Parallel domestication has been widely acknowledged but its genetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate genetic improvement and breeding of rice and crops in general.

中文翻译：

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陆稻平行驯化的基因组景观及其意义

平行驯化已得到广泛认可，但其遗传基础仍不清楚。作为重要的水稻生态型，陆稻在两个水稻亚种（In稻和粳稻）中被多次驯化。），并为探索平行驯化的遗传基础提供了可行的系统。为了揭示旱稻和低陆稻之间遗传分化的全基因组模式，并探索旱稻驯化过程中遗传变化的平行性，我们获得了95个水稻地方品种的全基因组序列，并获得了代表性种质的五个组织的全基因组表达数据。高地和低地水​​稻。我们的系统进化分析确认了两个水稻亚种中陆地生态型的多种驯化。根据重测序数据进行的基因组扫描确定了高地和低地生态型之间的显着差异，在eco稻和粳稻这两种生态型之间的基因组基因组分别有11.4％和14.8％的差异， 分别。进一步的全基因组基因表达分析发现，有效表达的基因中有30％在两种生态型之间有显着差异，这表明调节变化对陆稻的驯化很重要。重要的是，我们发现，只有1.8％的基因组差异和差异表达基因的1.6％是由高地共享籼稻和高地粳稻，主要是无与伦比的遗传改变的暗示旱稻驯化过程。这些发现不仅为在基因组规模上平行驯化的遗传基础提供了新的见解，而且还可以总体上促进水稻和农作物的遗传改良和育种。