Development and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)

Title:
Development and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)
Authors:
Guo, Rui; Landis, Jacob B.; Moore, Michael J.; Meng, Aiping; Jian, Shuguang; Yao, Xiaohong; Wang, Hengchang
Abstract:
Actinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41.3 Mb), of which 21,730 were annotated using protein databases. A total of 8,658 EST-SSR loci were identified in 7,495 unigene sequences, for which primer pairs were successfully designed for 3,842 loci (44.4%). Among these, 183 primer pairs were assayed for PCR amplification, yielding 69 with detectable polymorphism in A. eriantha. Additionally, 61 of the 69 polymorphic loci could be successfully amplified in at least one other Actinidia species. Of these, 14 polymorphic loci (mean N-A = 6.07 +/- 2.30) were randomly selected for assessing levels of genetic diversity and population structure within A. eriantha. Finally, a neighbor-joining tree and Bayesian clustering analysis showed distinct clustering into two groups (K = 2), agreeing with the geographical distributions of these populations. Overall, our results will facilitate further studies of genetic diversity within A. eriantha and will aid in discriminating outlier loci involved in local adaptation.
Citation:
Guo, Rui., Jacob B. Landis, Michael J. Moore, et al. 2017. "Development and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)." Frontiers in Plant Science 8:1383.
Publisher:
Frontiers Media
DATE ISSUED:
2017-08-25
Department:
Biology
Type:
Article
PUBLISHED VERSION:
10.3389/fpls.2017.01383
Additional Links:
http://journal.frontiersin.org/article/10.3389/fpls.2017.01383/full
PERMANENT LINK:
http://hdl.handle.net/11282/620492

Full metadata record

DC FieldValue Language
dc.contributor.authorGuo, Ruien
dc.contributor.authorLandis, Jacob B.en
dc.contributor.authorMoore, Michael J.en
dc.contributor.authorMeng, Aipingen
dc.contributor.authorJian, Shuguangen
dc.contributor.authorYao, Xiaohongen
dc.contributor.authorWang, Hengchangen
dc.date.accessioned2017-09-13T12:07:28Z-
dc.date.available2017-09-13T12:07:28Z-
dc.date.issued2017-08-25-
dc.identifier.citationGuo, Rui., Jacob B. Landis, Michael J. Moore, et al. 2017. "Development and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)." Frontiers in Plant Science 8:1383.en
dc.identifier.issn1664-462X-
dc.identifier.urihttp://hdl.handle.net/11282/620492-
dc.description.abstractActinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41.3 Mb), of which 21,730 were annotated using protein databases. A total of 8,658 EST-SSR loci were identified in 7,495 unigene sequences, for which primer pairs were successfully designed for 3,842 loci (44.4%). Among these, 183 primer pairs were assayed for PCR amplification, yielding 69 with detectable polymorphism in A. eriantha. Additionally, 61 of the 69 polymorphic loci could be successfully amplified in at least one other Actinidia species. Of these, 14 polymorphic loci (mean N-A = 6.07 +/- 2.30) were randomly selected for assessing levels of genetic diversity and population structure within A. eriantha. Finally, a neighbor-joining tree and Bayesian clustering analysis showed distinct clustering into two groups (K = 2), agreeing with the geographical distributions of these populations. Overall, our results will facilitate further studies of genetic diversity within A. eriantha and will aid in discriminating outlier loci involved in local adaptation.en
dc.language.isoen_USen
dc.publisherFrontiers Mediaen
dc.identifier.doi10.3389/fpls.2017.01383-
dc.relation.urlhttp://journal.frontiersin.org/article/10.3389/fpls.2017.01383/fullen
dc.subject.departmentBiologyen_US
dc.titleDevelopment and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)en_US
dc.typeArticleen
dc.identifier.journalFrontiers in Plant Scienceen
dc.subject.keywordActinidia erianthaen_US
dc.subject.keywordHigh-throughput sequencingen_US
dc.subject.keywordTranscriptomeen_US
dc.subject.keywordEST-SSRsen_US
dc.subject.keywordPopulation genetic structureen_US
dc.identifier.volume8en_US
dc.rightsArchived with thanks to Frontiers in Plant Scienceen
All Items in The Five Colleges of Ohio Digital Repository are protected by copyright, with all rights reserved, unless otherwise indicated.