Insights into the genomic architecture of seed and pod quality traits in the U.S. peanut mini-core diversity panel

Authors: PATEL, JINESH - Auburn University; Wang, Ming; Dang, Phat; Butts, Christopher - Chris; Lamb, Marshall; CHEN, CHARLES - Auburn University

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2022
Publication Date: 3/22/2022
Citation: Patel, J.D., Wang, M.L., Dang, P.M., Butts, C.L., Lamb, M.C., Chen, C.Y. 2022. Insights into the genomic architecture of seed and pod quality traits in the U.S. peanut mini-core diversity panel. Plants. 11(7):837. https://doi.org/10.3390/plants11070837.
DOI: https://doi.org/10.3390/plants11070837

Interpretive Summary: One primary goal of peanut breeding and genetics is to determine which genes are responsible for specific desired traits. Some traits such as seed size and the percentage of intact seed kernels produced after shelling are important because they affect the quality and yield of the crop at harvest. Seed dormancy is also important in preventing the kernels from sprouting prematurely in their pods before harvest which can also affect total yield. Because peanut collections show large amounts of variation in many important traits, and we used a sample of the USDA collection to measure the variation in seed size, shelling percentage, kernel quality, and dormancy. Then we studied the genetics of the population using the most recently developed analytical tools and compared these results to the trait variation to pinpoint and identify the genes that code for the traits. Using this powerful technique of trait association, we were able to determine several possible candidate genes which can be analyzed in more detail in the future. Knowing these genes will then help peanut researchers to breed peanut lines with improved kernel quality and total crop yield.

Technical Abstract: Traits like seed weight, shelling percent, percent sound mature kernels and seed dormancy determines quality of peanut seed. Few QTL studies using bi-parental mapping populations have identified QTL for seed dormancy and seed grade traits on different genomic regions. Here, we report a genome-wide association study (GWAS) to detect marker-trait associations for seed germination, dormancy and seed grading traits in peanut. A total of 120 accessions from U.S. peanut mini core collection were evaluated for seed quality traits and genotyped using Axiom SNP array for peanut. We observed significant variation for seed quality traits in different accessions and different botanical varieties. Through GWAS, we were able to identify multiple regions associated to sound mature kernels, seed weight, shelling percent, seed germination and dormancy. Some of genomic regions that were SNP associated to these traits aligned with previously known QTLs. For instance, QTL for seed dormancy has been reported on chromosome A05 and we also found SNP on same chromosome associated with seed dormancy explaining around 20% of phenotypic variation. In addition, we found novel genomic regions associated with seed grading, seed germination and dormancy traits. Numerous genes were identified in the surrounding regions of the associated SNP that play vital roles during seed development. In summary, our work will provide markers that could be incorporated in breeding program to accelerate selection process for seed quality, improve fresh seed dormancy and explore the function of candidate genes to understand the complex genetic network that governs seed quality.