ArticleBMC genomics2012
Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Genome-wide development of simple sequence repeat (SSR) markers at 2-Mb intervals in lotus (Nelumbo Adans.).BMC genomics · 2025Article
- Identification of QTLs and Putative Candidate Genes for Plant Architecture of Lotus Revealed by Regional Association Mapping.Plants (Basel, Switzerland) · 2023Article
- Article
- Identification of QTLs and a putative candidate gene involved in rhizome enlargement of Asian lotus (Nelumbo nucifera).Plant molecular biology · 2022Article
- Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology.BMC genomics · 2021Article
- The Establishment of an Efficient Callus Induction System for Lotus (Plants (Basel, Switzerland) · 2020Article
- Identification of genomic regions associated with early plant vigour in lentil (Journal of genetics · 2020Article
- Proteomic analysis showing the signaling pathways involved in the rhizome enlargement process in Nelumbo nucifera.BMC genomics · 2019Article
- The Latest Studies on Lotus (International journal of molecular sciences · 2019Review
- Construction of a high-density, high-quality genetic map of cultivated lotus (Nelumbo nucifera) using next-generation sequencing.BMC genomics · 2016Article
- Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
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- Article
- RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera).PloS one · 2015Article
- LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study.Database : the journal of biological databases and curation · 2015Article
- Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map.BMC genomics · 2014Article
- Characterization of flower-bud transcriptome and development of genic SSR markers in Asian lotus (Nelumbo nucifera Gaertn.).PloS one · 2014Article
- Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).Genome biology · 2013Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence.
resultsA total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%). Of 500 SSR primers tested, 386 (77.20%) produced scorable alleles with an average of 2.59 per primer, and 185 (37.00%) showed polymorphism among two parental genotypes, N. nucifera 'Chinese Antique' and N. lutea 'AL1', and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of 'Chinese Antique'. The 97 contigs were merged into 60 scaffolds.
conclusionGenetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of 'Chinese Antique'. The present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection.
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