Genotyping by sequencing (GBS) and SNP marker analysis of diverse accessions of pecan (Carya illinoinensis)

Abstract

Pecan (Carya illinoinensis) is an outcrossing, highly heterozygous, and slow-to-mature tree native to North America. In order to better understand cultivar characteristics, appreciate regional adaptation, and improve selection in pecan breeding programs, improved genomic tools that are cost-effective and capable of high-throughput screening are necessary. A diverse panel of 108 cultivars and accessions from the National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya) was selected to represent regionally adapted native pecans, controlled cross progeny and their parents, selected wild relative species, and interspecific hybrids between those species and pecans. We implemented a genotyping-by-sequencing (GBS) technique to discover 87,446 informative single nucleotide polymorphisms (SNPs) throughout the pecan genome. SNPs were used to develop genomic profiles to confirm, refute, or inform questions of cultivar origin. Native accessions show strong genetic relationships by geographic region of origin. Matrices were developed to facilitate evaluation of pedigree relationships between cultivars. A genome-wide association study (GWAS) was performed to discover 17 SNPs from a contiguous region significantly associated with the expression of the simply inherited trait controlling flowering type (dichogamy). The information, techniques, and resources developed will benefit the pecan community by improving the ability to characterize germplasm and use marker data for marker-assisted breeding. This should reduce breeding time by facilitating more informed and efficient selection of parents and progeny.