Genetic Diversity of Philippine Mallard Duck (Anas platyrhynchos domesticus L.) based on SSR Markers

Veneranda A. Magpantay1*, Angel L. Lambio1, Rita P. Laude2,
Consorcia E. Reaño3, and Maria Genaleen Q. Diaz2

1Institute of Animal Science, College of Agriculture and Food Science,
University of the Philippines Los Baños, College 4031 Laguna, Philippines
2Institute of Biological Sciences, College of Arts and Sciences,
University of the Philippines Los Baños, College 4031 Laguna, Philippines
3Institute of Crop Science, College of Agriculture and Food Science,
University of the Philippines Los Baños, College 4031 Laguna, Philippines

*Corresponding Author: This email address is being protected from spambots. You need JavaScript enabled to view it.





The study was conducted to assess the genetic diversity of Philippine mallard duck populations from four duck-producing provinces – namely Davao del Norte, Iloilo, Pampanga, and Quezon – using 22 microsatellite (SSR) markers. A total of 120 duck blood samples (60 males and 60 females) were obtained for genomic DNA extraction. All SSR markers were optimized and amplified using polymerase chain reaction (PCR) and the allele sizes were determined using an automated fragment analyzer. Results showed that all the SSR loci were not in Hardy-Weinberg equilibrium (HWE) but have high polymorphism information content (PIC), indicating their effectiveness in assessing diversity. The four populations showed high numbers of observed, effective, and private alleles. However, the observed heterozygosity (Ho) was very low. The FIS estimate indicated a deficit of heterozygotes in all populations across loci. The farthest genetic distance was observed between Davao del Norte and Quezon duck populations and that there was already significant moderate population differentiation noted. The phylogenetic tree showed that the Davao del Norte and the Iloilo duck populations are grouped into one cluster, while the Pampanga and the Quezon ducks are grouped into another. Overall results indicated that the Philippine mallard duck populations from the selected major duck-producing provinces in the country showed high genetic diversity and serve as a reservoir of desirable genes. This could aid researchers and decision-makers in developing local egg-type mallard duck breeds.




The Philippines, being an archipelago, is home to diverse plant and animal genetic resources. Recent reports showed that the Philippines is the center of biodiversity for chicken and marine life (Thomson et al. 2014, Carpenter and Springer 2005). Philippine mallard ducks, locally known as “Pateros,” are very popular for balut and salted egg processing. The majority of the inventory is concentrated in the Central and Southern Luzon, Cagayan Valley, Western Visayas, and Davao regions (PSA 2018). The mallard duck populations are being kept under varied production environments, from free-ranging to complete confinement, and exhibit diversity in physical traits (Lambio 2010). This phenotypic diversity needs to be further validated using the molecular technique as it provides more reliable information for assessing the degree, structure, divergence, and distribution of diversity within and among populations found in different locations. Currently, the most widely used genetic marker for diversity analysis is the SSR or short tandem repeat (STR). SSRs are repeat motifs of one to six nucleotides long. They are relatively abundant and distributed in the coding and non-coding regions of the genome. Their co-dominant property, relative ease of detection by PCR, versatility, low cost, high level of polymorphism, and ability to generate higher statistical power and discriminate among populations made this technique invaluable for various types of biological research (Moges et al. 2016, Seilsuth et al. 2016). They have been employed as an important biological marker for genome analysis (Su and Chen 2009, Lyimo et al. 2012, Farrag et al. 2013). The results could aid in the ongoing egg-type mallard duck breed development in the Philippines. . . . read more




