Development of InDel markers for Brassica rapa based on whole-genome re-sequencing

doi:10.1007/s00122-012-1976-6

	Development of InDel markers for Brassica rapa based on whole-genome re-sequencing
	Liu, Bo; Wang, Yan; Zhai, Wen; Deng, Jie; Wang, Hui; Cui, Yang; Cheng, Feng; Wang, Xiaowu; Wu, Jian
刊名	THEORETICAL AND APPLIED GENETICS
	2013
卷号	126 期号:1 页码:231-239
ISSN号	0040-5752
DOI	10.1007/s00122-012-1976-6
通讯作者	Liu, Bo
英文摘要	Genome-wide detection of short insertion/deletion length polymorphisms (InDels, < 5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3-5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77 %) yielded single PCR fragments and showed polymorphisms, 7 (1 %) did not amplify a product, and 141 (22 %) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77 %) were polymorphic, 111 (22 %) were not polymorphic and 5 (1 %) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90 % amplified a PCR product; 132 (25 %) showed polymorphism between the two B. napus accessions and 41 (8 %) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa.
学科主题	Agronomy ; Plant Sciences ; Genetics & Heredity ; Horticulture ; AGRONOMY ; GENETICS & HEREDITY ; HORTICULTURE ; PLANT SCIENCES
语种	英语
出版者	SPRINGER
WOS记录号	WOS:000313056900020
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101077]
专题	蔬菜花卉研究所_生物技术研究室
作者单位	Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100081, Peoples R China
推荐引用方式 GB/T 7714	Liu, Bo,Wang, Yan,Zhai, Wen,et al. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing[J]. THEORETICAL AND APPLIED GENETICS,2013,126(1):231-239.
APA	Liu, Bo.,Wang, Yan.,Zhai, Wen.,Deng, Jie.,Wang, Hui.,...&Wu, Jian.(2013).Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.THEORETICAL AND APPLIED GENETICS,126(1),231-239.
MLA	Liu, Bo,et al."Development of InDel markers for Brassica rapa based on whole-genome re-sequencing".THEORETICAL AND APPLIED GENETICS 126.1(2013):231-239.