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Success of SNP: Genomics work one highlight of 2016

By Allison Floyd

University of Georgia, Peanut & Mycotoxin Innovation Lab

Mapping the genome of cultivated peanut’s progenitors marked a great accomplishment for research of the crop. And in 2016, researchers working with PMIL made another stride in research that makes genetic information available to plant breeders working around the globe to create varieties that deal with real-world problems.

Work through the Translational Genomics project of the Feed the Future’s Peanut and Mycotoxin Innovation Lab – a project led by Peggy Ozias-Akins, professor at the University of Georgia – is making the knowledge gained through genome mapping accessible to breeders, which will accelerate variety development and create peanut varieties with the traits farmers need.

This year, researchers were able to define a complete array of SNPs, or single-nucleotide polymorphisms, markers can then be linked to important traits, such as tolerance to drought or resistance to diseases and pests. While researchers and breeders have used genetic markers and marker-assisted selection extensively in other crops, the complexity of the peanut genome made that work more difficult for many of the world’s peanut scientists.

Without genetic markers, breeders must grow out plants to see if they show the desired trait, work that is time-consuming and often less accurate than simply checking to see if the right markers are there.

The recently developed SNP array now makes molecular markers available to scientists throughout the world even if they don’t have state-of-the-art equipment or expertise in molecular genetics. Essentially, the SNP array creates a toolkit for breeders to analyze their peanut germplasm for specific traits, rather than buying expensive lab equipment and repeating genetic research in their own labs around the world.

For example, if a breeder is looking for resistance to a certain disease, he can sample plants and submit them to a service provider for SNP analysis using the array to see if the plants contain the appropriate genes for the trait. The breeder then selects only the plants that have the trait to advance further.

The benefits are obvious for a single trait, but begin to compound when selecting for multiple traits, such as high oleic content, multiple disease resistance, drought tolerance, low aflatoxin contamination, etc.

Leading up to the development of the complete array, graduate students, Carolina Chavarro and Josh Clevenger, working with Ozias-Akins, re-sequenced the genome of 20 genotypes, eight of direct relevance to the Peanut and Mycotoxin Innovation Lab, to generate additional sequence information for SNP discovery. Ultimately, they identified a total of 58,233 SNPs to be included in the array.

The SNPs used for array development will be deposited in the National Center for Biotechnology Information’s Short Genetic Variations database (SNPdb), a public repository. Researchers are already planning to use the array to genotype all lines being tested for resistance to pre-harvest aflatoxin contamination.

Until now, technology transfer has primarily been related to SNP marker discovery, but with the availability of the SNP array, breeders in partner countries can now be provided with a useful marker platform to accelerate their breeding programs.

Ultimately, the array makes trait selection practical, so that breeders throughout the world can select and use genes that benefit a peanut plant in disease resistance, drought tolerance, seed size and nutritional quality.

The array is giving everyone working on peanuts the ability to do modern genetic analysis to find markers that can accelerate crop improvement.

Pubished November 30, 2016