Jun 3, 2014

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

BMC Genomics
Qiong ZhangRay Ming

Abstract

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. 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 ...Continue Reading

  • References24
  • Citations8

References

Mentioned in this Paper

Genus - Lotus
Quantitative Trait Loci
Genome
Chromosome Map
Avian Crop
LUC7L3 gene
Genome Mapping
Nelumbo nucifera
Genomics
Sequencing

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