Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

Abstract

Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (~2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.

Elimination of a Retrotransposon for Quenching Genome Instability in Modern Rice

“…breeding. In support of this hypothesis, we were able to detect the HUO sequence in 5 out of 10 archaeological rice grains (about 1200-7000 years old) found in the lower Yangtze River corridor of China (Figure 5D and 5E) (Fan et al, 2011), which was one of the original regions where modern cultivated rice was grown (Fuller et al, 2009;Huang et al, 2012). The sequences of fragments amplified from these archaeological grains showed high sequence identity with the HUO sequence (Supplemental Figure 11).…”

Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

“…This suggests that japonica rice with the qSH1 mutation was present by at least 7000 years ago25 when the initial paddy system for cultivating rice was established7. This is supported by a DNA extracted from rice husks at Tianluoshan that links the rice to japonica28.…”

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

“…While recent work has shown encouraging results, studies leveraging the information in the DNA (and/or RNA) fragments present in plant subfossils are still scarce (for review, see Gutaker and Burbano [102]). The number of the species studied spans a large taxonomic range and includes barley [103, 104], wheat [105–109], maize [110–118], sunflower [119], grape [120–122], bottle gourd [123], radish [124], sorghum [125], papyri [126], rice [127], olive [128], orchid [129], Prunus [130], Arabidopsis [131], cotton [132], and trees [133–136]. Similarly, the primary material used for DNA extraction includes a whole variety of tissues, such as fruits, seeds, leaves, and woods, preserved in a wide range of conditions, including charred, waterlogged, desiccated, or mineralized remains.…”

“…Further DNA investigation of plant remains from archaeological sites in Egypt have been also reported for sorghum [125]. In rice, genomic sequences from remains found at Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze, were compared to current domesticated and wild rice populations in order to investigate the genetic changes underlying the domestication syndrome [127]. Microsatellite loci have also been used to investigate the origins of grape seeds preserved by waterlogging and charring at several European Celtic, Greek, and Roman sites [120, 122].…”