Genomic landscape of parallel domestication of upland rice and its implications

Abstract

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.

Natural variation of DROT1 confers drought adaptation in upland rice

“…During the long process of adaptation to arid environments, the typical upland japonica rice ecotype became genetically differentiated from that of cultivated lowland rice 44 . Upland japonica rice adapts to drought by developing a robust (long and thick) root system 11 .…”

Altitude‐related shift of relative abundance from insect to sunbird pollination in Elaeagnus umbellata (Elaeagnaceae)

“…The concept of “ecotypes” of floral traits linked to abiotic factors was clearly illustrated by phenotypic variation in plant functional traits in a long‐term study undertaken by Jens Clausen and his colleagues at three elevations in the Sierra Nevada (CA, USA) (see Lowry, 2012). The ecotype has been widely recognized in natural, experimental, and agricultural plants (Wang et al, 2021). However, there is still little evidence for pollination ecotypes linked to altitude, where changes in floral traits associated with changes in pollinators among populations of a plant species are linked to altitudinal differences (Tong et al, 2021).…”

Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS

“…Parallel evolution is a widespread and well-studied phenomenon in plants [ 39 – 41 ]. The domestication of upland rice might have involved the evolution of different adaptive strategies in response to different artificial selection pressures in xian (indica) and geng (japonica) , as suggested by a previous study that explored the parallelism of genetic changes during upland rice domestication [ 42 ]. Although many studies have been conducted, the patterns of selection that have fostered the evolution of different rice ecotypes during domestication remain unclear.…”