Abstract
BackgroundLotus 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.
Highlights
Lotus is a diploid plant with agricultural, medicinal, and ecological significance
Among the unmasked genome, repeat masked genome and gene models, the optimal reference sequences to call restriction-site associated DNA sequencing (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
We report the construction of two high-resolution genetic linkage maps for lotus using RADseq markers and a segregating F1 population crossed between Nelumbo nucifera ‘Chinese Antique’ and N. lutea ‘AL1’, the same mapping population used for linkage mapping with simple sequence repeats (SSRs)
Summary
Lotus is a diploid plant with agricultural, medicinal, and ecological significance. The Nelumbonaceae is a perennial, aquatic plant family, which comprises only one genus, Nelumbo, consisting of two species: Chinese lotus N. nucifera Gaertn (Asia, Australia, Russia) and American lotus N. lutea Pers (eastern and southern North America) [1]. Lotus is a diploid plant (2n = 2× = 16) with agricultural, medicinal, Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P.R. China. Full list of author information is available at the end of the article and ecological significance. Gaertn) is cultivated for its edible rhizomes, seeds, and leaves, which have been consumed as food for thousands of years in Asia.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
