(Press-News.org) The term "single-nucleotide polymorphism" (SNP) refers to a single base change in DNA sequence between two individuals. SNPs are the most common type of genetic variation in plant and animal genomes and are, thus, an important resource to biologists. The ubiquity of these markers and the fact that these polymorphisms show variation at such a fine scale (i.e., at the individual level) makes them ideal markers for many applications, such as population-level genetic diversity studies and genetic mapping in plants.
The growing popularity of next-generation sequencing has made SNPs a pervasive genetic marker in many areas of plant biology. The ever-increasing throughput of sequencing platforms has resulted in the ability to easily identify and genotype thousands of SNPs across numerous individuals to uncover genetic variation among and within populations. This technique, however, becomes quite challenging when the species of interest has undergone whole genome duplication events (i.e., polyploidy), as is common in many plant lineages.
Researchers at Texas A&M and the Southern Plains Agricultural Research Center have developed a strategy that simplifies the discovery of useful SNPs within the complex genome of cotton. The protocol is freely available in a recent issue of Applications in Plant Sciences.
"Cotton presents a challenge for SNP marker discovery due to the polyploid origin of the two most widely grown species," says Dr. Alan Pepper, an author of the study. "All plants have duplicated sequences, whether due to whole genome duplication, duplication of segments of chromosomes, duplication by retroviruses, or duplication by unequal crossing over. When you are looking for potential SNPs, particularly without a reference genome, you run the risk of identifying sequence differences between duplicated sequences rather than differences between individuals. This problem is particularly acute in recent allopolyploids."
Allopolyploid species are the product of hybridization between two divergent taxa. The genomes of these plants, therefore, contain two very similar copies of their genes--one from each parent.
According to Pepper, "A problem arises when our computational methods accidentally align DNA regions that are duplicated within the genomes of the plants being studied, rather than mapping the orthologous regions between the plants."
Enter the strategy presented by Pepper and colleagues.
Using the Illumina next-generation sequencing platform, over 50 million DNA reads were collected from restriction enzyme-digested DNA from four Gossypium species. The team then filtered these reads to enrich for orthologous DNA fragments.
Pepper explains, "One of the exciting things about this approach is that it employs a widely used, well-supported, off-the-shelf bioinformatics software known as Stacks (written by Julian Catchen at the University of Oregon) as a "filter" to enrich for pairs of fragments that are likely to be alleles of a single, orthologous region, rather than paralogs or homeologs."
The new method allows for the detection of polymorphisms between individuals, which will be useful for downstream applications such as marker-assisted selection, linkage and QTL mapping, and genetic diversity studies.
Pepper concludes, "The overall strategy for genotyping-by-sequencing, marker discovery, and annotation that we have provided in this study will be useful for researchers working with the many economically important allotetraploid species (such as the crop brassicas), but can be extended to any species, including those that do not currently have a reference genome."
INFORMATION:
Carlo Jo Logan-Young, John Z. Yu, Surender K. Verma, Richard G. Percy, and Alan E. Pepper. 2015. SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing. Applications in Plant Sciences 3(3): 1400077. doi:10.3732/apps.1400077
Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal focusing on new tools, technologies, and protocols in all areas of the plant sciences. It is published by the Botanical Society of America, a nonprofit membership society with a mission to promote botany, the field of basic science dealing with the study and inquiry into the form, function, development, diversity, reproduction, evolution, and uses of plants and their interactions within the biosphere. APPS is available as part of BioOne's Open Access collection.
For further information, please contact the APPS staff at apps@botany.org.
Massachusetts' health reform may be a crystal ball for researchers and policymakers in forecasting the potential impact of the Affordable Care Act. Many see the ACA as the backbone of efforts toward closing the nation's health gap. Because minorities and low-income populations are more likely to be uninsured, health coverage is widely assumed to be the most essential strategy to eliminating disparities in health outcomes.
However, new research published Wednesday in the BMJ, examining use of joint replacement and preventable hospital admissions, shines fresh light on ...
