Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley
Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley
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转录组分析揭示了现代栽培大麦的镶嵌基因组起源
DOI：
10.1073/pnas.1414335111
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发表时间：
2014-09-16
影响因子：
11.1
通讯作者：
Zhang, Guoping
中科院分区：
文献类型：
--
作者：
Dai, Fei;Chen, Zhong-Hua;Zhang, Guoping
考古学、历史学和分子学研究表明，近东的新月沃土是栽培大麦的起源和驯化的主要中心。然而，近年来越来越多的证据支持大麦多系起源的理论。据我们所知，这是首次尝试利用RNA测序技术和基因组相似性分析来研究大麦的驯化。我们证实了栽培大麦的多系起源，我们的研究结果表明，现代栽培大麦的基因组起源是来自近东和西藏，每个染色体上的不同贡献。这些发现推进了我们对农业文化早期传播的理解，并有望引起进化遗传学家和植物育种家的广泛兴趣。栽培大麦的驯化一直被用作研究农业文化起源和早期传播的模式系统。我们的研究结果表明，青藏高原及其邻近地区是栽培大麦驯化的中心之一。在这里，我们揭示了多个起源的驯化大麦使用转录组分析的栽培和野生大麦基因型。在12个割手密和9个普通大麦种质中产生了大约48-Gb的干净的转录本序列。我们在所有21个样本中报告了12，530个从头组装的转录本。群体结构分析表明，西藏青稞可能存在于驯化的早期。基于大量独特的基因组区域显示栽培大麦和野生大麦群体之间的相似性，我们提出现代栽培大麦的基因组起源来自新月沃土（主要在染色体1H，2 H和3 H）和西藏（主要在染色体4 H，5 H，6 H和7 H）的野生大麦基因型。这项研究表明，大麦的驯化可能发生在地理上不同的地区。
Significance Archaeological, historic, and molecular studies have indicated that the Fertile Crescent in the Near East is a major center of origin and domestication of cultivated barley. However, growing evidence in recent years supports the theory of a polyphyletic origin of barley. To our knowledge, this is the first attempt using RNA sequencing techniques and genomic similarity analysis to study the domestication of barley. We confirmed the polyphyletic origin of cultivated barley and our results revealed the genomic origin of modern cultivated barley is from both the Near East and Tibet, with different contributions on each chromosome. These findings advance our understanding of the early spread of agrarian culture, and are expected to be of wide interest to evolutionary geneticists and plant breeders. The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions.