genetic diversity and estimation of inbreeding coefficient within caspian

horse population using microsatellite markers, Afr. J. Biotec 9 (2010) 293–299.

A. C. M. Silva, S. R. Paiva, M. S. M. Albuquerque, A. A. Egito, S. A. Santos, F. C. Lima, S. T. Castro, A. S. Mariante, P. S. Correa, C. M. McManus, Genetic variability in local brazilian horse lines using microsatellite markers, Genetics and Molecular Research 11 (2012) 881–890.

M. Tolone, S. Mastrangelo, A. J. M. Rosa, Genetic diversity and population structure of sicilian sheep breeds using microsatellite markers, Small Rumin Res 102 (2012) 18–25.

M. Sodhi, M. Mukesh, S. P. S. Ahlawat, R. C. Sobti, G. C. Gehlot, S. C. Mehta, B. Prakash, B. P. Mishra, Genetic diversity and structure of two prominent zebu cattle breeds adapted to the arid region of india inferred from microsatellite polymorphism, Biochemical Genetics 46 (2008) 124–136.

R. Sharma, A. Maitra, A. K. Pandey, Genetic structure and differentiation of four indian autochthonous cattle populations,

Russian Journal of Genetics 48 (2012) 611–617.

A. A. Egito, S. R. Paiva, M. M. Albuquerque, A. S. Mariante, L. D. Almeida, S. R. Castro, D. Grattapaglia, Microsatellite based genetic diversity and relationships among ten creole and commercial cattle breeds raised in brazil, BMC Genet 8 (2007) 83.

W. Sun, H. Chen, C. Lei, Genetic variation in eight chinese cattle breeds based on the analysis of microsatellite markers,

Genet Sel Evol 40 (2008) 681–692.

R. Jose Ocampo, J. F. Mart ´ ´ınez, Assessment of genetic diversity and population structure of colombian creole cattle using microsatellites, Tropical Animal Health and Production 53 (2021) 122.

R. J. Petit, E. I. Mousadik, O. Pons, Identifying populations for conservation on the basis of genetics: simulated genetic

markers, Conserv Biol 12 (1998) 844–855.

B. G. Cassell, V. Adamec, R. E. Pearson, Effect of incomplete pedigrees on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in holsteins and jerseys, J. Dairy Sci 86 (2003) 2967–2976.

I. Alvarez, J. Capote, A. Trao ´ ´re, N. Fonseca, K. Perez, M. Cuervo, I. Fernandez, F. Goyache, Genetic relationships of the cuban hair sheep inferred from microsatellite polymorphism, Small Ruminant Research 104 (1-3) (2012) 89–93.

M. A. Cleveland, H. D. Blackburn, R. M. Enns, D. J. Garrick, Changes in inbreeding of u.s. herefords during the twentieth century, J. Anim. Sci 83 (2005) 992–1001.

G. Gandini, A. Bagnato, F. Miglior, G. Pagnacco, Inbreeding in the italian hafl inger horse, J. Anim. Breed. Genet 109 (1992) 433–443.

J. Sierszchulski, M. Helak, A. Wolc, T. Szwaczkowski, W. Schlote, Inbreeding rate and its effects on three body conformation traits in arabian mares, Anim. Sci. Pap. Rep 23 (2005) 51–59.

E. Barczak, A. Wolc, J. Wojtowski, P. ´ Sl´ osarz, ´ T. Szwaczkowski, Inbreeding and inbreeding depression

on body weight in sheep, J. Anim. Feed Sci 18 (2009) 42–50,

K. Ubolrat, S. Laopiem, K. Nunklang, J. Phavaphutanon, Genetic diversity and inbreeding situation of korat and siamese

cats based on microsatellite markers, Veterinary Integrative Sciences 17 (1) (2019) 51–64.

M. Nei, Molecular evolutionary genetics, Columbia University Press, New York, 1987.

E. Krupa,E. Zˇ akov ´ a Z. Krupov ´ a, Evaluation of inbreeding and ´genetic variability of five pig breeds in czech republic, AsianAustralasian journal of animal sciences 28 (1) (2015) 25–36,