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Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons
Author(s) -
Flamio Richard,
Swift Dominic G.,
Portnoy David S.,
Chojnacki Kimberly A.,
DeLonay Aaron J.,
Powell Jeffrey,
Braaten Patrick J.,
Heist Edward J.
Publication year - 2025
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13742
Subject(s) - biology , sturgeon , microsatellite , polyploid , ploidy , locus (genetics) , introgression , genetics , genetic marker , evolutionary biology , endangered species , hybrid , allele , fishery , gene , ecology , botany , habitat , fish <actinopterygii>
Abstract Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon ( Scaphirhynchus albus ) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon ( S. platorynchus ) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site‐associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced‐representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.