DOI: 10.5061/dryad.b8gtht7gg
title: Genotype data of Philippine native pigs, Duroc, Landrace, Large White and Berkshire, using 20 ISAG-FAO recommended microsatellite markers

description: 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.
description: We analyzed 7 Philippine
 populations, including Benguet <em>n</em> = 22,
 Kalinga<em> n</em> = 27, Nueva Viscaya<em> n</em>
 = 20,  Isabela<em> n</em>= 23, Quezon<em> n</em> =
 25, Marinduque<em> n</em> = 20, and Samar
 <em>n</em> = 20; and 4 commercial transboundary breeds,
 including Berkshire (BAI
 BS) <em>n</em> = 10 (from the National Swine and Poultry
 Research and Development Center, Bureau of Animal Industry
 (BAI)), Large White (LW)
 <em>n</em> = 11, Landrace (LR)
 <em>n</em> = 9, and Duroc (DC)<em> n</em> = 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. 
description: .txt file can be opened with Notepad, Microsoft Excel, Numbers,
 LibreOffice, WPS .fsa file can be opened with
 PeakScanner™ v1.0 (available free from www.thermofisher.com); NCBI's Osiris (Open Source Independent Review and Interpretation System) (https://www.ncbi.nlm.nih.gov/osiris/); and in R Studio using the Fragman package (Covarrubias-Pazaran et al., 2016).
description: # Genotype data of Philippine native pigs, Duroc, Landrace, Largewhite and
 Berkshire using 20 ISAG-FAO recommended microsatellite markers The
 genotype data presented contains the microsatellite alleles of domestic
 pigs in the Philippines. We used PCR and fragment analysis performed in
 3730xl Genetic Analyzer to achieve comparable results across batches. The
 data was used for the genetic diversity study of Philippine native pigs.
 This dataset includes both the processed file (.txt) and the raw file
 (.fsa). ## Description of the Data and file structure **Part 1. The
 processed file consist of manual allele scores of 196 pig samples
 genotyped with 20 ISAG-FAO recommended microsatellite markers.** A. The
 manual allele scores are made available in a text file, which you can open
 with a Notepad, Excel, WPS, LibreOffice or other similar software. It
 follows the formatting requirement of GenAlex v6.5, without the Genalex
 parameters, and labeled in rows 1 to 3 (to satisfy Dryad's table
 requirement). Below the dataset is other information such as minimum
 allele size, maximum allele size, count of alleles, and the list of unique
 alleles per marker. <br> B. Codes in the file Sequence\_Population
 Sequence Population\_Name Population\_Code n ABN A Benguet BN 22 BK B
 Kalinga K 27 CN C Nueva Vizcaya N 20 DI D Isabela I 23 EQ E Quezon\_native
 Q 25 FM F Marinduque M 20 GE G Samar S 20 HBS H Berskhire BS 10 ILW I
 Largewhite LW 11 JLR J Landrace LR 9 KD K Duroc D 9 **Part 2. Raw .fsa
 files** A. The dataset is contained in 8 folders based on the multiplex
 group number (G1 to G7) as follows: 1. G1 2. G2 3. G3 4. G4 5. G5 6. G6 7.
 G7 8. Anchor Samples Anyone from the two anchor samples (S0005 x N182; or
 S0005 x Q475) were included in each plate during Fragment Analysis to
 confirm consistent sizing. Each sample ID also starts with the Multiplex
 Group number (G1 to G7). B. We used GeneScan 400HD ROX for the most
 accurate sizing. GeneScan 400HD ROX is designed for sizing DNA fragments
 in the 50 to 400 bp range, and provides 21 single-strand labeled fragments
 of 50, 60, 90, 100, 120, 150, 160, 180, 190, 200, 220, 240, 260, 280, 290,
 300, 320, 340, 360, 380, and 400 bases. C. Primers Note: Forward primers-
 HPLC purified with 5' fluorophore; Reverse primers - HPLC purified
 Reference: FAO, 2011. Molecular genetic characterization of animal genetic
 resources. FAO Animal Production and Health Guidelines. No. 9. Rome. 85pp.
