Supplemental Material for Neik et al., 2019
Creators: name: Neik, Ting Xiang
name: Chai, Jing-Yun
name: Seow-Yeen Tan
name: Sudo, Maggie Pui San
name: Yongxia Cui
name: Jayasyaliny Jayaraj
name: Su-Sin Teo
name: Olsen, Kenneth M.
name: Beng-Kah Song
Publisher: name: Figshare
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 60409 Molecular Evolution

description: Supplementary Information of the manuscript entitled "When West meets East: The origins and spread of weedy rice between continental and island Southeast Asia" <br><b>Supplementary Information</b> <br>Figure S1. Representatives of five groups of weedy and cultivated rice accessions classified according to seed morphological features: (A) strawhulled, awnless (SH); (B) strawhulled, awned (SHA); (C) brown-striped-hulled, awnless types (BR); (D) brown-striped-hulled, awned (BRA); (E) cultivars. Figure S2. STRUCTURE analysis of the Sabah, Peninsular Malaysian, and other countries’ rice samples. (A) Plot of Ln P(D) vs. K. showed an increase in the posterior probability [Ln P(D); L(K)] for a K value up to 20 populations. (B) Plot of ΔK vs. K. Value of ΔK at K = 2 (511.7) was removed to ease illustrations of the second highest peak at K = 5 in the plot. (C) deltaK values calculated as a function of K. ΔK at K = 5 is highlighted in yellow (ΔK = 7.813). (D) Alternate outcomes at K = 4. (E) Alternate outcomes at K = 10.<br>Figure S3. Principal Coordinate Analysis (PCoA) plot of Sabah, Peninsular Malaysia, and worldwide rice samples. (A) PCoA analysis of 358 rice accessions from Sabah (weedy, cultivated and landrace rice), Peninsular Malaysia (cultivars), Indonesian Kalimantan (landrace), Indonesian Java (landrace), Brunei (landrace), Philippines (landrace), East Malaysian Sarawak state (landrace), Thailand (wild rice), Myanmar (wild rice) and US (tropical japonica). (B) PCoA analysis of 478 rice accessions from Sabah (weedy, cultivated and landrace rice), Peninsular Malaysia (weedy and cultivated rice), Thailand (wild rice), Myanmar (wild rice) and US (tropical japonica). Keys to rice sample names: SbCV, Sabah cultivated rice; PMCV, Peninsular Malaysia cultivated rice; SbSH, Sabah weedy rice with strawhulls and no awns; PMSH, Peninsular Malaysia weedy rice with strawhulls and no awns; PMmSH, Peninsular Malaysia weedy rice with intermediate strawhull and no awns; PMmSHA, Peninsular Malaysia weedy rice with intermediate strawhulls and awns; SbSHA, Sabah weedy rice with strawhulls and awns; PMSHA, Peninsular Malaysia weedy rice with strawhulls and awns; SbBR, Sabah weedy rice with browhulls and no awns; PMBR, Peninsular Malaysia weedy rice with browhulls and no awns; SbBRA, Sabah weedy rice with browhulls and awns; PMBRA, Peninsular Malaysia weedy rice with browhulls and awns; PMBH, Peninsular Malaysia weedy rice with blackhulls and no awns; PMBHA, Peninsular Malaysia weedy rice with blackhulls and awns; TropJap, tropical japonica; SbLr, Sabah landrace accessions; PMOr, Peninsular Malaysia <i>Oryza rufipogon</i>; SEAOr, Southeast Easian <i>O. rufipogon</i>; KN, Indonesian Kalimantan; JV, Indonesian Java; BN, Brunei; PHI, Philippines; SW, Sarawak; TropJap, <i>tropical japonica</i>. Figure S4. Haplotype network relationships for the <i>An-1</i> haplotypes identified in this study (Table S6). Each circle represents a haplotype and circle size is proportional to haplotype frequency. Vertical line indicates number of SNP. <br>Supplementary Table S1. Population code, location, number of sample, range of coordinates, coexisting rice varieties of the weedy rice populations and cultivated rice samples used in this study. <br>Supplementary Table S2. Distribution, morphotype code and number of sample of weedy rice accessions used according to hull color and awn presence. <br>Supplementary Table S3. Oryza accession information, haplotype of the An-1 gene, and coefficents of ancestry inferred by STRUCTURE. <br>Supplementary Table S4. Genetic diversity in Sabah weedy rice samples grouped by sampling location. Abbreviations of genetic diversity parameters are as follows: P, percentage of polymorphic loci; <i>H</i><sub>o</sub>, observed heterozygosity; <i>H</i><sub>e</sub>, expected heterozygosity; I, Shannon diversity index. <br>Supplementary Table S5. Pairwise population FST values generated by location-based clustering.<br>Supplementary Table S6. Compilation of the ten mutations identified in the sequenced region of <i>An-1</i> gene. Mutations n2*, n4*, and n6* are functional nucleotide polymorphisms (FNPs) identified in Luo <i>et al</i>. (2013) study.