Abstract：
Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. 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) on 11 chromosomes, significantly more than that expected by chance, 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. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.
摘要：
生境差异导致的生态差异在新物种的形成中起着突出的作用,但是生态物种形成过程中的遗传结构和表型差异的潜在机制仍然知之甚少。水稻的两个野生祖先（Oryzarufipogon和Oryzanivara）是具有生态差异的祖先衍生物种对，为研究生态适应/物种形成提供了独特的系统。这里,我们构建了高分辨率连锁图谱，并使用两个Oryza物种之间的杂交产生的F2种群对19个表型性状进行了数量性状基因座（QTL）分析。我们确定了与16个数量性状的种间差异相关的113个QTL，就解释变异百分比(PVE)而言，效应大小在1.61%到34.1%之间。QTL效应大小的分布遵循负指数，这表明少数影响大的基因和许多影响小的基因是表型差异的原因。我们在11条染色体上观察到18簇QTL（QTL热点），远远超过了偶然的预期，证明了基因座/基因共同遗传在生态适应/物种形成中的重要性。效应方向和v检验统计分析表明，大多数性状的种间分化是由发散的自然选择驱动的。支持这样的论点，即在多个性状的协调选择下，生态适应/物种形成将迅速进行。我们的发现为理解植物生态适应和物种形成的遗传结构提供了新的见解，并有助于在水稻育种中有效操纵特定基因或基因簇。
