Liliaceae Mico-Satellite Marker database [LiMdb]
Genomic resource for the improvement of family Liliaceae

Welcome to LiMdb

The plant family Liliaceae is well known for its colorful flowers. This family composed with 15 genera and 705 known species (Christenhusz & Byng 2016). It is monocotyledonous, perennial herbs. The leaves are linear in shape, with their veins usually arranged parallel to the edges, single and arranged alternating on the stem, or in a rosette at the base. Most of the Liliaceae species grown from bulbs, but some of them from rhizomes. Lily is commercially cultivated in France, Chile, the USA, Japan, and New Zealand, as well as in the Netherlands, the worlds leading producer and exporter. Lilium species belonging to the same section are cross-compatible and produce fertile hybrids. They are also highly heterozygous because they evolved from a series of interspecific crosses. However, the precise levels of heterozygosity within Lilium remain unexplored because there is lack of appropriate molecular markers for this species.
Publicly available SSR markers remains insufficient for many downstream breeding applications in lily; for example, genotyping, identifying cultivars, estimating genetic diversity, positional cloning, trait-tagging, and comparative mapping. To boost the breeding program of this valuable crop species, functional molecular markers must be developed.
In this database, we developed and deposited large number of SSR markers those were obtained from large-scale transcriptome data mining of the Lilium sp.


Sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We develop and characterize SSR (simple sequence repeat) markers from larger set of transcriptome data of Lilium sp. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.


db Info: LiMdb: Version 1. Current version of Lily SSR marker database contains 3560 SSR markers
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