Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae)

Area of Science:

• Plant genetics
• Molecular biology
• Bioinformatics

Background:

• Microsatellite markers (SSRs) are crucial for plant population genetics but their development is challenging.
• Traditional SSR development involves laborious cloning and sequencing methods.

Purpose of the Study:

• To evaluate next-generation sequencing (NGS) as an efficient approach for developing SSR markers.
• To develop a large set of SSR markers for five species within the Neotropical cactus genus Pilosocereus.

Main Methods:

• Utilized restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform.
• Applied bioinformatics to identify microsatellite loci from sequencing data.
• Validated polymorphic SSRs in Pilosocereus machrisii populations.

Main Results:

• Identified an average of 165 microsatellites per individual across five Pilosocereus species.
• Found di- and trinucleotide repeats to be the most abundant motifs.
• Developed 72 potentially amplifiable and 22 validated polymorphic SSR markers.

Conclusions:

• NGS, specifically RAD-seq, is an efficient strategy for isolating multispecies microsatellites, even in non-model plants.
• This method overcomes traditional challenges in SSR marker development.
• The developed SSRs will aid in population genetic studies of Pilosocereus cacti.