Identification of Markers Contributing to White Mold Resistance in Peanut Using Quantitative Trait Loci Sequencing

Undergraduate #16
Discipline: Biological Sciences
Subcategory: Genetics

Estrella Gutierrez - New Mexico Highlands University
Co-Author(s): Josh Clevenger, University of Georgia, GA; Michael Gonzales, University of Georgia, GA; Scott Jackson, University of Georgia, GA

Cultivated peanuts (Arachis hypogea) are an important crop in several regions of the world for their high essential vitamin properties. Peanuts and peanut oil are used for human and animal consumption, and in a variety of consumer items including paint and furniture polish. Peanut production in the Southeast U.S. is afflicted by white mold, Sclerotium rolfsii, and has been for as long as peanuts have been produced in the United States. White mold is the number one cause of yield loss in a season and is particularly hard to manage with fungicides in arid climates. This study utilizes Quantitative Trait Loci sequencing (QTL-seq) to test if markers for white mold resistance can be developed faster and more efficiently. QTL-seq is an approach done by whole-genome resequencing of DNA from two populations showing a desired phenotypical trait and its opposite (i.e. resistance and susceptibility) for a rapid identification of plant QTLs. Our hypothesis is that QTL-seq methods can identify chromosomal regions and markers important to white mold resistance in peanuts. In this study, we phenotyped three years of recombinant inbred lines and ranked the top 5% mold-resistant and bottom 5% mold-susceptible phenotypes. The resistant and susceptible groups were sequenced and mapped to two reference genomes. We estimated allele frequencies at single nucleotide polymorphism sites for both groups, and we observed peaks indicating resistance on chromosomes A01 and A05. We then identified and developed markers spanning resistance hotspots on these chromosomes. These resistance markers are expected to facilitate future selection for mold resistance, which will help farmers cultivate healthier, higher yield crops and reduce the use of fungicides. With this information, the future direction would be to use QTL-seq to find resistance to other diseases peanut, or other plants, are facing.

Funder Acknowledgement(s): The National Science Foundation (NSF) SoyMap Summer Research Program (SSRP) University of Georgia (UGA)

Faculty Advisor: Dr. Josh Clevenger, jclev@uga.edu

Role: My part of the experiment was mapping the genome sequences of the resistant and susceptible bulks to the reference genome, counting alleles at SNP sites genomewide, and identifying significant peaks indicting the regions of resistance. I also developed and implemented markers to select plants for the validation test.