Chinook Salmon Genetics

Recreational Fishing Grants Program Research Report

May 2013

Executive summary


Chinook salmon (Onchorhynchus tshawytscha), the largest species of Pacific salmon, is naturally distributed along the west coast of North America and in north-east Asia. The species was first introduced to Victorian waters in 1877, and in the late 1960s a captive breeding program was established at Snobs Creek to produce fish for a recreational capture and trophy fishery in western district crater lakes (Lake Purrumbete and Lake Bullen Merri). Since 1980, 932,500 Chinook salmon have been released.

The production of Chinook salmon from Snobs Creek has fallen dramatically over the past six years, and no fish have been released since 2007. This decline in production has been attributed to many factors including poor broodstock condition, changes in husbandry practices over time, and genetic factors. As part of a series of activities to improve production of Chinook salmon, this study was undertaken to describe and characterise the genetic structure of the captive population at Snobs Creek using microsatellite DNA markers, and to develop broodstock management guidelines to ensure the long-term genetic "fitness" of the stock and viability of the fishery.

Over the 13 microsatellite loci examined, 87 alleles were detected from samples of Chinook salmon held in captivity at Snobs Creek. Genetic analyses indicated reduced genetic diversity in this population compared to North American Chinook salmon populations. All genetic diversity indices (HeHo, number of alleles, allele richness and Ne) observed in the Snobs Creek Chinook salmon were lower than that reported in the Lower Columbia River lineage of Chinook salmon, the original source area of the Snobs Creek population. Although there was no evidence of bottleneck or inbreeding, a small number of individuals were closely related and had the inbreeding levels equivalent to halfsib parents or closer (if assuming no previous inbreeding). These results demonstrate the need to improve the management of the Snobs Creek Chinook salmon to ensure the long-term genetic "fitness" of the population.

Results from this study, along with information from other published genetic guidelines for breeding programs, were used to develop guidelines, in the form of 14 recommendations, for improved genetic management of Chinook salmon broodstock held at Snobs Creek.

These recommendations, which specifically aim to prevent loss of genetic diversity and minimise inbreeding within the population, include:

  • Create a "broodstock population", which will be kept separate from fish that are reared for stocking ("stocking population")
  • Spawn as many broodstock from the "broodstock population" as possible each year
  • Split the "broodstock population" across several culture systems, locations or facilities to minimise the impact of a dramatic loss of broodstock numbers from mortality events
  • Spawn an equal number of female and male fish each year
  • Consider establishing a frozen sperm bank to improve management of broodstock numbers and sex ratio
  • Spawn each male broodstock once only
  • Undertake single-pair (one female and one male) matings only
  • Consider 2 x 2 partial factorial mating design
  • Incubate eggs from each single-pair mating separately
  • Retain equal numbers of progeny from each spawning (family) as potential future broodstock. Nominally this number should be 50 randomly selected larvae per spawning
  • Avoid mating siblings by using males from a different year class to females
  • Maintain detailed and accurate breeding records
  • Re-assess the genetic status of the Chinook salmon "broodstock population" every 3 to 4 years
  • Develop BMP for Chinook salmon breeding and rearing at Snobs Creek.

Adoption of these recommendations will enhance production of more genetically "fit" seedstock for both breeding and release to the recreational fishery.

Further Information

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