ArticlePloS one2015
Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo nucifera).
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Article
- The population chloroplast genomes of Populus reveal the phylogenetic relationship between three new taxa of sect. Leucoides and their parents.BMC genomics · 2025Article
- Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta.BMC plant biology · 2025Article
- Genome-wide development of simple sequence repeat (SSR) markers at 2-Mb intervals in lotus (Nelumbo Adans.).BMC genomics · 2025Article
- Chloroplast genome analysis and phylogenetic position of Polygonatum sinopubescens and comparison with related species.PloS one · 2025Article
- Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome.BMC genomics · 2024Article
- Article
- Comparative analysis of the complete mitogenomes ofFrontiers in plant science · 2024Article
- Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom.International journal of molecular sciences · 2023Article
- Comparative Analysis of the Complete Mitochondrial Genomes ofInternational journal of molecular sciences · 2023Article
- Identification of QTLs and Putative Candidate Genes for Plant Architecture of Lotus Revealed by Regional Association Mapping.Plants (Basel, Switzerland) · 2023Article
- Studies on Lotus Genomics and the Contribution to Its Breeding.International journal of molecular sciences · 2022Review
- Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.).Planta · 2021Article
- Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology.BMC genomics · 2021Article
- The Latest Studies on Lotus (International journal of molecular sciences · 2019Review
- Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop.Annals of botany · 2018Article
- Detection of Highly Differentiated Genomic Regions Between Lotus (Frontiers in plant science · 2018Article
- The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae).International journal of molecular sciences · 2017Article
- The Complete Chloroplast Genome Sequences of the Medicinal Plant Pogostemon cablin.International journal of molecular sciences · 2016Article
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6 authors.
Funding
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Abstract
Genomic resources such as single nucleotide polymorphism (SNPs), insertions and deletions (InDels) and SSRs (simple sequence repeats) are essential for crop improvement and better utilization in genetic breeding. However, the resources for the sacred lotus (Nelumbo nucifera Gaertn.) are still limited. In the present study, to dissect large-scale genomic molecular marker resources for sacred lotus, we re-sequenced a Thailand sacred lotus cultivar 'Chiang Mai wild lotus' and compared with the reported lotus genome 'Middle lake wild lotus'. A total of 3,180,059 SNPs, 328, 251 InDels and 14,191 SVs were found between the two genomes. The functional impact analyses of these SNPs indicated that they may be involved in metabolic processes, binding, catalytic activity, etc. Mining the genome sequences for SSRs showed that 191,657 SSRs were identified with a frequency of one SSR per 4.23 kb and 103,656 SSR primer pairs were designed. Furthermore, 14, 502 EST-SSRs were also indentified using the available RNA-seq data in the NCBI. A subset of 150 SSRs (genomic and EST-SSRs) was randomly selected for validation and genetic diversity analysis. The genotypes could be easily distinguished using these SSR markers and the 'Chiang Mai wild lotus' was obviously differentiated from the other Chinese accessions. This study provides considerable amounts of genomic resources and markers for the quantitative trait locus (QTL) identification and molecular selection of the species, which could have a potential role in various applications in sacred lotus breeding.
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