Genotype data of Philippine native pigs, Duroc, Landrace, Large White and Berkshire, using 20 ISAG-FAO recommended microsatellite markers
Data files
Oct 04, 2023 version files 67.20 MB
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DRYAD_DATASET_A.txt
35.34 KB
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Microsatellite_raw_data_.fsa_Banayo_2023.zip
67.16 MB
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README.md
4.84 KB
Abstract
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.
README: 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.
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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:
- G1
- G2
- G3
- G4
- G5
- G6
- G7
- 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):
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.
Usage notes
.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).