Featured Research

from universities, journals, and other organizations

Simple sequence repeats for population-level studies of pines

Date:
April 30, 2014
Source:
American Journal of Botany
Summary:
Scientists have compared a set of plastid simple sequence repeat loci across over 100 pine species and tested them in groups of Ponderosa pine. The results of this study will be useful in delimiting species complexes in Pinus, and the demonstrated multiplex method can be easily applied to other plant groups.

This image shows locations of 15 cpSSR loci within the Pinus ponderosa plastome (GenBank FJ899555).
Credit: Wofford et al. From Wofford, A. M., K. Finch, A. Bigott, and A. Willyard. 2014.

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 chloroplast genome 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 evolutionary relationships 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 genetic structure within this group. By showing which primers were in conserved regions of the genome, 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."


Story Source:

The above story is based on materials provided by American Journal of Botany. Note: Materials may be edited for content and length.


Journal Reference:

  1. Austin M. Wofford, Kristen Finch, Adam Bigott, Ann Willyard. A Set of Plastid Loci for use in Multiplex Fragment Length Genotyping for Intraspecific Variation inPinus(Pinaceae). Applications in Plant Sciences, 2014; 2 (5): 1400002 DOI: 10.3732/apps.1400002

Cite This Page:

American Journal of Botany. "Simple sequence repeats for population-level studies of pines." ScienceDaily. ScienceDaily, 30 April 2014. <www.sciencedaily.com/releases/2014/04/140430161327.htm>.
American Journal of Botany. (2014, April 30). Simple sequence repeats for population-level studies of pines. ScienceDaily. Retrieved July 29, 2014 from www.sciencedaily.com/releases/2014/04/140430161327.htm
American Journal of Botany. "Simple sequence repeats for population-level studies of pines." ScienceDaily. www.sciencedaily.com/releases/2014/04/140430161327.htm (accessed July 29, 2014).

Share This




More Plants & Animals News

Tuesday, July 29, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Rodents Rampant in Gardens Around Louvre

Rodents Rampant in Gardens Around Louvre

AP (July 29, 2014) Food scraps and other items left on the grounds by picnickers brings unwelcome visitors to the grounds of the world famous and popular Louvre Museum in Paris. (July 29) Video provided by AP
Powered by NewsLook.com
Jane Goodall Warns Great Apes Face Extinction

Jane Goodall Warns Great Apes Face Extinction

AFP (July 29, 2014) The world's great apes face extinction within decades, renowned chimpanzee expert Jane Goodall warned Tuesday in a call to arms to ensure man's closest relatives are not wiped out. Duration: 00:58 Video provided by AFP
Powered by NewsLook.com
How Your Face Can Leave A Good Or Bad First Impression

How Your Face Can Leave A Good Or Bad First Impression

Newsy (July 29, 2014) Researchers have found certain facial features can make us seem more attractive or trustworthy. Video provided by Newsy
Powered by NewsLook.com
Rat Infestation at Paris' Tuileries Garden

Rat Infestation at Paris' Tuileries Garden

AFP (July 29, 2014) An infestation of rats is causing concern among tourists at Paris' most famous park -- the Tuileries garden next to the Louvre Museum. Duration: 00:54 Video provided by AFP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins