Abstract
Traditional rice landraces grown under on‐farm conservation conditions by indigenous farmers are extremely important for future crop improvement. However, little is known about how the natural selection and agriculture practices of indigenous farmers interact to shape and change the population genetics of rice landraces grown under on‐farm conservation conditions during the domestication. In this study, we sequenced DNA from 108 core on‐farm conserved rice landraces collected from the ethnic minority regions of Yunnan, China, including 56 accessions collected in 1980 and 52 accessions collected in 2007 and obtained 2,771,245 of credible SNPs. Our findings show that most genetic diversity was retained during the 27 years of domestication by on‐farm conservation. However, SNPs with marked allele frequency differences were found in some genome regions, particularly enriched in genic regions, indicating changes in genic regions may have played a much more prominent role in the short‐term domestication of 27 years. We identified 186 and 183 potential selective‐sweep regions in the indica and japonica genomes, respectively. We propose that on‐farm conserved rice landraces during the short‐term domestication had a highly polygenic basis with many loci responding to selection rather than a few loci with critical changes in response to selection. Moreover, loci affecting important agronomic traits and biotic or abiotic stress responses have been particularly targeted in selection. A genome‐wide association study identified 90 significant signals for six traits, 13 of which were in regions of selective sweeps. Moreover, we observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Our results provide insights into short‐term evolutionary processes and shed light on the underlying mechanisms of on‐farm conservation.
Highlights
Rice (Oryza sativa L.) was domesticated between 8,000 and 10,000 years ago from its wild ancestor, Oryza rufipogon, a broadly distributed native species of Asia (Oka, 1988)
Compared with mod‐ ern cultivars, traditional rice landraces grown by indigenous farmers represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of ge‐ netic variation
We observed no enrichment for SNPs with high ΔAF in intergenic regions, but we found a significant excess of SNPs in genic regions with ΔAF of 0.30–0.35
Summary
Rice (Oryza sativa L.) was domesticated between 8,000 and 10,000 years ago from its wild ancestor, Oryza rufipogon, a broadly distributed native species of Asia (Oka, 1988). Indigenous locals practice the conservation of diverse traditional rice landraces on their farms, referred to as “on‐farm conservation,” for the conservation of highly productive landraces and for ones more resistant to diseases and pests and tolerant of extreme environmental conditions, as well as cultural de‐ mands (e.g., ethnic dietary customs, medical uses, festival, and reli‐ gious ceremony; Gao, 2003) These landraces selected by on‐farm conservation likely cannot be replaced by modern improved varieties because they undoubtedly have their own outstanding fea‐ tures and some of these landraces have been planted for more than 50 years. | 292 of genome‐wide selection footprints and genetic diversity may help reveal the short‐term evolutionary processes and contribute to our understanding of the mechanisms of on‐farm conservation
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