Supplementary Information

Transcription

1 Supplementary Information Figure S1 Sequencing quality. Sample screenshot of re-sequencing raw file quality generated by FastQC. For both the graphs, scores were based on the Illumina 1.5 quality score. The X-axis represents the base positions of the raw reads, whereas Y-axis represent the quality score. (A) Sequencing quality of forward-end Illumina reads. (B) Sequencing quality of reverse-end Illumina reads. A B

2 Figure S2. Example of SNP graphs observed using the Illumina Infinium Genotyping Assay. SNP graphs were illustrated using the Software Illumina GenomeStudio, version (A) The normalized theta (Norm Theta) value is the ratio of the signal intensities assayed for the A and B forms (B) of the SNP marker allele against normalized R (signal intensity Norm R). Fig. A and B below represent the same SNP marker.

3 Figure S3. Full dendrogram. Related to Figure 2. An unrooted radial tree generated to show the full relationships among 312 individual palms according to pairwise genetic distance. The assayed palms were assigned to five clusters, including I. UR x AVROS (red), II. JL x AVROS (purple), III. Nigerian x AVROS (green), IV. GM x DA (yellow) and V. JL x DA (blue).

4 Table S1. Summary of SNP selection criteria. The SNP selection steps for the genotyping array design. The threshold values for each SNP filter parameter is given in second column. Filter Filter description Number of SNPs filtered out Remaining SNPs Interspecific Neighboring* Coverage** GQ** Ambiguities* Interspecific and nonsegregating SNPs Pairs of SNPs with distance <= 60 bp are removed SNPs with coverage < 17 or coverage > 53 are removed SNPs with GQ <= 7 are removed SNPs with ambiguous nucleotide «N» or «X» within 60 bp (upstream and downstream) are removed. SNPs with less than 60 bp (upstream or downstream) are also removed. 1,085,204 6,670,745 5,174,660 1,496, , ,135 5, ,046 10, ,054 Indels* Filter out indels 56, ,697 Biallelic* MAF** SNP type* Filter out SNPs which are not biallelic SNPs with MAF <= 0.05 are removed (A/T and C/G SNPs are removed) *Filter due to technical requirement for synthesis of Illumina Infinium SNPs chip **Filter due to quality control ,289 71, ,236 88, ,888

5 Table S2. Transcripts/genes detected in the selection sweep. Related to Figure 4. The full list of transcripts/genes found in genomic regions under the selection sweep with their physical positions. (Excel file: Table S2.xlsx)

6 Table S3. Chi-square test values (p-value) for the Gene Ontology (GO) and the Enzyme Class (EC) annotations detected in the selective sweep regions. The full list of p-values are provided together with GOs/ECs and their annotations. GO/ EC ID Chi-sq test (pvalue) Annotation GO: E-30 structural constituent of cytoskeleton GO: E-29 response to light stimulus GO: E-25 cytoskeleton GO: E-25 GO: E-24 peroxisome fission beta-n-acetylglucosaminylglycopeptide beta-1,4- galactosyltransferase activity GO: E-23 integral component of peroxisomal membrane GO: E-21 regulation of defense response GO: E-17 seed germination EC: E-16 sucrose synthase GO: E-16 regulation of protein localization GO: E-15 proteasomal protein catabolic process GO: E-15 cell division GO: E-14 cytoskeleton organization GO: E-13 sucrose synthase activity GO: E-13 response to auxin GO: E-13 glucose catabolic process EC: E-11 4-Coumarate-CoA ligase GO: E-11 root hair elongation GO: E-09 systemic acquired resistance GO: E-08 biosynthetic process GO: E-08 SNARE binding GO: E-08 sulfur compound biosynthetic process GO: E-08 4-coumarate-CoA ligase activity EC: E-08 beta-ketoacyl-[acyl-carrier-protein] synthase I

7 GO: E-08 coenzyme biosynthetic process GO: E-08 regulation of lipid metabolic process GO: E-07 sulfur amino acid metabolic process GO: E-07 3-oxoacyl-[acyl-carrier-protein] synthase activity GO: E-07 chloroplast stroma GO: E-07 pollen tube reception EC: E-07 glycogen phosphorylase EC: E-07 shikimate dehydrogenase EC: E-07 3-dehydroquinate dehydratase GO: E-06 cold acclimation GO: E-06 oxidoreduction coenzyme metabolic process GO: E-06 NEDD8 transferase activity GO: E-06 CAAX-box protein maturation GO: E-06 aromatic amino acid family metabolic process GO: E-06 phosphorylase activity GO: E-06 alkylbase DNA N-glycosylase activity EC: E-05 DNA-3-methyladenine glycosylase II EC: E-05 fructose-bisphosphate aldolase GO: E-05 glycine catabolic process GO: E-05 isocitrate dehydrogenase (NADP+) activity GO: E-05 synergid death GO: E-05 cuticle development GO: E-05 establishment of cell polarity GO: E-05 identical protein binding GO: E-05 cellulose metabolic process EC: E-05 sedoheptulose-bisphosphatase EC: E-05 phenylalanine ammonia-lyase GO: E-04 3-dehydroquinate dehydratase activity GO: E-04 alditol:nadp+ 1-oxidoreductase activity

