Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

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Abstract

Abstract The Cactaceae family is native to the American continent with several centers of diversity. In South America, one of these centers is the Central Andes and many species are considered to be threatened or vulnerable according to the International Union for Conservation of Nature (IUCN). Stetsonia coryne is an emblematic giant columnar cacti of the Chaco phytogeographic province. It has an extensive geographical distribution in many countries of the continent. However, to date there are no specific molecular markers for this species, neither reports of population genetic variability studies, such as for many cactus species. The lack of information is fundamentally due to the lack of molecular markers that allow these studies. In this work, by applying a Genotyping by Sequencing (GBS) technique, we developed polymorphic SSR markers for the Stetsonia coryne and evaluated their transferability to phylogenetically close species, in order to account for a robust panel of molecular markers for multispecies-studies within Cactaceae.

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Primer3—new capabilities and interfaces

Andreas Untergasser, Ioana Cutcutache, Triinu Koressaar … (2012)

Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

Robert Elshire, Jeffrey C. Glaubitz, Qi-ying Sun … (2011)

Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

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Stacks: an analysis tool set for population genomics.

Julian Catchen, Paul Hohenlohe, Susan Bassham … (2013)

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics. © 2013 John Wiley & Sons Ltd.

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Author and article information

Journal

Journal ID (publisher-id): aabc

Title: Anais da Academia Brasileira de Ciências

Abbreviated Title: An. Acad. Bras. Ciênc.

Publisher: Academia Brasileira de Ciências (Rio de Janeiro, RJ, Brazil )

ISSN (Print): 0001-3765

ISSN (Electronic): 1678-2690

Publication date (Print and electronic): 2021

Volume: 93

Issue: suppl 3

Electronic Location Identifier: e20201778

Affiliations

[2] Salta-Salta Salta orgnameUniversidad Nacional de Salta orgdiv1Facultad de Ciencias Naturales Argentina

[3] Buenos Aires Buenos Aires orgnameUniversidad de Buenos Aires orgdiv1formerly Instituto de Biotecnología Argentina

[1] Ciudad Autónoma de Buenos Aires orgnameConsejo Nacional de Investigaciones Científicas y Técnicas (CONICET) orgdiv1Godoy Cruz 2290 Argentina

Article

Publisher ID: S0001-37652021000600801 Publisher ID: S0001-3765(21)09300000801

DOI: 10.1590/0001-3765202120201778

SO-VID: 283e537d-68b2-4885-a6de-96f488e5f342

License:

This work is licensed under a Creative Commons Attribution 4.0 International License.

History

Date received : 13 November 2020

Date accepted : 08 April 2021

Page count

Figures: 0, Tables: 0, Equations: 0, References: 68, Pages: 0

Product

SciELO Brazil

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