Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

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.

Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)

“…The observed heterozygosity ( Ho ), expected heterozygosity ( He ) and polymorphism information content ( PIC ) was estimated using power marker software version 3 87 , 88 . Further, the dendrogram was constructed on the basis of Nei’s genetic distance matrix using neighbour-joining (NJ) methodology with 1000 bootstrap replicates 28 , 50 , 85 , 89 , 90 . Further, for genetic mapping analysis, tea being a cross pollinated plant species, four alleles representing five different segregation patterns viz.…”

Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)

“…Although only a minor portion of the B. rotunda genome at around 0.35%, microsatellites are the key elements in plant genomes. Among these, short sequence repeat mi-crosatellites (SSRs) have found wide utility as co-dominant markers useful in breeding and diversity studies [86,87]. In this study, we identified the genomic and EST-SSRs from B. rotunda, designing primers and showing several to have a transferability to Musa and Ensete genomes, mostly in silico analysis, but with 14 tested in PCR experiments.…”

Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (Boesenbergia rotunda)

“…Although only a minor portion of the B. rotunda genome at around 0.35%, microsatellites are key elements in plant genomes. Among these, short sequence repeat microsatellites (SSRs) have found wide utility as co-dominant markers useful in breeding and diversity studies 85, 86 . In this study, we identified genomic and EST-SSRs from B. rotunda , designing primers and showing several to have transferability to Musa and Ensete genomes, mostly in silico analysis, but with 14 tested in PCR experiments.…”

“…Although only a minor portion of the B. rotunda genome at around 0.35%, microsatellites are key elements in plant genomes. Among these, short sequence repeat microsatellites (SSRs) have found wide utility as co-dominant markers useful in breeding and diversity studies 85,86 .…”