Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

Abstract

Background The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus. Results In this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility. Conclusions This study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

“…Advances in high-throughput sequencing technology and reduced sequencing costs have enhanced the efficiency and convenience of using transcriptomics data to identify SSR loci with large numbers of polymorphisms 32 . Compared with genomic-SSR molecular markers, EST-SSR molecular markers have lower development costs, greater versatility and conservation, and favorable associations with phenotypic traits 33 . In the present study, www.nature.com/scientificreports/ 2,510 SSR loci were identified from 37,538 unigenes in the A. heimuer transcriptome; the SSR frequency of 6.69% was higher than the rates for edible mushrooms such as Auricularia polytricha (4.70%) and Pleurotus eryngii (3.09%) 34,35 , indicating that the A. heimuer transcriptome contains abundant SSR loci.…”

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

“…In A. humile , 85% of the 14 tested cashew SSRs amplified ( Soares et al., 2013 ); in A. microcarpum , A. pumilum , and A. nanum , 92% of the 12 cashew SSRs amplified ( Croxford et al., 2006 ); and in A. microcarpum and A. othonianum , 100% of 54 transcriptome-based SSRs amplified ( Savadi et al., 2022a ). The relatively lower rate of transferability of genomic SSRs compared to genic SSRs could be attributed to the higher conservation of genic sequences compared to sequences from the anonymous regions of the genomes ( Ellis and Burke, 2007 ; Jiang et al., 2020 ). Thus, we contemplate that the SSR markers developed in this study can be a potential marker repository for not only cashew but also the related Anacardium species and could be employed for macro-syntenic comparisons, germplasm characterizations, genetic mapping, molecular breeding involving interspecies hybridizations, etc.…”

Research Article In silico microsatellite transferability from Psidium guajava to Eucalyptus globulus validated by PCR

“…The theoretical transferability described here has a significant potential to help genetic mapping, comparative genomics, and transferability studies as it can 'filter' large amounts of molecular information before experimental steps. Jiang et al (2020) reported that the increase in the number of species sequenced by NGS technologies would increase the information in databases such as GenBank, providing abundant material to be explored using BLAST-like tools. Theoretical transferability may be applied to any marker.…”