+Supplementary Materials Genetic Structure of Omani Goats Reveals Admixture among Populations from Geographically Proximal Sites Nasser Ali Al-Araimi a* , Raed Mahmoud Al-Atiyat b , Agusto Luzuriaga- Neira a , Osman Mahgoub Gaafar c , Isam T. Kadim d , Waleed Al- Marzooqi c , Hamza A. Babiker e , Mohammed N. Al-Kindi e , Aliya S. Al- Ansari f , Ali H. Al-Lawati g , Albano Beja-Pereira a,h a Research Center in Biodiversity and Genetic Resources (CIBIO), InBIO, University of Porto, R. Padre Armando Quintas 7, 4485-661 Vairão, Porto, Portugal b Department of Animal Production, Faculty of Agriculture, Mutah University, Al-Karak 61710, Jordan c Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Postal Code 123, Al-Khod, Sultanate of Oman d Department of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, P.O. Box 33, Postal Code 616, Birkat Al-Mouz, Sultanate of Oman e Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, P.O. Box 35, Postal Code 123, Al-Khod, Sultanate of Oman 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
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ars.els-cdn.com · Web viewgThe Oman Animal and Plant Genetic Resources Center, The Research Council, P.O. Box 1422, Postal Code 130, Muscat, Sultanate of Oman hDepartment of Geosciences,
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+Supplementary Materials
Genetic Structure of Omani Goats Reveals Admixture among Populations from
Geographically Proximal Sites
Nasser Ali Al-Araimia*, Raed Mahmoud Al-Atiyatb, Agusto Luzuriaga-Neiraa, Osman Mahgoub
Gaafarc, Isam T. Kadimd, Waleed Al-Marzooqic, Hamza A. Babikere, Mohammed N. Al-Kindie,
Aliya S. Al-Ansarif, Ali H. Al-Lawatig, Albano Beja-Pereiraa,h
aResearch Center in Biodiversity and Genetic Resources (CIBIO), InBIO, University of Porto, R.
Padre Armando Quintas 7, 4485-661 Vairão, Porto, PortugalbDepartment of Animal Production, Faculty of Agriculture, Mutah University, Al-Karak 61710,
JordancDepartment of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences,
Sultan Qaboos University, P.O. Box 34, Postal Code 123, Al-Khod, Sultanate of OmandDepartment of Biological Sciences and Chemistry, College of Arts and Sciences, University of
Nizwa, P.O. Box 33, Postal Code 616, Birkat Al-Mouz, Sultanate of OmaneDepartment of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos
University, P.O. Box 35, Postal Code 123, Al-Khod, Sultanate of OmanfDepartment of Biology, College of Sciences, Sultan Qaboos University, P.O. Box 36, Postal
Code 123, Al-Khod, Sultanate of OmangThe Oman Animal and Plant Genetic Resources Center, The Research Council, P.O. Box 1422,
Postal Code 130, Muscat, Sultanate of OmanhDepartment of Geosciences, Environment and Spatial Planning, Faculty of Sciences, University
of Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
a Cr, chromosome location; b F and R, forward and reverse primer, respectively; c accession no; * loci were excluded from further analysis based on inconsistent banding patterns, HWE and linkage disequilibrium.
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3132
Table S2. MICRO-CHECKER summary results of the presence of null alleles by population.
Locus/Population
Jabal Akhdar
Batinah Dhofar Ash
SharqiyahMusanda
mSomali
a Iran Pakistan India
SRCRSP05 no yes yes no no no no no noSRCRSP08 no no no no no no no yes noMAF65 no no no no no no no no noINRA005 no no no no no no no no noINRA006 no no no no no no yes no noINRA063 no no no no no no no no noILSTS19 no no yes no no no no no noSRCRSP23 no no no no no no no no noILSTS08 no no no no no no no no noCSRD247 no no no no no no no no noMcM527 no no no no no no no no noOarFCB20 no no no no yes no no no noINRA023 no no no no no no no no noILSTS87 no no no no no no no no no
MICRO-CHECKER summary results by population. The program highlighted the possible presence of null alleles in only six
instances (shown in bold yes).
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Table S3. FST estimates with and without ENA correction.
Locus FST not using ENA FST using ENASRCRSP5 0.081 0.076SRCRSP8 0.211 0.202MAF65 0.089 0.087INRA005 0.053 0.053INRA006 0.054 0.055INRA063 0.117 0.115ILSTS19 0.140 0.137SRCRSP23 0.063 0.063ILSTS008 0.107 0.105CSRD247 0.107 0.106McM527 0.051 0.051OarFCB20 0.100 0.104INRA023 0.071 0.071ILSTS87 0.125 0.125All loci 0.096 0.095Bootstrap 95% CI 0.076-0.121 0.076-0.117
FreeNA output. The global FST (Weir and Cockerham, 1996) was estimated with and without ENA correction, as described in Chapuis
and Estoup (2007).
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Table S4. Significant exact probability (P) of Hardy-Weinberg departures for each locus-population combination.
Locus/Population
Jabal Akhdar
Batinah
Dhofar
Ash Sharqiyah
Musandam
Somalia
Iran
Pakistan
India
HWEd ‡
SRCRSP5 no no no no no no no no no 0SRCRSP8 no no no no no no no no yes 1MAF65 no no no no no no no no no 0INRA005 no no no no no no no no no 0INRA006 no no no no no no yes no yes 2INRA063 no no no no no no no no no 0ILSTS19 no no no no no no no no no 0SRCRSP23 no no no no no no no no no 0ILSTS008 no no no no no no no no no 0CSRD247 no no no no no no no no no 0McM527 no no no no no no no no no 0OarFCB20 no no no no no no no no no 0INRA023 no no no no no no no no no 0ILSTS87 no no no no no no yes no no 1HWEd
‡ 0 0 0 0 0 0 2 0 2 0Bold yes indicates a locus-population combination that is still significant (P ≤ 0.001) following adjustments for multiple tests with
Holm–Bonferroni sequential correction (Holm, 1979); ‘no’ indicates not significant. HWEd ‡: No. of significant population and locus
departures from HWE at P ≤ 0.001 after Holm–Bonferroni sequential correction (Holm, 1979).
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Table S5. Genotypic linkage disequilibrium tests. The number of significant (P < 0.001) locus combinations of 819 is listed for
each breed following adjustments for multiple tests with Holm–Bonferroni sequential correction (Holm, 1979).