Nav: Home

Simplifying SNP discovery in the cotton genome

March 31, 2015

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."
-end-
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.

Botanical Society of America

Related Genome Articles:

Breakthrough in genome visualization
Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome.
Sturgeon genome sequenced
Sturgeons lived on earth already 300 million years ago and yet their external appearance seems to have undergone very little change.
A sea monster's genome
The giant squid is an elusive giant, but its secrets are about to be revealed.
Deciphering the walnut genome
New research could provide a major boost to the state's growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California's 4,800 growers.
Illuminating the genome
Development of a new molecular visualisation method, RNA-guided endonuclease -- in situ labelling (RGEN-ISL) for the CRISPR/Cas9-mediated labelling of genomic sequences in nuclei and chromosomes.
A genome under influence
References form the basis of our comprehension of the world: they enable us to measure the height of our children or the efficiency of a drug.
How a virus destabilizes the genome
New insights into how Kaposi's sarcoma-associated herpesvirus (KSHV) induces genome instability and promotes cell proliferation could lead to the development of novel antiviral therapies for KSHV-associated cancers, according to a study published Sept.
Better genome editing
Reich Group researchers develop a more efficient and precise method of in-cell genome editing.
Unlocking the genome
A team led by Prof. Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells.
Why do we need one pair of genome?
Scientists have unraveled how the cell replication process destabilizes when it has more, or less, than a pair of chromosome sets, each of which is called a genome -- a major step toward understanding chromosome instability in cancer cells.
More Genome News and Genome Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at Radiolab.org/donate.