USGS, Southern Illinois University researchers advance genome mapping for critically-endangered sturgeon

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This scientific advancement can lead to the development of new genetic markers that will help scientists distinguish between pallid sturgeon and the shovelnose sturgeon, another sturgeon species that looks similar but is more common.

In a genetics breakthrough that may help detect and conserve one of North America’s most endangered fish species, researchers from the U.S. Geological Survey’s Columbia Environmental Research Center and Southern Illinois University Carbondale recently produced offspring of endangered pallid sturgeon with DNA from only a single parent. These offspring are not ‘clones’, which are exact copies of an individual, they have only half the DNA from just the female parent.  

This scientific advancement can lead to the development of new genetic markers that will help scientists distinguish between pallid sturgeon and the shovelnose sturgeon, another sturgeon species that looks similar but is more common. 

“Genetic identification of pure pallid sturgeon is critical to guide species recovery and management efforts and preserve genetic diversity” said USGS biologist Kimberly Chojnacki, a co-author of the scientific paper about this important step in pallid sturgeon conservation.

The pallid sturgeon is a rare species native to the Mississippi and Missouri River basins. Pallid sturgeon are known to hybridize with the more common and closely related shovelnose sturgeon and produce fertile offspring which are not endangered.  

The two species are so similar in appearance that biologists sampling fish in rivers cannot tell the difference between pallid sturgeon and pallid-shovelnose hybrids using body characteristics.  This complicates efforts to monitor and recover the endangered species.

Furthermore, existing genetic markers cannot reliably distinguish among pure pallid sturgeon, shovelnose sturgeon and hybrids of the two species. Researchers need a panel of hundreds to thousands of genetic markers as references so they can make these distinctions.

The long evolutionary history of sturgeon, stretching back millions of years, has left the pallid sturgeon with twice as many paired chromosomes as most other species. This complicates genetic studies, but scientists used a novel strategy to overcome this complication which will allow for the identification of additional genetic markers. 

Scientists used genetically deactivated sperm from distantly related male paddlefish, and eggs from a female pallid sturgeon, to successfully produce pallid sturgeon offspring with the genetic makeup of only the female parent, which simplifies genetic analysis. 

 

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Left, a haploid pallid sturgeon specimen (DNA only from one parent) at approximately 11-12 days after hatching. The simplified DNA of these specimens is needed to develop new genetic markers; however none of the specimens were reared beyond the collection of tissue for genetic analyses.  Right, a  pallid sturgeon with two parents. Photo credit: U.S. Geological Survey. 

“This joint research is the first critical step in the development of thousands of new, cost-effective genetic markers necessary to unravel differences between the two species and conserve the distinctiveness of one of North America's most endangered large river species,” said USGS ecologist Aaron DeLonay, co-author on the study. 

This is the first time scientists have successfully overcome complications of the complex genome of the pallid sturgeon.  

“This is an innovative method for developing genetic tools for organisms, such as the pallid sturgeon, with unusually large genomes,” said the study’s lead author, Richard Flamio Jr., Southern Illinois University, Carbondale.   

The paper “Production of haploid gynogens to inform genomic resource development in the paleotetraploid pallid sturgeon (Scaphirhynchus albus)” was published in Aquaculture on March 1, 2021 and can be found here:https://doi.org/10.1016/j.aquaculture.2021.736529