 Primer Name Forward\_Sequence (5' to 3') Reverse\_Sequence
 (5' to 3') Chromosome Fluorophore (for Forward primer only)
 Group S0005 TCCTTCCCTCCTGGTAACTA GCACTTCCTGATTCTGGGTA 5 TAMRA G1 S0155
 TGTTCTCTGTTTCTCCTCTGTTTG AAAGTGGAAAGAGTCAATGGCTAT 1 FAM G1 S0026
 AACCTTCCCTTCCCAATCAC CACAGACTGCTTTTTACTCC 16 HEX G1 S0355
 TCTGGCTCCTACACTCCTTCTTGATG TTGGGTGGGTGCTGAAAAATAGGA 15 TAMRA G2 Sw830
 AAGTACCATGGAGAGGGAAATG ACATGGTTCCAAAGACCTGTG 10 FAM G2 Sw2410
 ATTTGCCCCCAAGGTATTTC CAGGGTGTGGAGGGTAGAAG 8 HEX G2 Swr1941
 AGAAAGCAATTTGATTTGCATAATC ACAAGGACCTACTGTATAGCACAGG 13 TAMRA G3 Sw632
 TGGGTTGAAAGATTTCCCAA GGAGTCAGTACTTTGGCTTGA 7 FAM G3 Sw24
 CTTTGGGTGGAGTGTGTGC ATCCAAATGCTGCAAGCG 17 HEX G3 S0228
 GGCATAGGCTGGCAGCAACA AGCCCACCTCATCTTATCTACACT 6 FAM G4 S0218
 GTGTAGGCTGGCGGTTGT CCCTGAAACCTAAAGCAAAG X HEX G4 Sw936
 TCTGGAGCTAGCATAAGTGCC GTGCAAGTACACATGCAGGG 15 TAMRA G4 S0097
 GACCTATCTAATGTCATTATAGT TTCCTCCTAGAGTTGACAAACTT 4 FAM G5 Sw857
 TGAGAGGTCAGTTACAGAAGACC GATCCTCCTCCAAATCCCAT 14 TAMRA G5 Sw122
 TTGTCTTTTTATTTTGCTTTTGG CAAAAAAGGCAAAAGATTGACA 6 HEX G5 Sw2406
 AATGTCACCTTTAAGACGTGGG AATGCGAAACTCCTGAATTAGC 6 TAMRA G6 IGF1
 GCTTGGATGGACCATGTTG CATATTTTTCTGCATAACTTGAACCT 5 FAM G6 Sw240
 AGAAATTAGTGCCTCAAATTGG AAACCATTAAGTCCCTAGCAAA 2 HEX G6 S0090
 CCAAGACTGCCTTGTAGGTGAATA GCTATCAAGTATTGTACCATTAGG 12 TAMRA G7 S0226
 GCACTTTTAACTTTCATGATACTCC GGTTAAACTTTTNCCCCAATACA 2 FAM G7 Sw72
 ATCAGAACAGTGCGCCGT TTTGAAAATGGGGTGTTTCC 3 HEX G7 D. Individual animal ID
 Individual animal ID used the following codes: Benguet B Kalinga K Nueva
 Vizcaya N Isabela I Quezon Q Marinduque M Samar S Berskhire BS Largewhite
 LW Landrace LR Duroc D Volante V Exotic breeds were sex-identified, if
 available, whether male (M) or female (F). Final sample codes for the .fsa
 files are Multiplex Group number - Population initials - Animal number -
 (optional) Notes (i.e. a, b, \_retrial, etc), for example: Multiplex Group
 1 Large White Male number 3: G1LWM3.fsa; Multiplex Group 2 Benguet native
 pig number 050: G2B050.fsa; Multiplex Group 3 Benguet native pig number
 099, b: G2B099b.fsa. NOTE: The partial mitochondrial d-loop nucleotide
 sequence data of most samples are available in the DDBJ/EMBL/GenBank
 databases under the accession numbers OM363266 - OM363454. ##
 Sharing/access Information Links to other publicly accessible locations of
 the data: None Was data derived from another source? No If yes, list
 source(s):