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Open Access Research article

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

Qiong Zhang12, Leiting Li23, Robert VanBuren2, Yanling Liu1, Mei Yang1, Liming Xu1, John E Bowers4, Caihong Zhong1, Yuepeng Han1, Shaohua Li1 and Ray Ming125*

Author Affiliations

1 Key Laborary of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P.R. China

2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

3 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China

4 Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA

5 FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fijian 350002, China

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BMC Genomics 2014, 15:372  doi:10.1186/1471-2164-15-372

Published: 15 May 2014

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.

Keywords:
Chinese lotus; Genome assembly; Genotyping by sequencing; Restriction associated sequencing; Megascaffold