New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing1

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Abstract

Premise of the study:

Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars.

Methods and Results:

A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19.

Conclusions:

The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management.

Related collections

Most cited references 5

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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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Current trends in microsatellite genotyping.

E Guichoux, L Lagache, S. Wagner … (2011)

Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling. © 2011 Blackwell Publishing Ltd.

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Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences.

Juan E Zalapa, Hugo Cuevas, Huayu Zhu … (2012)

The application of next-generation sequencing (NGS) technologies for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in the botanical sciences is described. Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been a difficult and costly process. NGS technologies allow the efficient identification of large numbers of microsatellites at a fraction of the cost and effort of traditional approaches. The major advantage of NGS methods is their ability to produce large amounts of sequence data from which to isolate and develop numerous genome-wide and gene-based microsatellite loci. The two major NGS technologies with emergent application in SSR isolation are 454 and Illumina. A review is provided of several recent studies demonstrating the efficient use of 454 and Illumina technologies for the discovery of microsatellites in plants. Additionally, important aspects during NGS isolation and development of microsatellites are discussed, including the use of computational tools and high-throughput genotyping methods. A data set of microsatellite loci in the plastome and mitochondriome of cranberry (Vaccinium macrocarpon Ait.) is provided to illustrate a successful application of 454 sequencing for SSR discovery. In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.

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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: August 2016

Publication date (Electronic): 29 July 2016

Volume: 4

Issue: 8

Electronic Location Identifier: apps.1600021

Affiliations

[2 ]Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, F-34398 Montpellier, France

[3 ]Vanuatu Agricultural Research and Technical Centre (VARTC), P.O. Box 231, Santo, Vanuatu

[4 ]Institut Agronomique néo-Calédonien (IAC), P.O. Box 73, 98890 Païta, New Caledonia

Author notes

[1]

The authors thank H. Vignes for assistance with the construction of the library, X. Argout for assistance with bioinformatics analysis, C. Hamelin for data curation of TropGeneDB, X. Perrier for helpful comments on the manuscript, and P. Biggins for editorial input.

[5 ]Author for correspondence: fabien.de_bellis@ 123456cirad.fr

Article

Publisher ID: apps1600021

DOI: 10.3732/apps.1600021

PMC ID: 5001855

SO-VID: f50a9d7a-0e1d-4416-9c54-e3f5d6abb3ec

License:

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