Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing

doi:10.1007/s00122-013-2218-2

	Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing
	Chen, Wei 1; Chen, Haodong 1,2; Zheng, Tianqing 3; Yu, Renbo 1,2,4; Terzaghi, William Bryan 5; Li, Zhikang 3,6; Deng, Xing Wang 1,2,4; Xu, Jianlong 3,6; He, Hang 1,2
刊名	THEORETICAL AND APPLIED GENETICS
	2014
卷号	127 期号:2 页码:297-307
ISSN号	0040-5752
DOI	10.1007/s00122-013-2218-2
通讯作者	Chen, Wei
英文摘要	Key message A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing.Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 "high quality" SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.
学科主题	Agronomy ; Plant Sciences ; Genetics & Heredity ; Horticulture
语种	英语
出版者	SPRINGER
WOS记录号	WOS:000330723900004
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4935]
专题	作物科学研究所_分子生物学系
作者单位	1.Peking Univ, Coll Life Sci, Natl Lab Prot Engn & Plant Genet Engn, Peking Yale Joint Ctr Plant Mol Genet & Agrobiote, Beijing 100871, Peoples R China 2.Shenzhen Inst Crop Mol Design, Shenzhen 518107, Peoples R China 3.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100081, Peoples R China 4.Frontier Labs Syst Crop Design Co Ltd, Beijing 100085, Peoples R China 5.Wilkes Univ, Dept Biol, Wilkes Barre, PA 18766 USA 6.Chinese Acad Agr Sci, Shenzhen Inst Breeding & Innovat, Shenzhen 518083, Peoples R China
推荐引用方式 GB/T 7714	Chen, Wei,Chen, Haodong,Zheng, Tianqing,et al. Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing[J]. THEORETICAL AND APPLIED GENETICS,2014,127(2):297-307.
APA	Chen, Wei.,Chen, Haodong.,Zheng, Tianqing.,Yu, Renbo.,Terzaghi, William Bryan.,...&He, Hang.(2014).Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing.THEORETICAL AND APPLIED GENETICS,127(2),297-307.
MLA	Chen, Wei,et al."Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing".THEORETICAL AND APPLIED GENETICS 127.2(2014):297-307.