Automated DNA sample preparation and sequencing could help researchers identify genetic markers associated with wheat yield, disease resistance and other agronomic traits.
A new genotyping platform at Embrapa Wheat in Brazil is expanding researchers’ capacity to analyse wheat DNA and support the development of improved cultivars.
The technology automates DNA sample preparation, reducing a process that previously took several days to approximately 12 hours. It is expected to lower research costs and accelerate the identification of genetic markers linked to yield, disease resistance and other important crop characteristics.
The platform represents the latest stage in the modernization of genotyping, a process used to identify variations within an organism’s DNA.
“In two decades, the protocol has been modernized, with the replacement of manual gel analysis by electrophoresis systems – which use electric field to separate molecules – and, more recently, by sequencing, which allows large-scale and high-precision genotyping,” says laboratory technician Jordalan Muniz.
A Year’s Work Reduced to One Week
Second-generation sequencing was incorporated into the routine of Embrapa Wheat’s Biotechnology Laboratory following the installation of two instruments, according to a press release.
The ION Chef automates sample preparation, while the ION GeneStudio S5 Plus performs DNA sequencing.
“We can say that the one-year job can now be done in just one week. It is an efficiency gain that reduces costs and accelerates the obtaining of molecular data in support of the wheat genetic improvement program at Embrapa,” explains researcher Luciano Consoli.
The increased capacity is particularly valuable for wheat research because the crop’s genome is five times larger than the human genome. The publication of the wheat reference genome in 2018 provided researchers with new opportunities to develop biotechnology tools for crop improvement.
Thousands of Wheat and Barley Markers Available
Embrapa Wheat’s Molecular Genetics team currently holds information on approximately 5,000 wheat molecular markers and 3,500 barley markers that are compatible with the new platform.
Markers associated with genes of interest can help breeders select lines carrying desirable agronomic characteristics.
Researchers have also developed a marker panel for use in wheat breeding. The sequencing platform can simultaneously analyse 384 samples against 202 markers, producing approximately 80,000 data points.
The system can also examine specific regions within DNA sequences, providing researchers with a more detailed picture of the genetic variation available to breeding programs.
“The first result of the use of this technology for the generation of molecular genotyping data is the increase in the efficiency of the process of generating new cultivars and in the identification of alleles or parts of genes of interest for breeding programs. If before we had a cartographic representation, now we have something more detailed, with streets and signboards,” says Consoli.
Supporting Selection for Disease Resistance
Wheat cultivars and breeding lines carrying markers of interest can be selected for use in crossing programs.
Embrapa Wheat has already applied molecular analysis and marker-assisted selection to efforts to broaden genetic resistance to diseases such as wheat blast, known in Brazil as brusone.
“Identified, in a given cultivar, the presence of a molecular marker associated with resistance, such as brusone, its plants can be incorporated into the breeding program for crossing,” points out researcher Gisele Torres.
However, molecular markers do not eliminate the need to evaluate plants under field conditions. Breeders must still determine whether plants carrying a particular marker express effective resistance when exposed to the disease-causing pathogen.
“The simple presence of a certain marker, even when DNA fragments are known to confer resistance, is not enough for the plants that have it to be resistant. The work of biotechnology is complementary to the work of improvement. Thus, to verify the effectiveness of a given molecular marker, it is essential that breeders evaluate the reaction of plants to the pathogen in the field,” adds Torres.
Additional Applications for Wheat Research
The Embrapa team is exploring several other applications for the sequencing platform.
Researchers could extract DNA from soil samples to identify microorganisms that may benefit wheat production in particular regions. The resulting molecular soil profiles could then be compared with production factors and crop performance.
The technology could also support research into wheat for people with celiac disease by helping scientists characterize markers associated with genes that code for proteins involved in the immune response to gluten.
Additional possibilities include gene-expression analysis through RNA sequencing and the sequencing of small genomes, including those of microorganisms.
“In the past we used a magnifying glass, moved to the microscope and evolved to see what is inside the plants. Now, we can identify all kinds of variations present in the plant’s DNA fragments that are associated with defense and the use of environmental resources,” Consoli says.
