DOI: 10.5061/dryad.9zw3r22ng
title: SNP data for F2 population derived from Oryza rufipogon and O. nivara

description: To elucidate the genetic architecture underlying phenotypic divergence is
 essential to the understanding of ecological adaptation and speciation.
 Two wild rice species (O. rufipogon and O. nivara) are a
 progenitor-daughter species pair with ecological divergence and provide a
 unique system for studying ecological adaptation/speciation. Here, we
 constructed a high-resolved linkage map and conducted a quantitative trait
 locus (QTL) analysis of 19 phenotypic traits using an F2 population
 generated from a cross between the perennial O. rufipogon and annual O.
 nivara. We identified 113 QTLs associated with interspecific divergence of
 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in
 terms of the percentage of variation explained (PVE). The distribution of
 effect sizes of QTLs followed a negative exponential, suggesting that a
 few genes of large effect and many genes of small effect were responsible
 for the phenotypic divergence. We observed 18 clusters of QTLs (QTL
 hotspots), with each involving multiple adaptive traits, demonstrating the
 importance of coinheritance of loci/genes in ecological
 adaptation/speciation. Analysis of effect direction and v-test statistics
 revealed that interspecific differentiation of most traits was driven by
 divergent natural selection, supporting the argument that ecological
 adaptation/speciation would proceed rapidly under coordinated selection on
 multiple traits.
description: Fresh leaves of two parental lines and 600
 F<sub>2</sub> individuals randomly chosen from the 862
 F<sub>2</sub> population were collected and dried by
 silica-gel. Genomic DNA was extracted using the cetyltrimethylammonium
 bromide (CTAB) method (Murray & Thompson, 1980). The libraries of
 mapping parents were constructed following the manufacturer’s
 recommendations (Illumina) for 500 bp insert size and sequenced by
 BGIseq500 platform (BGI; Shenzhen, China) with 150 bp paired-end reads.
 The F<sub>2</sub> individuals were genotyped by a
 specific-locus amplified fragment-sequencing (SALF-seq) method (Sun
 <em>et al.,</em> 2013). In brief, two restriction enzymes
 (<em>RsaI</em> and <em>HaeIII</em>) were selected
 to digest the genomic DNA. The digested fragments (SLAF tags) were ligated
 to the adapters with T4 DNA ligase. After PCR amplification, purification,
 sample mixing and electrophoresis with agarose gels, the size of fragments
 ranging from 264–314 bp were obtained and purified. Subsequently, the
 products were sequenced using Illumina HiSeq 2500 platform (Illumina; San
 Diego, U.S.) with 125 paired-end reads according to the manufacturer’s
 instruction. The short reads of parental lines and
 F<sub>2</sub> individuals were filtered by removing
 low-quality reads with more than 10% of bases missing. Then, short reads
 were aligned to the reference sequence of Nipponbare genome (IRGSP-1.0)
 (Kawahara <em>et al.,</em> 2013) using BWA (Li &
 Durbin, 2010) with the MEM algorithm. Furthermore, Samtools (Li
 <em>et al</em>., 2009) were applied to sort the mapping
 results and build an index for each BAM file. Variant calling was
 conducted using the Genome Analysis Toolkit (GATK, version 4.0.2.1) (Van
 der Auwera <em>et al</em>., 2013). SNPs were filtered with
 VariantFiltration of GATK “AC &lt; 2 || QD &lt; 2.0 || FS &gt;
 60.0 || MQ &lt; 40.0 || MQRankSum &lt; -12.5 || ReadPosRankSum
 &lt; -8.0” as suggested by the manual.
description: # SNP data for F2 population derived from Oryza rufipogon and O. nivara
 A F2 population was
 generated from cross between O. rufipogon and O. nivara. ## Description of
 the data and file structure The SLAF-seq data of F2 population and
 resequencing data parental lines was aligned to IRGSP-1.0 by GATK
 according to suggested pipeline. The SNPs was selected and then filtered.