2017 ASHS Annual Conference

Pecan (Carya illinoinensis) is an outcrossing, highly heterozygous, and slow to mature tree native to North America. The USDA ARS Pecan Breeding Program worked with verified pecan cultivar collections of the National Collection of Genetic Resources for Pecans and Hickories to develop microsatellite molecular markers capable of verifying cultivar identity and parentage. By working within range-wide provenance collections of pecan and other Carya species, patterns of regional genetic variation have been observed. In order to better understand cultivar characteristics, appreciate regional adaptation, and improve selection in the USDA ARS and other pecan breeding programs, improved genomic tools are necessary that are cost effective and capable of high-throughput screening. A diverse panel of 108 cultivars and accessions was selected to represent historic use by regional pecan producers, with many controlled cross progeny and both parents represented within the panel. A 169 member biparental mapping population designed to segregate on reaction to pecan scab (Venturia effusa) was also analyzed. We have implemented a genotyping by sequencing (GBS) technique to discover over 87,446 single nucleotide polymorphisms (SNPs) throughout the pecan genome. This is the first reported use of this technology in pecan and represents a large step forward in the industry’s ability to measure genetic relationships with high resolution. From these markers, we have discovered, confirmed, and refuted many pedigree-level relationships between cultivars. Twenty-one accessions of known geographic origin show strong regional genetic variations and have been utilized to characterize the genetic backgrounds of cultivars of ambiguous origin. A genome wide association study (GWAS) was performed to discover 39 SNPs across five contigs significantly associated with expression of the simply inherited trait controlling flowering type (heterodichogamy). Finally, 6,756 SNPs segregating in the mapping population were used to develop a genetic linkage map. These resources are intended to benefit the pecan community by improving the ability to characterize germplasm and utilize marker data to reduce breeding time by facilitating more informed and efficient selection.