Abstract Detail

Hybrids and Hybridization

Literman, Robert [1], Ott, Brittany [2], Wen, Jun [3], Grauke, L.J. [4], Schwartz, Rachel [5], Handy, Sara [6].

Reference-free discovery of millions of SNPs permits species and hybrid identification in Carya (Hickory).

DNA-based species identification assays like the development of species-specific PCR primers or the profiling of single-nucleotide polymorphisms (SNPs) are required when morphological identification is not possible, as is case for many processed food products and dietary supplements. Most DNA-based pipelines rely on the ability to identify and compare homologous sequences; yet, in the absence of genomic resources (i.e. well-annotated genomes or large annotated locus sets) the development of these assays can become restricted to a small set of well-characterized loci. In plants, chloroplast genomes are smaller and more well-characterized than their nuclear counterpart; yet much of the chloroplast genome is conserved among closely related species, and the utility of chloroplast markers will be restricted if variable sites evolve either too quickly or slowly to capture and maintain reliable signal. Additionally, in clades where consumable species readily hybridize such as in the genus Carya (pecan and hickories), chloroplast markers alone are typically unable to identify hybrid specimens due to their maternal inheritance. Here, we present a bioinformatics pipeline requiring no underlying reference genome or annotation data and apply it to low-coverage Carya genome skim data to identify over one million nuclear species-diagnostic SNPs capable of distinguishing samples among diploid Carya species. These SNPs were also useful for identifying hybrid specimens, even at low sequencing depths. Because many clades still lack even basic genomic resources, including clades of allergenic concern like nut-bearers, reference-free pipelines like this will provide a powerful tool aiding in the development of robust and reliable species assays.

1 - United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-706, 5001 Campus Dr. , College Park, MD, 20740, USA
2 - United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-706, 5001 Campus Dr., College Park, MD, 20740, United States
3 - Botany, MRC-166 National Museum Of Natural History, 10th St. & Constitution Ave., NW, Mrc 166, Washington/DC, 20013, United States
4 - United States Department of Agriculture (Retired), Agricultural Research Service Pecan Breeding & Genetics, Somerville, TX, United States
5 - University of Rhode Island, Department of Biological Sciences, Kingston, RI, United States
6 - HFS-717, 5001 Campus Dr., College Park, MD, 20740, United States

Keywords:
hybridization
Carya
bioinformatics
genomics.

Presentation Type: Oral Paper
Session: HH1, Hybrids and Hybridization I
Location: /
Date: Wednesday, July 21st, 2021
Time: 10:30 AM(EDT)
Number: HH1003
Abstract ID:291
Candidate for Awards:Margaret Menzel Award