Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map

doi:10.1186/1471-2164-15-372

CORC > 武汉植物园 > 中国科学院武汉植物园

	Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map
	Zhang,Qiong 1,2; Li,Leiting 2,3; VanBuren,Robert 2; Liu,Yanling 1; Yang,Mei 1; Xu,Liming 1; Bowers,John E 4; Zhong,Caihong 1; Han,Yuepeng 1; Li,Shaohua 1
刊名	BMC Genomics
	2014-05-15
卷号	15 期号:1
关键词	Chinese lotus Genome assembly Genotyping by sequencing Restriction associated sequencing Megascaffold
ISSN号	1471-2164
DOI	10.1186/1471-2164-15-372
英文摘要	AbstractBackgroundLotus is a diploid plant with agricultural, medicinal, and ecological significance. Genetic linkage maps are fundamental resources for genome and genetic study, and also provide molecular markers for breeding in agriculturally important species. Genotyping by sequencing revolutionized genetic mapping, the restriction-site associated DNA sequencing (RADseq) allowed rapid discovery of thousands of SNPs markers, and a crucial aspect of the sequence based mapping strategy is the reference sequences used for marker identification.ResultsWe assessed the effectiveness of linkage mapping using three types of references for scoring markers: the unmasked genome, repeat masked genome, and gene models. Overall, the repeat masked genome produced the optimal genetic maps. A high-density genetic map of American lotus was constructed using an F1 population derived from a cross between Nelumbo nucifera ‘China Antique’ and N. lutea ‘AL1’. A total of 4,098 RADseq markers were used to construct the American lotus ‘AL1’ genetic map, and 147 markers were used to construct the Chinese lotus ‘China Antique’ genetic map. The American lotus map has 9 linkage groups, and spans 494.3?cM, with an average distance of 0.7?cM between adjacent markers. The American lotus map was used to anchor scaffold sequences in the N. nucifera ‘China Antique’ draft genome. 3,603 RADseq markers anchored 234 individual scaffold sequences into 9 megascaffolds spanning 67% of the 804?Mb draft genome.ConclusionsAmong the unmasked genome, repeat masked genome and gene models, the optimal reference sequences to call RADseq markers for map construction is repeat masked genome. This high density genetic map is a valuable resource for genomic research and crop improvement in lotus.
语种	英语
出版者	BioMed Central
WOS记录号	BMC:10.1186/1471-2164-15-372
内容类型	期刊论文
源URL	[http://202.127.146.157/handle/2RYDP1HH/437]
专题	中国科学院武汉植物园
通讯作者	Ming,Ray
作者单位	1.Chinese Academy of Sciences; Key Laborary of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden 2.University of Illinois at Urbana-Champaign; Department of Plant Biology 3.Nanjing Agricultural University; College of Horticulture 4.University of Georgia; Department of Crop and Soil Sciences 5.Fujian Agriculture and Forestry University; FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology
推荐引用方式 GB/T 7714	Zhang,Qiong,Li,Leiting,VanBuren,Robert,et al. Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map[J]. BMC Genomics,2014,15(1).
APA	Zhang,Qiong.,Li,Leiting.,VanBuren,Robert.,Liu,Yanling.,Yang,Mei.,...&Ming,Ray.(2014).Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map.BMC Genomics,15(1).
MLA	Zhang,Qiong,et al."Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map".BMC Genomics 15.1(2014).