AGATEP RC, LAMBIO AL, VEGA RS, CAPITAN SS, MENDIORO MS, YEBRON MGN. 2016. Microsatellite-based genetic diversity and relationship analyses of three genetic groups of domesticated mallard ducks (Anas platyrhynchos domesticus L). Philipp J Vet Anim Sci 42(2): 102–111.
AHMADI AK, RAHIMI G, VAFAEI A, SAYYAZADEH H. 2007. Microsatellite Analysis of Genetic Diversity in Pekin (Anas platyrhynchos) and Muscovy (Cairina moschata) duck populations. Int J Poult Sci 6(5): 378–382.
CARPENTER KE, SPRINGER VG. 2005. The center of the center of marine shore fish biodiversity: the Philippine Islands. Environ Biol of Fishes 72: 467–480.
CLEMENTINO C, BARBOSA F, CARVALHO A, COSTA-FILHO R. 2010. Microsatellite DNA loci for population studies in Brazilian chicken ecotypes. Int J Poult Sci 9(12): 1100–1106.
EARL DA, VONHOLDT BM. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet 4(2): 359–361.
EVANNO G, REGNAUT S, GOUDET J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol 14(8): 2611–2620.
[FAO] Food and Agriculture Organization. 2010. Molecular characterization of animal genetic resources [FAO Animal Production and Health Guidelines No. 11]. Rome, Italy.
FARRAG SA, SOLTAN ME, ENAB AA. 2013. Genetic Variation Analysis of Sinai Chicken and Japanese Quail Populations Using Microsatellite DNA Markers. International Conference on Food and Agricultural Sciences. Singapore: IACSIT Press.
FRANCIS RM. 2017. POPHELPER: An R package and web app to analyze and visualize population structure. Mol Ecol Resour 17: 27–32.
ISMOYOWATI, PURWANTINI D. 2010. An estimation of genetic variation in Indonesian local duck using microsatellite marker. Asian J of Poultry Sci 4: 198–204.
LAMBIO AL. 2010. Poulty Production in the Tropics, 1st Edition. Laguna, Philippines: The University of the Philippines Press. 263p.
LI HF, LI BC, CHEN KW, YANG N, MA YH, TANG QP, TU YJ. 2006. Study on Molecular Genetic Diversity of Native Duck Breeds in China. Acta Veterinaria et Zootechnica Sinica 11: 1107–1113.
LYIMO CM, WEIGEND A, JANBEN-TAPKEN U, MSOFFE PL, SIMIANER H, WEIGEND S. 2012.  Assessing genetic diversity of five Tanzanian chicken ecotypes using microsatellite markers and mitochondrial DNA D-loop sequencing. Proceeding of the Conference on International Research on Food Security, Natural Resource Management and Rural Development by Georg-August Universität Göttingen and University of Kassel-Witzenhausen; 19–21 Sep 2012.
MOGES AD, ADMASSU B, BELEW D, YESUF M, NJUGUNA J, KYALO M, GHIMIRE SR. 2016. Development of microsatellite markers and analysis of genetic diversity and population structure of colletotrichum gloeosporioides from Ethiopia. PLoS ONE 11(3): 1–18.
PRITCHARD JK, STEPHENS M, DONNELLY P. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945–959.
[PSA] Philippine Statistics Authority. 2018. Duck situation report: January to December 2018. Retrieved from on 18 Sep 2019.
PEAKALL R, SMOUSE PE. 2006. GenAlEx 6: Genetic analysis in Excel; Population genetic software for teaching and research. Mol Ecol Notes 6: 288–295.
PEAKALL R, SMOUSE PE. 2012. GenAlEx 6.5: Genetic analysis in Excel; Population genetic software for teaching and research – An update. Bioinformatics 28: 2537–2539.
PERRIER X, JACQUEMOUD-COLLET JP. 2006. DARwin software. Retrieved from
POSSAMAI MHP, BATTILANA J, PALUDO E, HERKENHOFF ME, PÉRTILE F, LIMA-ROSA CADV. 2015. Genotypic characterization of ten microsatellite loci in two Brazilian free range (Caipira) chicken lines. Cienc Rural 45(5): 877–883.
SEILSUTH S, SEO JH, KONG HS, JEON GJ. 2016. Microsatellite Analysis of the Genetic Diversity and Population Structure in Dairy Goats in Thailand. Asian-Australas J Anim Sci 29(3): 327–332.
SEO D, BHUIYAN MSA, SULTANA H, HEO JM, LEE JH. 2016. Genetic diversity analysis of south and east asian duck populations using highly polymorphic microsatellite markers. Asian-Australas J Anim Sci 29(4): 471–478.
SU Y, CHEN GH. 2009. DNA microsatellite analysis of genetic diversity among Chinese indigenous laying-type ducks
(Anas platyrhynchos). Czech J Anim Sci 54(3): 128–135.
TADANO R, KATAOKA Y. 2014. Genetic diversity in a small chicken population inferred from microsatellite polymorphism. J Poult Sci 51(3): 242–247.
TADANO R, KINOSHITA K, MIZUTANI M, TSUDZUKI M. 2014. Comparison of microsatellite variations between Red Junglefowl and a commercial chicken gene pool. Poult Sci 93(2): 318–325.
THOMSON VA, LEBRASSEUR O, AUSTIN JJ, HUNT TL, BURNEY DA, DENHAM T, RAWLENCEA NJ, WOOD JR, GONGORA J, FLINK LG, LINDERHOLM A, DOBNEY K, LARSON G, COOPER A. 2014. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proc Natl Acad of Sci USA 111(13): 4826–4831.
WU F, HUANG Y, MA Y, HU S, HAO J, LI N. 2009. Evaluation of genetic diversity and relationships within and between two breeds of duck based on microsatellite markers. Prog Nat Sci 19(11): 1581–1586.