Nuclear and Mitochondrial SNP Development for Molecular Discrimination of Bighead Carp, Silver Carp, and Their Hybrids

Although interspecific hybridization among bighead and silver carp is known to occur beyond the F₁ generation in the United States, the extent of backcrossing and subsequent hybridization events can be masked by an inadequate number of loci examined and the lack of discriminating power of the existing molecular probes.  We have identified several thousand nuclear SNPs diagnostic to parental bighead and silver carp that can be consistently assayed from US and Chinese populations to detect parental bighead carp, parental silver carp, and their multiple levels of admixture.  Additionally, we obtained one mitochondrial SNP diagnostic for each parental species to investigate the species-specific gender contribution to the hybrid offspring.   SNPs were identified by shotgun sequencing of pooled US and Chinese bighead and silver carp, separately.   The Illumina reads were mapped to bighead and silver carp mitochondrial genomes and also zebrafish nuclear genome.  A representative sample of 60-80 markers were selected from the nuclear SNPs based on their chromosomal position and location within functional genes of evolutionary significance.  The resulting markers will assist in detection of multi-generational hybrids, the directionality of hybridization, their prevalence throughout the Mississippi River basin, and hybridization implications on fitness and morphology.