气候变化领域集成服务门户(CCPortal): High-throughput genotyping by whole-genome resequencing

CCPortal

DOI	10.1101/gr.089516.108
	High-throughput genotyping by whole-genome resequencing
	Huang, Xuehui; Feng, Qi; Qian, Qian; Zhao, Qiang; Wang, Lu; Wang, Ahong; Guan, Jianping; Fan, Danlin; Weng, Qijun; Huang, Tao; Dong, Guojun; Sang, Tao; Han, Bin
发表日期	2009
ISSN	1088-9051
EISSN	1549-5469
卷号	19 期号:6
英文摘要	The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was; 203 faster in data collection and 353 more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution'' gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
学科领域	Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
来源期刊	GENOME RESEARCH
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/111563
作者单位	Chinese Acad Sci, Natl Ctr Gene Res, Shanghai 200233, Peoples R China
推荐引用方式 GB/T 7714	Huang, Xuehui,Feng, Qi,Qian, Qian,et al. High-throughput genotyping by whole-genome resequencing[J]. 中国科学院西北生态环境资源研究院,2009,19(6).
APA	Huang, Xuehui.,Feng, Qi.,Qian, Qian.,Zhao, Qiang.,Wang, Lu.,...&Han, Bin.(2009).High-throughput genotyping by whole-genome resequencing.GENOME RESEARCH,19(6).
MLA	Huang, Xuehui,et al."High-throughput genotyping by whole-genome resequencing".GENOME RESEARCH 19.6(2009).