Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection

Authors: OTYAMA, PAUL - Iowa State University; WILKEY, ANDREW - Oak Ridge Institute For Science And Education (ORISE); KULKARNI, ROSHAN - Oak Ridge Institute For Science And Education (ORISE); ASSEFA, TESHALE - Oak Ridge Institute For Science And Education (ORISE); CHU, JULIET - University Of Georgia; CLEVENGER, JOSH - University Of Georgia; O'CONNER, DAN - Peanut Company Of Australia; WRIGHT, GRAEME - Peanut Company Of Australia; DZERN, STANLEY - University Of Florida; MACDONALD, GREGORY - University Of Florida; ANGLIN, NOELLE - International Potato Center; CANNON, ETHALINDA - Iowa State University; OZIAS-AKINS, PEGGY - University Of Georgia; Cannon, Steven

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2019
Publication Date: 6/11/2019
Citation: Otyama, P.I., Wilkey, A., Kulkarni, R., Assefa, T., Chu, Y., Clevenger, J., O'Conner, D.J., Wright, G.C., Dezern, S.W., MacDonald, G.E., Anglin, N.L., Cannon, E.K.S., Ozias-Akins, P., Cannon, S.B. 2019. Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics. https://doi.org/10.1186/s12864-019-5824-9.
DOI: https://doi.org/10.1186/s12864-019-5824-9

Interpretive Summary: An important challenge for improvement of any crop is to identify genetic markers that can be used to efficiently select for valuable traits. For peanut, a new resource to assist with this process is a high-density array (a "genotyping array") for determining the DNA bases at approximately fifty thousand chromosomal locations, for any given plant sample. Those DNA bases can then be used as genetic markers and tested for associations with traits. The genotyping array was used to characterize the DNA marker states for a set of 107 diverse plant samples comprising the U.S. "mini core" collection of peanut varieties, as well as six selected commercial varieties. The genetic markers for these plant varieties were then checked for associations with seventeen traits of interest, including oil quality and other nutritional characteristics. This research reports marker-trait associations for three of the traits, including for two varieties of fatty acids and for blanchability (an important peanut processing characteristic). This research will be used by breeders to develop peanut varieties with improved nutrition and processing characteristics.

Technical Abstract: A high-density SNP array with 58,000 positions was used to genotype the U.S. peanut mini core collection of 107 diverse accessions plus six select commercial varieties. This research is a report of linkage disequilibrium (LD), population structure, and genetic diversity in the U.S. peanut mini core, using 13,527 markers from the full SNP array, selected to be informative and interpretable within this collection. LD persists over long distances in the collection, decaying to r2 = half decay distance at 3.78Mb. Structure within the collection is best explained when separated into four or five groupings, with accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing data or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market class. Genome wide association (GWA) analysis was performed on these lines for 17 seed quality traits. Strong marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. A reduction of these fatty acids is a possible breeding objective. Other traits such as blanchability showed significant associations in multiple tests, with plausible candidate genes. Blanchability is an important processing trait for uses such as for confectionary and peanut butter. Based on genome-wide association analysis and population structure results, as well as additional simulation results, we find that the primary limitations of this collection for GWA studies are population size and significant remaining structure. These results can be used to improve GWA results in future studies.