SNP data for F2 population derived from Oryza rufipogon and O. nivara

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.