Abstract
Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. 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.
Highlights
Belongs to family liliaceae, which mainly propagates vegetatively
Xi et al.[15] suggested that ISSR may be useful in identification of L. longiflorum mutants instated of RAPD
Di- and trinucleotide repeats found more abundant than other SSR repeats and di-nucleotide repeat was twofold higher than tri-nucleotide repeats
Summary
Belongs to family liliaceae, which mainly propagates vegetatively. sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. Characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. Based on 13 morphological characters the Lilium species are taxonomically classified into seven sections; Martagon, Pseudolirium, Lilium (Liriotypus), Archelirion, Sinomartagon, Leucolirion, and Oxypetalum[3,4] All cultivars from these sections were further categorized into three main groups: Longiflorum (L), Asiatic (A), and Oriental (O) h ybrids[5]. Several DNA markers, such as RAPD (randomly amplified polymorphic DNA), ISSR (inter simple sequence repeat), AFLP (amplified fragment length polymorphism), DArT (Diversity Arrays Technology), SSR and SNP (Single Nucleotide Polymorphism) have been developed in lily for studying genetic diversity[9,10,11,12,13], germplasm characterization, identifying h ybrids9,13,14, mutants[15], and genetic m apping[16]. A representative portion of SSR markers were validated and utilized to figure out the lily genetic diversity and population structure of Korean core lily collection
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