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There and back again: Using whole genome sequencing to identify the genes associated with migration patterns in rainbow trout
Sachdeva, Shriya
Sachdeva, Shriya
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Date
2022
Additional date(s)
5/19/2022
Abstract
Migration, which is defined as the seasonal movement for survival or reproductive advantage such as access to resources, is a behavioral phenomenon exhibited by many species including the salmonid Oncorhynchus mykiss. More commonly known as rainbow trout, O. mykiss exists in two life histories: migrants (steelhead trout), and residents (rainbow trout). While there are many factors that contribute to this variation in migration behavior, one of the reasons is their genetic makeup since there is an apparent correlation between the migratory behavior of parents and their offspring. The primary objective of this research project is to identify single nucleotide polymorphisms (SNPs), or genetic differences, which are associated with migratory behavior in rainbow trout. To that end, I used whole genome sequence data from five migrant and five resident rainbow trout. These data were aligned to the trout genome and used to locate genetic differences between the two migratory types. Quantitative PCR (DMAS-qPCR) approaches were used to validate the SNPs and genotype them in a larger set of twenty-five migratory steelhead. Research findings exhibited that Sashin Lake is producing smolts (young migratory steelhead) that are successfully returning to the lake and reproducing at the end of their life cycle. Additionally, while there was not a significant difference seen in terms of marine survival between the sexes, females were more likely to migrate compared to their male counterparts due to the reproductive advantage and greater access to resources that migration offers. This data will support future studies observing trout migratory behavior with larger sample sizes and from different generations and settings and will benefit conservation studies regarding population decline in migratory species.
Contents
Subject
Genes
Rainbow
Trout
Migration
Sashin
Steelhead
O. mykiss
Salmon
Salmonid
Oncorhynchus mykiss
Alaska
PCR
Hardy-Weinberg Equilibrium
genome
sequencing
bioinformatics
samtools
sam
bam
ANGSD
PCR
qPCR
Rainbow
Trout
Migration
Sashin
Steelhead
O. mykiss
Salmon
Salmonid
Oncorhynchus mykiss
Alaska
PCR
Hardy-Weinberg Equilibrium
genome
sequencing
bioinformatics
samtools
sam
bam
ANGSD
PCR
qPCR
Subject(s)
Research Projects
Organizational Units
Journal Issue
Genre
Description
Format
Department
Biology