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

Abstract

Pecan ( Carya illinoinensis (Wangenh.) K. Kock) is a high value nut crop cultivated in many parts of the world. Several types of genetic markers have been developed for pecan and are useful for understanding pedigrees of native trees and improved cultivars. 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 relationship between wild pecan populations as well as that of improved cultivars. Population statistics derived from the provenance collection will help direct conservation efforts for the species. The impacts of the identified genetic variants were also evaluated at the amino acid level using an in silico approach. In addition, the amplification-refractory mutation system was used to highlight an ad-lib method for developing molecular markers from the resequencing information to help identify unknown individuals.

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