Development of microsatellite loci for the endangered seagrass Zostera japonica (Zosteraceae)1

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Abstract

Premise of the study:

New microsatellite markers were developed for the Asian endangered seagrass Zostera japonica (Zosteraceae) to assess genetic diversity and population structure of this species. In China, Z. japonica populations have drastically decreased since the 1970s.

Methods and Results:

A total of 12 polymorphic tetranucleotide microsatellite loci were isolated and characterized in Z. japonica. The number of alleles per locus ranged from one to 11. The expected and observed heterozygosity ranged from 0 to 0.772 and from 0 to 1.000, respectively.

Conclusions:

The new microsatellites will be useful in evaluating clonality and population structure of Z. japonica and aiding in conservation and management of the endangered seagrass in Asia.

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Most cited references 11

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Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

T Thiel, W Michalek, R. K. Varshney … (2003)

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.

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Isolating microsatellite DNA loci.

Travis Glenn, Barbara Schable (2004)

A series of techniques are presented to construct genomic DNA libraries highly enriched for microsatellite DNA loci. The individual techniques used here derive from several published protocols but have been optimized and tested in our research laboratories as well as in classroom settings at the University of South Carolina and University of Georgia, with students achieving nearly 100% success. Reducing the number of manipulations involved has been a key to success, decreasing both the failure rate and the time necessary to isolate loci of interest. In our lab during the past 3 years alone, these protocols have been successfully used to isolate microsatellite DNA loci from at least 55 species representing three kingdoms. These protocols have made it possible to reduce the time to identify candidate loci for primer development from most eukaryotic species to as little as 1 week.

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Biodiversity and the functioning of seagrass ecosystems

JE Duffy (2006)

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Author and article information

Journal

Journal ID (nlm-ta): Appl Plant Sci

Journal ID (iso-abbrev): Appl Plant Sci

Journal ID (publisher-id): apps

Title: Applications in Plant Sciences

Publisher: Botanical Society of America

ISSN (Electronic): 2168-0450

Publication date Collection: September 2015

Publication date (Electronic): 1 September 2015

Volume: 3

Issue: 9

Electronic Location Identifier: apps.1500064

Affiliations

[2 ]Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, Shandong, People’s Republic of China

[3 ]University of the Chinese Academy of Sciences, No. 19A, Yuquan Road, Beijing 100049, People’s Republic of China

Author notes

[1]

The authors acknowledge funding from the National Science and Technology Basic Work Program (2015FY110600), the 100 Talents Program of the Chinese Academy of Sciences to J.X.L., and the National Marine Public Welfare Research Project (201305043).

[4 ]Authors for correspondence: yizhou@qdio.ac.cn (Y.Z.); jinxianliu@gmail.com (J.X.L.)

Article

Publisher ID: apps1500064

DOI: 10.3732/apps.1500064

PMC ID: 4578380

SO-VID: 3de1d962-f993-4530-b1f0-c0cfa059fbfc

License:

This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA).

History

Date received : 3 June 2015

Date accepted : 8 July 2015

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