Application of the Second Generation Sequencing Technology in Rice Genomics and Transcriptomics

doi:10.3969/j.issn.1001-7216.2015.02.013

Abstract

Abstract:

The second generation sequencing technology made a revolutionary breakthrough in the field of sequencing technology with advantages, including high throughput, high precision and low cost. It provided a new method for the research in rice genomics. Here, we reviewed the theory and development of the second generation sequencing technology including sequencing by synthesis and sequencing by ligation, and summarized its applications in genomics, involving structural genomics and functional genomics, and transcriptomics of rice. Finally, the prospects of current sequencing technologies and their applications in rice research were also discussed.

Key words: the second generation sequencing, rice, genomics, transcriptomics

摘要：

二代测序技术是测序技术的一次革命性突破,它具有高通量、高精度、低成本的优势,为水稻基因组学研究提供了新的研究方法和解决方案。概述了以使用合成法测序和连接法测序为原理的二代测序技术的特点和发展,并总结了其在水稻基因组学,包括结构基因组学和功能基因组学以及转录组学研究中的应用,并就当前测序技术的发展趋势作了展望。

关键词: 二代测序技术, 水稻, 基因组学, 转录组学

CLC Number:

Q755
S511.01

Yang GAO, Da-wei XUE, Qian QIAN, Zhen-yu GAO. Application of the Second Generation Sequencing Technology in Rice Genomics and Transcriptomics[J]. Chinese Journal OF Rice Science, 2015, 29(2): 208-214.

高阳, 薛大伟, 钱前, 高振宇. 二代测序技术在水稻基因组学和转录组学研究中的应用[J]. 中国水稻科学, 2015, 29(2): 208-214.

Figures/Tables 1

References 57

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测序对象 Sequencing objects	测序仪器 Sequencing machines	测序深度 Sequencing depth	目的 Purpose	文献
敏感型IR64 耐旱型Nagina22 耐盐碱型Pokkali	Illumina Hiseq2000	≈10×	挖掘对干旱和盐胁迫有差异反应的水稻品种的遗传变异及其与功能的关系	[21]
水稻限制酶切片段	Illumina GAⅡX	≈19×	证明简化基因组测序的可靠性和准确性	[24]
两优培九重组自交系亲本93-11 亲本培矮64S	Illumina Hiseq2000	≈4× ≈36× ≈48×	更新亲本基因组序列、QTL精细定位农艺性状基因	[25]
40个栽培稻 10个野生稻	Illumina GAⅡ	>15×	鉴定重要农艺性状基因、揭示栽培稻驯化中的基因选择	[27]
3000份水稻品种	Illumina Hiseq2000	≈14×	构建水稻遗传数据库	[28]
1083个栽培稻 446个野生稻	Illumina GAⅡX	≈1× ≈2×	水稻基因组多样性及栽培稻起源分析	[32]
澳洲普通野生稻澳洲南方野生稻	Illumina GAⅡX	6.2× 4.9×	研究水稻基因组的进化	[33]
淡绿叶突变体	Illumina GAⅡX	≤3×	利用MutMap鉴定突变位点	[38]
517个地方品种	Illumina GAⅡ	≈1×	GWAS分析14个农艺性状位点	[42]
950个栽培品种	Illumina GAⅡX	≤1×	GWAS研究花期和粒重相关位点	[43]
日本晴生长7d的苗和根	Illumina GAⅡX		定量水稻5号染色体着丝粒区域的基因表达	[46]
分蘖期和抽穗期的根	Illumina Hiseq2000		研究杂种优势的分子机理	[47,48]

测序对象 Sequencing objects	测序仪器 Sequencing machines	测序深度 Sequencing depth	目的 Purpose	文献
敏感型IR64 耐旱型Nagina22 耐盐碱型Pokkali	Illumina Hiseq2000	≈10×	挖掘对干旱和盐胁迫有差异反应的水稻品种的遗传变异及其与功能的关系	[21]
水稻限制酶切片段	Illumina GAⅡX	≈19×	证明简化基因组测序的可靠性和准确性	[24]
两优培九重组自交系亲本93-11 亲本培矮64S	Illumina Hiseq2000	≈4× ≈36× ≈48×	更新亲本基因组序列、QTL精细定位农艺性状基因	[25]
40个栽培稻 10个野生稻	Illumina GAⅡ	>15×	鉴定重要农艺性状基因、揭示栽培稻驯化中的基因选择	[27]
3000份水稻品种	Illumina Hiseq2000	≈14×	构建水稻遗传数据库	[28]
1083个栽培稻 446个野生稻	Illumina GAⅡX	≈1× ≈2×	水稻基因组多样性及栽培稻起源分析	[32]
澳洲普通野生稻澳洲南方野生稻	Illumina GAⅡX	6.2× 4.9×	研究水稻基因组的进化	[33]
淡绿叶突变体	Illumina GAⅡX	≤3×	利用MutMap鉴定突变位点	[38]
517个地方品种	Illumina GAⅡ	≈1×	GWAS分析14个农艺性状位点	[42]
950个栽培品种	Illumina GAⅡX	≤1×	GWAS研究花期和粒重相关位点	[43]
日本晴生长7d的苗和根	Illumina GAⅡX		定量水稻5号染色体着丝粒区域的基因表达	[46]
分蘖期和抽穗期的根	Illumina Hiseq2000		研究杂种优势的分子机理	[47,48]