Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence
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 dom...
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description | 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 ge- nomic 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 re- mains in the Tianluoshan site and the common rice field weeds such as mustards in southern China. |
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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 ge- nomic 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 re- mains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.</description><identifier>ISSN: 1001-6538</identifier><identifier>EISSN: 1861-9541</identifier><identifier>DOI: 10.1007/s11434-011-4691-9</identifier><language>eng</language><publisher>Heidelberg: SP Science China Press</publisher><subject>Chemistry/Food Science ; Domestication ; Earth Sciences ; Engineering ; Humanities and Social Sciences ; Life Sciences ; multidisciplinary ; Oryza sativa ; Physics ; Science ; Science (multidisciplinary) ; 中国南方 ; 分歧 ; 古DNA序列 ; 基因型 ; 大米 ; 水稻种子 ; 长江中游地区 ; 驯化过程</subject><ispartof>Chinese science bulletin, 2011-10, Vol.56 (28), p.3108-3113, Article 3108</ispartof><rights>The Author(s) 2011. 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Sci. Bull</addtitle><addtitle>Chinese Science Bulletin</addtitle><description>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 ge- nomic 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 re- mains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.</description><subject>Chemistry/Food Science</subject><subject>Domestication</subject><subject>Earth Sciences</subject><subject>Engineering</subject><subject>Humanities and Social Sciences</subject><subject>Life Sciences</subject><subject>multidisciplinary</subject><subject>Oryza sativa</subject><subject>Physics</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>中国南方</subject><subject>分歧</subject><subject>古DNA序列</subject><subject>基因型</subject><subject>大米</subject><subject>水稻种子</subject><subject>长江中游地区</subject><subject>驯化过程</subject><issn>1001-6538</issn><issn>1861-9541</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><recordid>eNp9kLlOAzEURUcIJMLyAXSmohrwNmO7jMIqRdBAAY3lOM-D0cRO7EkQfD2Ogihp3iLd85ZbVWcEXxKMxVUmhDNeY0Jq3ipSq71qRGRbioaT_VJjTOq2YfKwOsr5o3SMCDqq3sbBeggDun4cowyrNQQLGUWHkreAXIoLNLwD6uMnejWhG74BJdiA6VH2XfDOW1PoDkIcvpbeornfQOq2U06qA2f6DKe_-bh6ub15ntzX06e7h8l4Wlsm1VALxZnErWmoUti1dq4UA2qkmTlpqZSUWmclo04qPrNSUCksbZwgmDvJrGPH1cVu7jLFcn8e9MJnC31vAsR11goLIkTDaVGSndKmmHMCp5fJL0z60gTrrY16Z6MuNuqtjVoVhu6YXLShg6Q_4jqF8tC_0PnvovcYulXh_jYxxYUogf0A9DiAeA</recordid><startdate>20111001</startdate><enddate>20111001</enddate><creator>Fan, LongJiang</creator><creator>Gui, YiJie</creator><creator>Zheng, YunFei</creator><creator>Wang, Yu</creator><creator>Cai, DaGuang</creator><creator>You, XiuLing</creator><general>SP Science China Press</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>~WA</scope><scope>C6C</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope></search><sort><creationdate>20111001</creationdate><title>Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence</title><author>Fan, LongJiang ; Gui, YiJie ; Zheng, YunFei ; Wang, Yu ; Cai, DaGuang ; You, XiuLing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c389t-7943806a52990f6cd993e2a8abf8c28822cfc832f894bc87287c25f7104f83cf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Chemistry/Food Science</topic><topic>Domestication</topic><topic>Earth Sciences</topic><topic>Engineering</topic><topic>Humanities and Social Sciences</topic><topic>Life Sciences</topic><topic>multidisciplinary</topic><topic>Oryza sativa</topic><topic>Physics</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>中国南方</topic><topic>分歧</topic><topic>古DNA序列</topic><topic>基因型</topic><topic>大米</topic><topic>水稻种子</topic><topic>长江中游地区</topic><topic>驯化过程</topic><toplevel>online_resources</toplevel><creatorcontrib>Fan, LongJiang</creatorcontrib><creatorcontrib>Gui, YiJie</creatorcontrib><creatorcontrib>Zheng, YunFei</creatorcontrib><creatorcontrib>Wang, Yu</creatorcontrib><creatorcontrib>Cai, DaGuang</creatorcontrib><creatorcontrib>You, XiuLing</creatorcontrib><collection>维普_期刊</collection><collection>中文科技期刊数据库-CALIS站点</collection><collection>维普中文期刊数据库</collection><collection>中文科技期刊数据库- 镜像站点</collection><collection>Springer_OA刊</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><jtitle>Chinese science bulletin</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fan, LongJiang</au><au>Gui, YiJie</au><au>Zheng, YunFei</au><au>Wang, Yu</au><au>Cai, DaGuang</au><au>You, XiuLing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence</atitle><jtitle>Chinese science bulletin</jtitle><stitle>Chin. Sci. Bull</stitle><addtitle>Chinese Science Bulletin</addtitle><date>2011-10-01</date><risdate>2011</risdate><volume>56</volume><issue>28</issue><spage>3108</spage><epage>3113</epage><pages>3108-3113</pages><artnum>3108</artnum><issn>1001-6538</issn><eissn>1861-9541</eissn><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 ge- nomic 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 re- mains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.</abstract><cop>Heidelberg</cop><pub>SP Science China Press</pub><doi>10.1007/s11434-011-4691-9</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Chemistry/Food Science Domestication Earth Sciences Engineering Humanities and Social Sciences Life Sciences multidisciplinary Oryza sativa Physics Science Science (multidisciplinary) 中国南方 分歧 古DNA序列 基因型 大米 水稻种子 长江中游地区 驯化过程 |
title | Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence |
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