Grandparent Inference from Genetic Data

Steelhead hatcheries in the Snake River Basin support conservation and fisheries management but risk genetic introgression into wild populations through hatchery-origin straying. This study addresses multi-generational genetic monitoring of hatchery impacts on ESA-listed Snake River Steelhead using advanced grandparentage inference technology. A new genetic marker panel (Omy287), consisting of 287 microhaplotype loci, was developed and validated, achieving high genotyping success (>90%) and robust genetic diversity. Empirical error testing across hatchery broodstock showed minimal false-positive and acceptable false-negative rates, further improved by incorporating detailed hatchery metadata.



Analysis of wild steelhead adults (2020–2021) and juveniles (2018) identified hatchery genetic contributions across generations. Among adults, 19.1% had hatchery ancestry, primarily from Lyons Ferry, Sawtooth, Dworshak, and Pahsimeroi hatcheries. Juvenile assignments revealed hatchery-origin ancestry in 6.2%, with notable detection in Marsh Creek, an area managed strictly for wild fish.



The integration of grandparentage inference significantly enhances traditional parentage-based tagging, enabling robust assessment of multi-generational hatchery introgression. This technology supports adaptive management, conservation planning, and regulatory compliance, providing critical insights into long-term genetic effects of hatchery programs on wild steelhead populations.



Genotypes produced from this project are publicly available at the FishGen Database Repository (FishGen - A repository for salmon and steelhead genetic data). FishGen.net is a final repository for salmon and steelhead genetic data as part of Genetic Stock Identification and Parentage Based Tagging projects in the Columbia River basin and throughout the Pacific Coast of North America.



This project completed an amendment to extend and to increase by 10% of the award amount ($9,521) in October 2024. IDFG applied for and was awarded more funds ($30,000) in Round 27 in Dec 2024 and an extension to allow IDFG to develop and test the new genetic technology on juveniles as well as adults. This project was funded from FY20 and FY21 using Priority 2 funds. All funds were expended within the FY20 grant life cycle.

Quantifying straying in salmonid populations is difficult, particularly for steelhead that return to spawn on the peak of spring snowmelt when water flows are high and water is turbid. In addition, their iteroparous life-history means that few carcasses are available for recovery. These factors preclude the use of typical monitoring methods such as weir trapping and spawning ground surveys (Campbell et al 2012). Even if identifying and enumerating straying hatchery steelhead was possible, the major genetic concerns involve whether those fish successfully spawn with wild fish. If the feasibility of Grandparentage testing technology is demonstrated, this will provide a powerful new tool for monitoring risks posed from straying hatchery fish. This type of monitoring is directly called for in the NMFS recovery plan for Snake River steelhead (NMFS 2017).