8 GO: E-04 shikimate 3-dehydrogenase (NADP+) activity GO: E-04 shikimate metabolic process GO: E-04 very long-chain fatty acid metabolic process GO: E-04 regulation of RNA splicing GO: E-04 ribonuclease activity GO: cellular amino acid biosynthetic process GO: secondary metabolic process GO: mitochondrial mrna modification GO: glyoxylate cycle GO: pollen tube guidance GO: negative regulation of circadian rhythm GO: regulation of protein homodimerization activity GO: negative regulation of nuclear-transcribed mrna poly(a) tail shortening GO: organic anion transmembrane transporter activity EC: sterol 14alpha-demethylase EC: carbon-monoxide dehydrogenase (cytochrome b-561) GO: nucleotide metabolic process GO: protein processing GO: isocitrate metabolic process GO: cortical microtubule, transverse to long axis GO: response to wounding GO: cytidine to uridine editing GO: sterol 14-demethylase activity GO: response to organonitrogen compound GO: bis(5'-adenosyl)-pentaphosphatase activity GO: phenylpropanoid metabolic process GO: formate-tetrahydrofolate ligase activity GO: oxygen transporter activity

9 GO: acetylglutamate kinase regulator activity GO: regulation of fatty acid biosynthetic process GO: regulation of arginine biosynthetic process via ornithine GO: positive regulation of microtubule polymerization GO: double fertilization forming a zygote and endosperm GO: unsaturated fatty acid biosynthetic process GO: mrna stabilization GO: long-day photoperiodism, flowering GO: photosynthesis, light reaction EC: superoxide dismutase EC: primary-amine oxidase EC: lactoylglutathione lyase EC: adenosinetriphosphatase GO: glutamate-ammonia ligase activity GO: glutamine biosynthetic process GO: mitochondrial intermembrane space protein transporter complex GO: microtubule bundle formation GO: mrna export from nucleus GO: cellular protein localization GO: cellulose biosynthetic process GO: carboxy-lyase activity GO: acyl-[acyl-carrier-protein] desaturase activity GO: protein polyubiquitination GO: cell fate determination GO: DNA topoisomerase type I activity GO: chromatin DNA binding GO: protein import into mitochondrial inner membrane EC: Tyrosine decarboxylase EC: aromatic-l-amino-acid decarboxylase

10 EC: L-ascorbate oxidase EC: fructose-bisphosphatase EC: '(2'),5'-bisphosphate nucleotidase GO: base-excision repair GO: cell migration GO: histone H3-K4 methylation GO: preprophase band GO: aromatic-l-amino-acid decarboxylase activity GO: tyrosine decarboxylase activity GO: peroxisome matrix targeting signal-1 binding GO: abscisic acid glucosyltransferase activity GO: filiform apparatus GO: sedoheptulose-bisphosphatase activity GO: organic cyclic compound metabolic process GO: short-day photoperiodism GO: jasmonic acid biosynthetic process GO: phosphatidylethanolamine binding GO: post-embryonic root development GO: carotenoid biosynthetic process GO: longitudinal axis specification GO: transferase activity, transferring acyl groups other than aminoacyl groups GO: cytoplasmic mrna processing body GO: L-alanine:2-oxoglutarate aminotransferase activity GO: lactoylglutathione lyase activity GO: L-alanine catabolic process GO: short-day photoperiodism, flowering GO: tryptophan-trna ligase activity GO: tryptophanyl-trna aminoacylation

11 GO: regulation of nitrogen utilization GO: L-ascorbate oxidase activity GO: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (nonphosphorylating) activity GO: H3 histone acetyltransferase activity GO: negative regulation of transforming growth factor beta receptor signaling pathway GO: 'de novo' CTP biosynthetic process GO: carboxylic acid biosynthetic process GO: folic acid metabolic process GO: transcription from plastid promoter GO: regulation of cell division GO: fructose-bisphosphate aldolase activity GO: stem cell population maintenance EC: polygalacturonase GO: carbon-monoxide oxygenase activity GO: cortical microtubule organization GO: chloroplast relocation GO: intra-golgi vesicle-mediated transport GO: amine metabolic process GO: nitrogen fixation GO: cinnamic acid biosynthetic process GO: phenylalanine ammonia-lyase activity GO: copper ion binding GO: gluconeogenesis

12 Table S4. GWAS association scores. Related to Figure 5 and Table 1. The full GWAS result for the trait of S/F %. First column is the SNP identifier, second is the chromosome number, third is the position on chromosome, fourth is the p-value and fifth column is the log10(p-value). (Excel file: Table S4.xlsx)