A public mid-density genotyping platform for pecan [Carya illinoinensis (Wangenh.) K. Koch]

Pecan [Carya illinoinensis (Wangenh.) K. Koch] is the fifth-largest tree nut in global cultivation, with 80% of production occurring in the southern states of the United States. Despite the economic and health benefits of pecans, there is a lack of genomic tools available to breeders for crop improvement. The pecan breeding community is small, and most breeding programs have many barriers to adopting technology, particularly in the cost and know-how needed to create and use genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag (Diversity Array Technology [DArT]) panel of 3100 loci distributed across the diploid pecan genome for use in molecular breeding and genomic prediction. Here, we show the panel's ability to distinguish key parents and founders of cultivated pecan from other Carya species that may be used in pre-breeding. We also demonstrate that the resultant data can create a linkage map in a biparental population. The creation of this marker panel brings cost-effective and rapid genotyping capabilities to pecan breeding programs, making routine genotyping a reality for any pecan breeder. Furthermore, the open access provided by this platform enables the comparison and integration of genetic datasets generated on the marker panel across projects, institutions, and countries.