New Peanut Genomics Database Accelerates Research: Q&A With PeanutBase

By Lindsay Stevens

PeanutBase is a community resource for the international peanut research and breeding community. Originally led by Ethy Cannon, this database allows for peanut-related research from around the world to reside in one central database. To learn more, NPB spoke with PeanutBase personnel Sudhansu Dash, who was involved with the site development, curation and content management, and has served as the lead of PeanutBase since 2020; Andrew Farmer, who worked on the generation of data and analysis for the International Peanut Genome Initiative (IPGI); and Steven Cannon, who played a major role in the assembly and analysis of the genome and is the lead or core developer on several software projects to make genomic data accessible.

Q: What led to the creation of PeanutBase?

A: PeanutBase was started in 2013 as the primary repository and portal for genetic and genomic data generated by IPGI. PeanutBase has matured with IPGI, and now provides tools that allow researchers to explore the genomes of the peanut and its wild relatives, along with related genetic resources integrated into the database. PeanutBase has evolved to accommodate and integrate major data types from researchers and breeders. There are tools for exploring and visualizing the ancestral diploid and tetraploid genomes, along with genetic maps, markers, traits and information about varieties and diversity.

Q: What is PeanutBase? How can it be used?

A: PeanutBase is a repository for various data types from the research community and enables visualization and exploration of genetic and genomic data from IPGI and international research efforts. Site tools help users explore: the ancestral diploid and cultivated tetraploid genomes, along with genetic maps and markers from two genotyping chips; side-by-side comparison of genotype data; similarities between peanut genome regions and related genomes; browsing and mining genomic data; interactive geographic exploration of germplasm accessions; and phenotypic data visualization of the peanut mini core collection. Additional tools were integrated into PeanutBase to make genetic comparisons with other legume species. Molecular markers for important agronomic traits can be explored using the data and the tools. Researchers also deposit data here to fulfill journal publishing requirements.

The overarching objective is to make genomic data easily accessible and useful for incorporation into breeding programs, as well as to keep PeanutBase current with rapidly progressing research by integrating large amounts of new data.

Q: Where is PeanutBase Housed?

A: The USDA legume group at Iowa State University and the comparative legume group at the National Center for Genome Research (NCGR) in Santa Fe, New Mexico provided bioinformatic research support in legume genomics even before the initial legume genomes were sequenced. Because of their expertise, three legume databases are now established in Iowa (SoyBase, the Legume Information System (LIS) and PeanutBase).

When the ancestral diploid genomes were sequenced, it was better to establish PeanutBase to leverage the expertise and experience of this collaborative group in Iowa and New Mexico. It was a small step to initiate another legume genomics database in Iowa with a well-established computational hardware and software support system rather than starting from scratch elsewhere. Dr. Cannon's group provided the hardware support for PeanutBase. This saved the infrastructure cost for the Peanut Research Foundation (TPRF), helped PeanutBase mature rapidly, leveraged information-rich legume species at LIS and SoyBase, and took advantage of the expertise on comparative legume genomics at NCGR. The updated computational infrastructure for PeanutBase and LIS are now housed at NCGR in New Mexico.

Q: How will PeanutBase impact future research?

A: As researchers, we have a community-facing portal providing a single source for submitting, downloading and exploring genomics and related data. This saves time by avoiding having to go to multiple internet resources for data. Wherever possible the genetic data (maps, markers and mapped traits) have been integrated with the genomic data, making it possible for breeders to leverage the resource in their breeding programs. PeanutBase can acquire and integrate new data types when the community generates and needs them, e.g., pan-genome data involving many peanut cultivars and related wild species. Overall, it makes genomic data useful for peanut breeding programs for improved cultivar development.

Q: How have growers contributed to the creation of PeanutBase?

A: The mandate for the creation of PeanutBase came from the IPGI, which is supported by growers and other industry members. That initial stimulus from the growers along with the financial support from TPRF has catapulted PeanutBase as a successful portal for researchers. The continued financial support from TPRF reflects support from the grower community.

From A Researcher’s Perspective:

We also spoke to Dr. John Cason, Texas A&M AgriLife Research and Extension Center at Stephenville, to hear how researchers and peanut breeders, like himself, use PeanutBase.

Q: How have you used PeanutBase?

A: As part of an ongoing project, we used PeanutBase as a search engine for genes and gene families associated with drought-tolerance genes we identified in a wild species. We subjected two wild species to a midseason drought and collected RNA for a gene expression analysis. Once we had genes that were associated with drought, we searched PeanutBase for gene matches from the reference genome Arachis ipaensis. Currently, we are starting to use some of the markers to make early-generation selections and eliminate materials before investing a lot of money in them.

Q: How does PeanutBase add value to our industry?

A: The information starting to be available on PeanutBase is staggering. From my perspective in an applied breeding program, we need to screen for traits the industry wants as early as possible. Those are becoming increasingly available on PeanutBase. Personally, there has been a lag in deciding exactly how to use the information, but we have started putting things in place that allows us to take advantage of it. Now there are markers associated with traits we are interested in, and we have developed materials related to the parents the markers were found in. This makes it easy to deploy those markers in the program. All of that to say, large amounts of constantly growing research that is easily available in PeanutBase is a game changer for the progress that can be made and the speed at which we can make it.