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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #423114
Research Project: Healthy, Sustainable Pecan Nut Production

Location: Fruit and Tree Nut Research

Title: Comprehensive resequencing reveals new genetic polymorphisms applicable to wild and cultivated pecan

Author
item Brungardt, Jordan
item ALARCON, YANINA - University Of Texas Southwestern Medical Center
item MONTEROS, MARIA - Bayer Cropscience
item Chatwin, Warren
item RANDALL, JENNIFER - New Mexico State University
item BOCK, CLIVE - US Department Of Agriculture (USDA)

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2025
Publication Date: 12/15/2025
Citation: Brungardt, J.J., Alarcon, Y., Monteros, M.J., Chatwin, W.B., Randall, J.J., Bock, C.H. 2025. Comprehensive resequencing reveals new genetic polymorphisms applicable to wild and cultivated pecan. Genetic Resources and Crop Evolution. 73. Article 46. https://doi.org/10.1007/s10722-025-02651-1.
DOI: https://doi.org/10.1007/s10722-025-02651-1

Interpretive Summary: Pecan is a high value nut crop grown throughout the world. Genetic markers play an increasingly important role in breeding, pedigree analysis, and identification of value added traits. The amount of useful information for any given marker set often depends on the density with which it covers a given genome. Genotype-by-sequencing (GBS) implements high-throughput DNA sequencing to identify large amounts of genetic variation within a given species. Several previous GBS experiments using pecan have been performed, but have a relatively low amount of theoretical genome coverage, do not have publicly available markers, and/or have limited power due to using a fragmented genome as a reference. The research presented here exploited the large amount of genetic diversity found in the pecan provenance collection at the USDA-ARS Byron, GA location as well as historical pecan cultivars located at the USDA-ARS Sommerville, TX location to identify 12.8 thousand genetic markers of pecan via GBS. The method of performing GBS in this research was changed slightly to dramatically increase the amount of theoretical genomic marker coverage compared to previous research. The resulting information was used to infer pedigrees, identify mislabeled plants, and to develop a low-cost, flexible system for identifying specific cultivars and offspring of successful controlled crosses.

Technical Abstract: Pecan (Carya illinoinensis (Wangenh.) K. Kock) is a high value nut crop cultivated in many parts of the world. Genetic markers of different types have been developed for this species to address questions about pedigrees of improved cultivars and it’s early dissemination. Presented here is a publicly available 12.8 thousand marker-set developed from Illumina next-generation sequencing of sixty-three cultivars and 871 trees from a pecan provenance collection. The resulting information gives unprecedented resolution of the genetic relationships between wild pecan populations as well as that of improved cultivars. Consequences of the identified genetic polymorphisms were evaluated at the proteome level in silico. In addition, the amplified refractory mutation system was used to highlight an ad-lib method for developing molecular markers from this information to help identify unknown individuals.