Simple sequence repeats for population-level studies of pines

Apr 30, 2014
This image shows locations of 15 cpSSR loci within the Pinus ponderosa plastome (GenBank FJ899555). Credit: Applications in Plant Sciences 2(5): 1400002. doi:10.3732/apps.1400002.

Simple sequence repeats, abbreviated SSRs and frequently referred to as microsatellites, are highly variable sections of the genome. 'Sequence repeat' refers to the fact that a nucleotide motif is repeated. 'Simple,' because the repeated sequence often consists of only a couple of nucleotides—for example, ATAT.

Because these markers typically have high rates of molecular evolution, the number of repeats present in the genome often differs between individuals. By isolating SSRs and comparing length differences between taxa, evolutionary relationships can be inferred. Their high rate of change makes these markers particularly useful for fine-scale studies aimed at uncovering genetic structure within and between populations of a single species.

Scientists at Hendrix College have determined the location of a set of SSR regions that were originally found in the of two species of pines. They compared these regions in over 100 pine species and tested them using over 900 individuals. The results of their study are available for free viewing in the May issue of Applications in Plant Sciences.

"We compared published primer pairs with newly published plastomes for many species to select highly variable, unique fragments" says Dr. Ann Willyard, one of the authors of the study. "Additionally, by adopting a PCR multiplex technique that does not require primers to be fluorescently labeled for each locus, this approach is much more cost-effective than traditional methods."

Importantly, all loci used in this study were from the plastid genome. "Nuclear markers have historically been difficult to work with in pines," explains Willyard. "Although the nuclear genome is important to fully understand in plants, nuclear data sets are very difficult to obtain for large numbers of individuals and are complicated by issues of paralogy and shared ancestral polymorphisms, especially in long-lived outcrossing tree species like pines."

Willyard and her undergraduate colleagues tested the utility of these SSRs within groups of ponderosa pine. They found six markers to be particularly useful for understanding within this group. By showing which primers were in conserved regions of the , they were able to suggest that many of these loci are likely to be useful in other groups.

"The ponderosa pine species complex was used as a test case, but the resources that we have presented will make the technique easily adaptable to any group of pine species," explains Willyard.

The SSR regions identified in this study provide a jumping-off point for future studies. "We are particularly excited about the usefulness of these markers for delimiting species complexes," says Willyard. "Because next-generation sequencing is still cost prohibitive for population-level studies, fragment lengths of SSRs provide a quick and inexpensive way to look for patterns that are worth pursuing and testing with next-generation nucleotide sequences for one exemplar from each population of interest."

Explore further: Big data: A method for obtaining large, phylogenomic data sets

add to favorites email to friend print save as pdf

Related Stories

Loblolly pine's immense genome conquered

Mar 20, 2014

The massive genome sequence of the loblolly pine—the most commercially important tree species in the United States and the source of most American paper products—has been completed by a nationwide research ...

Sequencing hundreds of chloroplast genomes now possible

Jan 31, 2013

Researchers at the University of Florida and Oberlin College have developed a sequencing method that will allow potentially hundreds of plant chloroplast genomes to be sequenced at once, facilitating studies of molecular ...

Recommended for you

Vermicompost leachate improves tomato seedling growth

Nov 21, 2014

Worldwide, drought conditions, extreme temperatures, and high soil saline content all have negative effects on tomato crops. These natural processes reduce soil nutrient content and lifespan, result in reduced plant growth ...

Plant immunity comes at a price

Nov 21, 2014

Plants are under permanent attack by a multitude of pathogens. To win the battle against fungi, bacteria, viruses and other pathogens, they have developed a complex and effective immune system. And just as ...

Evolution: The genetic connivances of digits and genitals

Nov 20, 2014

During the development of mammals, the growth and organization of digits are orchestrated by Hox genes, which are activated very early in precise regions of the embryo. These "architect genes" are themselves regulated by ...

Surrogate sushi: Japan biotech for bluefin tuna

Nov 20, 2014

Of all the overfished fish in the seas, luscious, fatty bluefin tuna are among the most threatened. Marine scientist Goro Yamazaki, who is known in this seaside community as "Young Mr. Fish," is working to ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.