Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early japonica in South and Southeast Asia
Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early japonica in South and Southeast Asia
复制标题
DOI：
10.1007/s12520-015-0236-5
复制
发表时间：
2016-09-01
影响因子：
2.2
通讯作者：
Fuller, Dorian Q.
中科院分区：
文献类型：
--
作者：
Castillo, Cristina Cobo;Tanaka, Katsunori;Fuller, Dorian Q.
我们报告了一个成功的提取和测序的古代DNA从水稻颗粒（水稻）从六个考古遗址，包括两个来自印度和四个来自泰国，年龄从约。2500到1500 BP。总共对221个考古谷物进行了PCR扩增，并对主要靶向片段进行了测序，以与112个现代水稻群体（包括作物和野生品种）产生的现代序列进行比较。我们的研究结果包括来自叶绿体和核基因组的遗传序列，基于叶绿体的四个标记和核基因组的六个标记。这些标记可以区分籼稻和粳稻，这是亚洲水稻的两个主要亚种。被认为有不同的地理起源。一个核标记区分了热带和温带的亚种japonica。其他标记涉及在驯化下选择的表型变异，如不落粒、谷粒粘性（蜡质淀粉）和果皮颜色。从核标记物中回收和鉴定序列通常很差，而叶绿体序列的回收是成功的，在61%的考古谷物中回收了四种标记物中的至少一种。这使得成功分化的籼稻或粳稻亚种品种，与粳稻确定在所有的泰国材料和混合的籼稻和粳稻叶绿体在两个印度组合。水稻亚种还通过传统的考古植物学方法进行了评估，该方法依赖于谷物指标，基于对13个现代种群和499个考古谷物的测量。颗粒指标还表明，在东南亚网站的优势，粳稻型谷物和混合的粳稻和籼稻在印度的网站与少数籼稻。粒形测量与古DNA（aDNA）的相似结果证实了粒形测量在水稻亚种鉴定中具有一定的可靠性。该研究还强调了从考古水稻中恢复古代DNA的巨大潜力。在本研究中产生的数据增加了支持水稻进化的模式，包括杂交粳稻和原籼稻。
We report a successful extraction and sequencing of ancient DNA from carbonized rice grains (Oryza sativa) from six archaeological sites, including two from India and four from Thailand, ranging in age from ca. 2500 to 1500 BP. In total, 221 archaeological grains were processed by PCR amplification and primary-targeted fragments were sequenced for comparison with modern sequences generated from 112 modern rice populations, including crop and wild varieties. Our results include the genetic sequences from both the chloroplast and the nuclear genomes, based on four markers from the chloroplast and six from the nuclear genome. These markers allow differentiation of indica rice from japonica rice, the two major subspecies of Asian rice (O. sativa) considered to have separate geographical origins. One nuclear marker differentiates tropical and temperate forms of subspecies japonica. Other markers relate to phenotypic variation selected for under domestication, such as non-shattering, grain stickiness (waxy starch) and pericarp colour. Recovery and identification of sequences from nuclear markers was generally poor, whereas recovery of chloroplast sequences was successful, with at least one of four markers recovered in 61 % of archaeological grains. This allowed for successful differentiation of indica or japonica subspecies variety, with japonica identified in all the Thai material and a mixture of indica and japonica chloroplasts in the two Indian assemblages. Rice subspecies was also assessed through conventional archaeobotanical methods relying on grain metrics, based on measurements from 13 modern populations and 499 archaeological grains. Grain metrics also suggest a predominance of japonica-type grains in the Southeast Asian sites and a mixture of japonica and indica in the Indian sites with indica in the minority. The similar results of grain metrics and ancient DNA (aDNA) affirm that grain measurements have some degree of reliability in rice subspecies identification. The study also highlights the great potential of ancient DNA recovery from archaeological rice. The data generated in the present study adds support to the model of rice evolution that includes hybridization between japonica and proto-indica.