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Final Report Summary - QGEN-DS (Demographic and Selective effects on the Quantitative Genetics of Ninespine Sticklebacks)

-- Summary description of the project objectives
The goal of this project was to understand the genetics of size differences between different and unrelated populations of ninespine sticklebacks, a fish that is present across the Northern Hemisphere with a circumpolar distribution, in both fresh and salt waters. From a scientific standpoint our goals were multiple. The first was to broadly understand the genetics of body size, which is a major determinant of a large number of biological and evolutionary processes. The second was to ascertain whether the same genetic basis underlie the independent evolution of large body size in unrelated populations. Finally we were interested in understanding whether it is possible to maintain genetic variation for body size despite selection – this specific question would be particularly relevant for the genetic variability of organisms that are selected for commercial traits.

-- Description of the work
The approach we used was to cross fish from large and small-bodied populations, creating a hybrid population where each individual half the genetic material comes from the small population and half form the large population. Two full sibs are the crossed to create a recombinant progeny (technically a F2 generation) where each fish has a different genotype combination and a different body size. Both phenotypic and genetic information are then used to identify the genetic regions associated with the phenotypic differences.

We created three F2 generations from three independent crosses between small and large populations. We were successful in producing very large F2 generations in each cross (between 280-310 F2 individuals), giving us a unique power to detect association between genotype and phenotype. In addition each F2 fish was measured for growth at regular intervals, providing us with growth patterns and final body size.

Using Next Generation Sequencing techniques we also generated a wealth of genomic data for these three crosses, with the added benefit that a large amount of these genomic data can be used on any ninespine sticklebacks and not simply in our crosses. Specifically we have identifies in excess of 50000 Single Nucleotide Polymorphisms (SNP) markers on the ninespine genome.

-- Description of the main results achieved
Taking advantage of the data we generated we were able to create three genetic maps (one for each cross) and a more general consensus genetic map with data from all three crosses. This information has been already used in correctly assembling the data used to create a physical map of the ninespine genome.

We also successfully mapped the genomic architecture of brain size to different chromosomes using the genetic and phenotypic data from one of our crosses.

Additionally, using some of the markers developed from the F2 data we were able to identify that the ninspine collected from and Artic Swedish lake are one single population despite the fact the fish utilise discrete habitats within the lake.

Thanks to the uniquely large F2 generations we were also able to identify regions of the genome showing an abnormal pattern of inheritance between parents and offspring. We were able to identify different areas of the genome that contain recessive lethal alleles and to ascertain that these lethal alleles are unique to each cross.

Finally, we are now in the process of analysing the genetics of body size.

-- Final results and their potential impact and use (including the socio-economic impact and the wider societal implications of the project so far)
We see two different kinds of impacts from the work carried out during this fellowship. On one hand we have produced a wealth of genomic data and analytical methods that have been shared with the scientific community, allowing to use the ninespine stickleback as a new model organism and as an important testing grounds for the empirical verification of the generality of findings obtained from work on other species. On the other hand our work on the evolution of body size will have interesting consequences for aquaculture (in the specific) and animal and plant breeding (in a broader sense). Our goal to identify the loci affecting body size in different and unrelated populations will give us the ability to understand (1) what loci are involved in controlling body size and (2) whether the same loci are affecting body size in every circumstances where we observe variations between populations. Because body size is an important commercial trait it will be possible to understand how selection for body size and growth is affecting the level of genetic diversity in commercially kept stocks: if for instance it is possible to select for body size using different loci in different stocks it would be possible to preserve the largest amount of genetic variability in a species of economic interest, while at the same time maximising the productivity of the stock.

-- A summary of the progress of the researcher training activities/transfer of knowledge activities/integration activities (as it applies for the MC action)
After successfully passing a postgraduate teaching course provided his publication and research curriculum for external evaluation. His teaching competence was tested as he presented a lecture in front of a University Pedagogy Commission and based on his curriculum and his teaching skills the researcher was awarded the title of Docent by the University of Helsinki (Docentship HY/91/01.08.03/2016), providing him with a full Higher Education Teaching qualification for both undergraduate and postgraduate teaching, and the qualification to lead a research group at University level.

The work has been presented in two conferences (the 8th International Stickleback conference at Stony Brooks in 2015 and the Evolution Meeting in Austin in 2016), has produced three publications and has been presented to American and Canadian students participating in the EuroScholars program. The genetic data and the genetic map have also been used in collaboration with the Norwegian group led by Prof. Kjetill Sigurd Jakobsen who is creating a physical map of the ninespine genome.

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