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25 April 2024 |
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Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish | | Mikhail Spivakov
; Thomas O. Auer
; Ravindra Peravali
; Ian Dunham
; Dirk Dolle
; Asao Fujiyama
; Atsushi Toyoda
; Tomoyuki Aizu
; Yohei Minakuchi
; Felix Loosli
; Kiyoshi Naruse
; Ewan Birney
; Joachim Wittbrodt
; | | Date: |
16 Apr 2013 | | Abstract: | Background Oryzias latipes (Medaka) has been established as a vertebrate
genetic model for over a century, and has recently been rediscovered outside
its native Japan. The power of new sequencing methods now makes it possible to
reinvigorate Medaka genetics, in particular by establishing a near-isogenic
panel derived from a single wild population. Results Here we characterise the
genomes of wild Medaka catches obtained from a single Southern Japanese
population in Kiyosu as a precursor for the establishment of a near isogenic
panel of wild lines. The population is free of significant detrimental
population structure, and has advantageous linkage disequilibrium properties
suitable for establishment of the proposed panel. Analysis of morphometric
traits in five representative inbred strains suggests phenotypic mapping will
be feasible in the panel. In addition high throughput genome sequencing of
these Medaka strains confirms their evolutionary relationships on lines of
geographic separation and provides further evidence that there has been little
significant interbreeding between the Southern and Northern Medaka population
since the Southern/Northern population split. The sequence data suggest that
the Southern Japanese Medaka existed as a larger older population which went
through a relatively recent bottleneck around 10,000 years ago. In addition we
detect patterns of recent positive selection in the Southern population.
Conclusions These data indicate that the genetic structure of the Kiyosu Medaka
samples are suitable for the establishment of a vertebrate near isogenic panel
and therefore inbreeding of 200 lines based on this population has commenced.
Progress of this project can be tracked at
this http URL | | Source: | arXiv, 1304.4515 | | Services: | Forum | Review | PDF | Favorites | |
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