Genotype data of Philippine native pigs, Duroc, Landrace, Large White and Berkshire, using 20 ISAG-FAO recommended microsatellite markers

Microsatellite genotyping is a cost-effective method for the genetic diversity analysis of under-studied populations, such as the Philippine native pigs. We genotyped n = 196 pigs representing 7 Philippine native pig populations (n = 20 to 27 for each population) and 4 commercial transboundary breeds (n = 9 to 11 for each population). Twenty microsatellite markers, recommended by the International Society of Animal Genetics (ISAG)-FAO, were used to generate the dataset for population analysis (S0005, S0155, S0026, S0355, Sw830, Sw2410, Swr1941, Sw632, Sw24, S0228, Sw936, S0097, Sw857, Sw122, Sw2406, IGF1, Sw240, S0090, S0226, Sw72). S0218 was used as a sex marker (data not shown). All loci, except Sw24, did not deviate from Hardy Weinberg equilibrium. Each marker showed an average PIC of 0.779. A total of 260 alleles of length 86 to 272 bp were obtained. Using this dataset, we determined population structure and conservation priorities in the Philippine native pigs. This dataset contains both the raw files (.fsa) and the processed file (.txt). This dataset can be used by colleagues to increase their research coverage and achieve multi-population and multi-country comparisons, especially among Asian indigenous pigs.

Methods
We analyzed 7 Philippine populations, including Benguet n = 22, Kalinga n = 27, Nueva Viscaya n = 20,  Isabela n= 23, Quezon n = 25, Marinduque n = 20, and Samar n = 20; and 4 commercial transboundary breeds, including Berkshire (BAI BS) n = 10 (from the National Swine and Poultry Research and Development Center, Bureau of Animal Industry (BAI)), Large White (LW) n = 11, Landrace (LR) n = 9, and Duroc (DC) n = 9 (LW, LR and DC were from breeding farms accredited by the BAI, Philippines). Ear notch samples (20 mg) or hair follicles (5 pieces) were rehydrated in phosphate-buffered saline and extracted using GF-1 Tissue DNA Extraction Kit (Vivantis Technologies, Malaysia), following the manufacturer’s protocol. PCR was prepared in 25 µL volume using 20 ng DNA, 1x SuperPlex™ Premix (Takara Bio USA, Inc., California, USA) and 0.05-0.10 µM each primer. Twenty-one microsatellite markers recommended by the International Society of Animal Genetics (ISAG)-FAO were used (FAO, 2011) in multiplex groups (G) as follows G1 S0026, S0155, S0005; G2 S0355, Sw830, Sw2410; G3 Sw24, Sw632, Swr1941; G4 Sw936, S0218, S0228; G5 Sw122, Sw857, S0097; G5 Sw240, Sw2406, IGF1; G7 Sw72, S0226, S0090; except G3 and G4 which did not yield to multiplexing. Forward primers were 5’ labeled with either 6-FAM, HEX, or TAMRA. Fragment analysis was performed by a third-party service provider (Macrogen Inc., Seoul, Korea) on a 3730xl DNA analyzer (Applied Biosystems) using the GeneScan™ 400HD ROX™ internal lane standard (Applied Biosystems, USA). Raw files (.fsa) were opened in PeakScanner™ v1.0 (available free from www.thermofisher.com) and manually scored. Scoring was done by a single personnel to ensure consistent consideration of the stutter peak pattern. We made available both the raw file (.fsa) and processed genotype (.txt) data.