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

Authors: BENTLEY, NOLAN - Texas A&M University; Grauke, Larry; KLEIN, PATRICIA - Texas A&M University

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/13/2018
Publication Date: 2/1/2019
Citation: Bentley, N., Grauke, L.J., Klein, P. 2019. Genotyping by sequencing (GBS) and SNP marker analysis of diverse accessions of pecan (Carya illinoinensis). Tree Genetics and Genomes. 15:8. https://doi.org/10.1007/s11295-018-1314-5.
DOI: https://doi.org/10.1007/s11295-018-1314-5

Interpretive Summary: Pecan trees are native to North America and have been used by people for thousands of years, but orchards developed by grafting were first established in the mid 1800s. Pecan trees have many things that make them hard to work with in tree breeding programs. They have separate male and female flowers that mature at different times on the same tree, encouraging cross pollination with other nearby pecan trees and sometimes with related hickories. That makes regional populations of trees very diverse. Trees are very large, slow to flower and bear fruit, and they live a long time. The US National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya) is a very large collection of grafted pecan trees. The USDA ARS Pecan Breeding Program has been actively breeding improved pecans since the early 1930s, using these trees. In a breeding program, it helps to know the identity of each tree, and if possible to know which trees were its parents. We know the geographic region where many of these trees came from, and how they perform under different conditions. We used a special group of 108 selected trees from this collection to develop new methods for identifying each tree, determining its parents, and finding out what geographic region they came from. We used these new techniques to discover new information about parentage for several trees. Since the genetic code for an individual tree is unique and does not change, these tools provide "fingerprints" to identify these trees. That can help nursery producers be sure they sell the right trees with the right names. We also tested to see if all of the trees that have the same type of bloom pattern share genetic "markers" that can separate them from trees with a different bloom pattern. Those tests found 17 markers that clearly separate two important bloom types of pecan. These markers should tell the bloom pattern of a young seedling, even before it gets old enough to bloom. This is an example of marker-assisted selection, which will continue to be developed with these techniques. This will help reduce the time needed to breed better pecan trees.

Technical 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 relatives, and interspecific hybrids between those species and pecan. 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.