Characterization, validation, and cross-species transferability of newly developed EST-SSR markers and their application for genetic evaluation in crape myrtle (Lagerstroemia spp)

Ye, Yuanjun; Feng, Lu; Liang, Xiaohan; Liu, Tingting; Cai, Ming; Cheng, Tangren; Wang, Jia; Zhang, Qixiang

doi:10.1007/s11032-019-0936-0

Cited by 15 publications

(9 citation statements)

References 22 publications

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“…Similar observations, whereby dinucleotides was the most abundant motif in the plants' genomes, have been reported for other tree species such as grey mangrove (Avicennia marina) 25 , downy oak (Quercus pubescens) 26 and crape myrtle (Lagerstroemia spp.) 27 . A total of 19 transcriptome-based microsatellite markers (EST-SSR) were developed in this study.…”

Section: Discussionmentioning

confidence: 99%

Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Azman

et al. 2020

Sci Rep

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Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.

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Section: Discussionmentioning

confidence: 99%

Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Azman

et al. 2020

Sci Rep

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“…The use of molecular markers has been widely implemented in plant breeding (Ahmar et al., 2020; Jiang, 2013; Nadeem et al., 2017). Even in traditional breeding, molecular markers used in phylogenetic analyses could be useful tools for germplasm classification and identification of species, genetically identical (clones), or cultivars (Ye et al., 2019); marker‐based parentage analysis would facilitate pedigree reconstructions of offspring from open‐pollinated seeds of the breeding population or seed orchard, and thus recombination of genes from the best individuals can be achieved without controlled crosses (called ‘breeding without breeding’) for forest trees (El‐Kassaby & Lstiburek, 2009; Wang et al., 2010). Therefore, it is important to choose proper molecular markers before effectively using markers in plant breeding (Jiang, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genomic SSR and EST‐SSR markers for phylogenetic and pedigree reconstructions—A comparison in sea buckthorn

Luo-yun

Wang

et al. 2021

Plant Breeding

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Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non‐model species. We identified SSRs from expressed sequence tags (EST‐SSRs) and whole genome sequences (gSSRs), by analysing the transcriptome and genome of the Mongolian sea buckthorn (Hippophae rhamnoides subsp. mongolica) cultivar ‘Sunny’. Using the same number of loci, EST‐SSRs showed higher transferability to Hippophae than gSSRs, and phylogenetic trees based on EST‐SSRs demonstrated higher resolution for classifying Hippophae species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST‐SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST‐SSRs and gSSRs would provide insight into the trade‐off between differentiation and polymorphism in marker selection for breeding programs.

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“…In general, markers with PIC> 0.5 are defined as highly polymorphic [ 40 ]. In our case, the average PIC value of the 13 EST-SSR markers used, except LaES18 and LaES27, was 0.654, higher than many EST-SSR markers developed from transcriptome sequences, such as for Torreya grandis (0.357) [ 41 ], Mucuna pruriens (0.24) [ 42 ] and Lagerstroemia spp (0.589) [ 43 ]. The high PIC values observed in our work hinted a high efficiency of these set of markers in genetic analysis.…”

Section: Discussionmentioning

confidence: 65%

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

Jiang

Wang

et al. 2020

BMC Plant Biol

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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.

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Characterization, validation, and cross-species transferability of newly developed EST-SSR markers and their application for genetic evaluation in crape myrtle (Lagerstroemia spp)

Cited by 15 publications

References 22 publications

Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Genomic SSR and EST‐SSR markers for phylogenetic and pedigree reconstructions—A comparison in sea buckthorn

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

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