Generation of expressed sequence tags, development of microsatellite and single nucleotide polymorphism markers in Primula sieboldii E. Morren (Primulaceae) for analysis of genetic diversity in natural and horticultural populations

Abstract

Primula sieboldii is a self-incompatible ornamental plant that has been cultivated for more than 300 years in Japan. In order to increase the available genomic resources for this species, 5651 expressed sequence tags (ESTs) were generated from seedling and winter bud cDNA libraries. After clustering and assembling ESTs, 2960 unigene elements that contain an homologous sequence to an S locus-linked gene of P. vulgaris were identified. In total, 127 simple sequence repeats (SSRs) were found. The most frequent di-and tri-SSR motifs were GA (78.6%) and ATT (12.9%), respectively. Twenty SSR and 40 single nucleotide polymorphism (SNP) markers were developed. These markers were evaluated for polymorphisms using 24 individuals (Y) from a population in Yatsugatake and 14 individuals (PS) from across the distributional range of P. sieboldii in Japan. The average level of expected heterozygosity within Y and PS was 0.39 and 0.48, respectively for EST-SSR markers and 0.26 and 0.29, respectively for SNP markers. The level of polymorphism for EST-SSR markers was lower than that for genomic SSR markers developed in a previous study. We also surveyed the genetic diversity of 56 cultivars, which had lower allelic richness than the Y and PS populations.

Comparative transcriptome analysis and marker development of two closely related Primrose species (Primula poissonii and Primula wilsonii)

“…Traditional strategies for SSR marker development are labour-intensive and costly. In the case of Primula , up to now, only a few microsatellite primers have been available for Primula obconica , P. sieboldii and P. vulgaris [11-13], and this has impeded genetic analysis of this important garden plant. Based on the two Primula transcriptomes, 7,571 and 8,272 SSRs were found in P. poissonii and P. wilsonii , respectively.…”

“…In this region Primula shows a typical patterns of adaptive evolution and explosive speciation; however, research has been hampered by the fact that few Primula genomic resources are available. Up to now, only a few SSR primers from the three Primula species P. vulgaris , P. obconica , and P. sieboldii have been developed [11-13], and only one large EST collection, consisting of 5,651 ESTs generated from Primula sieboldii were available [13]. Paucity of genetic data such as genome sequences, transcriptome sequences and associated molecular markers has made Primula breeding or evolutionary analysis a challenging task.…”

Large-Scale Heat-Tolerance Screening and Genetic Diversity of Pea (Pisum sativum L.) Germplasms

“…SNaPshot technology is mainly used in forensic identification and SNP detection of human genes. In recent years, it has been applied in the field of plant genetics research due to its low cost, especially in research on forest trees and ornamental plants [ 51 , 52 , 54 ]. In the present study, the SNaPshot method was introduced for identification and evaluation of pea germplasms for the first time.…”

“…SNaPshot technology, also known as micro-sequencing technology, achieves mid-throughput SNP typing [ 47 , 48 ] and has been widely used in forensic medical identification [ 49 ] and in SNP detection of human genes [ 50 ] due to its high sensitivity, good repeatability, and lack of need for additional equipment. SNaPshot shows broad application prospects in the field of plant genetics research, such as SNP typing and marker development [ 51 ], molecular-marker-assisted breeding [ 52 ], and genetic diversity analysis [ 53 , 54 , 55 , 56 ]. To date, there have been only sporadic studies on the genetic diversity and population genetic structure of pea germplasms using SNP markers [ 57 ] and even fewer reports have analyzed pea genetics using SNaPshot technology.…”

Development of EST‐SSR Markers for Primula ovalifolia (Primulaceae) by Transcriptome Sequencing

“…In Primula , only a few genomic SSR markers have been developed for several species thus far, such as P. vulgaris Huds. ( Van et al, 2006 ), P. obconica Hance ( Yan et al, 2010 ), P. sieboldii E. Morren ( Ueno et al, 2011 ), P. veris L. ( Bickler et al, 2013 ), P. poissonii Franch., and P. wilsonii Dunn ( Zhang et al, 2013 ). Considering that these markers demonstrate low polymorphism and limited transferability, and that species of section Petiolares are phylogenetically distant from the above-named species, expressed sequence tag (EST)-SSRs specific to section Petiolares could provide useful tools for evolutionary and ecological studies in this section.…”