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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #316362

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

Title: Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

Author
item GARDNER, ELLIOT - Chicago Botanical Garden
item LARICCHIA, KRISTEN - Chicago Botanical Garden
item MURPHY, MATTHEW - Chicago Botanical Garden
item RAGONE, DIANE - National Tropical Botanical Garden (NTBG)
item Scheffler, Brian
item Simpson, Sheron
item WILLIAMS, EVELYN - Chicago Botanical Garden
item ZEREGA, NYREE J - Chicago Botanical Garden

Submitted to: Applications in Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2015
Publication Date: 9/10/2015
Citation: Gardner, E.M., Laricchia, K.M., Murphy, M., Ragone, D., Scheffler, B.E., Simpson, S.A., Williams, E., Zerega, N.C. 2015. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences. Applications in Plant Sciences. 3(9):1500049. doi:10.3732/apps.1500049.

Interpretive Summary: Breadfruit, breadnut and their related species represent important food trees for many parts of the world. The USA has a significant germplasm collection of breadfruit related species located in Kahaleo, Hawaii. Desired cultivars are vegetatively propagated and DNA markers can play an important role in identification of clonal lines. In this study, DNA markers were developed and validated on several species. These DNA markers are chloroplast specific and they have certain advantages over nuclear DNA markers. Chloroplast are more abundant in green tissue and thus less plant DNA is required for detection. Chloroplasts are also maternally inherited and thus it is possible to use DNA markers to also identify maternal lines. These markers will act as important tool, along with nuclear markers, for species, clonal and maternal identification of those species related to breadfruit and breadnut.

Technical Abstract: Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus (A.) altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: 15 simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. Conclusion: These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines—often important in vegetatively-propagated crops such as breadfruit.