title: Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map.
abstract: BACKGROUND
  Lotus 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Among 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.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Zhang
authors.forename: Leiting
authors.initials: L
authors.lastname: Li
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.forename: Yanling
authors.initials: Y
authors.lastname: Liu
authors.forename: Mei
authors.initials: M
authors.lastname: Yang
authors.forename: Liming
authors.initials: L
authors.lastname: Xu
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.forename: Caihong
authors.initials: C
authors.lastname: Zhong
authors.forename: Yuepeng
authors.initials: Y
authors.lastname: Han
authors.forename: Shaohua
authors.initials: S
authors.lastname: Li
authors.affiliation: Key Laborary of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P,R, China. rming@life.uiuc.edu.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
mesh_terms: D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant; D005838:Genotype; D006579:Heterozygote; D018895:Microsatellite Repeats; D031653:Nelumbo / Q000235:genetics*; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D014481:United States