气候变化领域集成服务门户(CCPortal): Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)

CCPortal

DOI	10.1186/1471-2164-11-656
	Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)
	Xu, Jianjun; Zhao, Qiang; Du, Peina; Xu, Chenwu; Wang, Baohe; Feng, Qi; Liu, Qiaoquan; Tang, Shuzhu; Gu, Minghong; Han, Bin; Liang, Guohua
发表日期	2010
ISSN	1471-2164
卷号	11
英文摘要	Background: Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics. Results: In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13x genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene. Conclusions: The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.
学科领域	Biotechnology & Applied Microbiology; Genetics & Heredity
语种	英语
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
来源期刊	BMC GENOMICS
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/111597
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	Xu, Jianjun,Zhao, Qiang,Du, Peina,et al. Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)[J]. 中国科学院西北生态环境资源研究院,2010,11.
APA	Xu, Jianjun.,Zhao, Qiang.,Du, Peina.,Xu, Chenwu.,Wang, Baohe.,...&Liang, Guohua.(2010).Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.).BMC GENOMICS,11.
MLA	Xu, Jianjun,et al."Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)".BMC GENOMICS 11(2010).