ATLANTA - April 1, 2015- While there has been substantial progress in some cancer control efforts in the past several decades, like reductions in smoking and increased utilization of cancer screening, progress in some areas is lagging, according to a new report. Among the areas of most concern: smoking rates among certain populations, obesity, indoor tanning, and low utilization of a new vaccine against human papillomavirus (HPV), which causes cervical and other cancers. Additionally, colorectal cancer screening, which not only detects tumors early but also may prevent ...
Bottom Line: The prevalence of childhood cancer survivors is estimated to have increased, and the majority of those who have survived five or more years beyond diagnosis may have at least one chronic health condition.
Journal in Which the Study was Published: Cancer Epidemiology, Biomarkers & Prevention, a journal of the American Association for Cancer Research
Author: Siobhan M. Phillips, PhD, MPH, assistant professor of preventive medicine at Northwestern University Feinberg School of Medicine in Chicago
Background: The goal of the study was to update prevalence ...
The European Respiratory Society (ERS) and American Thoracic Society (ATS) have published a statement describing the current evidence on the diagnosis, assessment and management of chronic obstructive pulmonary disease (COPD), identifying gaps in knowledge and making recommendations for the directions of future research.
ERS Guidelines Director, Professor Guy Brusselle, commented: "The World Health Organization predicts that COPD will become the third leading cause of death worldwide by 2030. It is therefore a critical time for us to act on improving the management of ...
(NEW YORK -- April 01, 2015) A new blood test promises to predict which people will have severe allergic reactions to foods according to a new study led by Mount Sinai researchers and published online today in the The Annals of Allergy, Asthma & Immunology.
To detect food allergies, physicians typically use skin prick tests or blood tests that measure levels of allergen-specific IgE (sIgE), a protein made by the immune system. However, these tests cannot predict the severity of allergic reactions. Oral food challenges, in which specific allergens are given to patients ...
PULLMAN, Wash.- A team led by Washington State University researchers has found that methane emissions from local natural gas distribution systems in cities and towns throughout the U.S. have decreased in the past 20 years with significant variation by region.
The researchers found that upgrades in metering and regulating stations, changes in pipeline materials, better instruments for detecting pipeline leaks as well as regulatory changes have led to methane emissions that are from 36% to 70% lower than current Environmental Protection Agency estimates when the data ...
DALLAS, March 31, 2015 -- A new scientific statement issued jointly by three medical organizations and published in the American Heart Association's journal Hypertension, addresses how low to aim when treating patients with high blood pressure who also have vascular diseases.
The document provides an up-to-date summary on treating hypertension in patients who have both high blood pressure and have had a stroke, heart attack or some other forms of heart disease, said Elliott Antman, M.D., President of the American Heart Association and professor of medicine at Harvard ...
Montréal, March 31, 2015 - A team of researchers at the IRCM led by Frédéric Charron, PhD, in collaboration with bioengineers at McGill University, uncovered a new kind of synergy in the development of the nervous system, which explains an important mechanism required for neural circuits to form properly. Their breakthrough, published today in the scientific journal PLoS Biology, could eventually help develop tools to repair nerve cells following injuries to the nervous system (such as the brain and spinal cord).
Researchers in Dr. Charron's laboratory ...
Women seek a greater variety of products and services when they are ovulating, according to a new study in the Journal of Consumer Research.
"Fertile women seek more options in men and this drives their desire for alternative options as consumers. If you are open to checking out alternatives, you are simply more likely to find the best option and it turns out that the desire for alternatives in mate choice impacts other choice situations," write authors Kristina M. Durante and Ashley Rae Arsena (both University of Texas, San Antonio).
In one study, women reported how ...
Why do some consumers make choices based on their feelings instead of rational assessments? According to a new study in the Journal of Consumer Research, consumers who consider themselves independent are more inclined to rely on feelings when making decisions.
"When making a decision, we can either base the decision on how we feel about the different options or on our logical reasoning about the specific features of the options. Our feelings often contradict logical assessments and the product that appeals more to our feelings is not the one that 'makes more sense' based ...
