Development and characterisation of novel microsatellite loci for the baldchin groper (Choerodon rubescens) and cross-amplification in seven other labrid species

Abstract

15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 2 Abstract 42We describe the development and characterisation of novel microsatellite loci for the baldchin groper, 43Choerodon rubescens. The purpose was to identify loci that can be used to resolve uncertainties about 44 the population (stock) structure of this fish species, which is endemic to a narrow region of the west 49Cross-amplification of the 12 loci in 7 other labrid species was often successful, especially in 50 congeners. 52Keywords Choerodon· Labridae · microsatellite marker · population structure 54The baldchin groper, Choerodon rubescens, is a large, long-lived labrid endemic to a region of 62Ideally, the processes that are put in place to manage the fisheries for C. rubescens should 63 operate at a spatial scale(s) relevant to the population (stock) structure of this species; as yet this 64 structure is unknown. This paper describes the development, characterisation and testing of novel 65 microsatellite markers for C. rubescens. These markers were developed primarily for resolving 66 uncertainties about the population structure of this species, however, their ability to cross-amplify loci 67 in 7 other labrid species was also assessed. Very few studies have published microsatellite markers for 109The 12 loci were also tested on 7 other labrid species, using the same conditions as described 110 above for C. rubescens. In general, the loci worked very well with the cogeners C. schoenleinii and C. 111cyanodus, for which, respectively, 8 and 9 loci were amplified with 100% success (Table 2). At least 112 one polymorphic locus (and usually more) was amplified with 100% success from each of the 7 species 113(see Table 2). 114 Acknowledgments 115We thank Frances Brigg (SABC, Murdoch University) for advice about fragment analysis and 116 operating the ABI 3730. We also thank David Fairclough, Gary Jackson, Jeff Norriss and other staff of 117

Fisheries genomics of snapper (Chrysophrys auratus) along the west Australian coast

“…Although the time periods covered preclude investigation across multiple generations, they are adequate for assessing interpopulation migration and population range shifts as a result of temporal variation in recruitment or population density (information important in fisheries management). The Cockburn Sound samples were collected by DPIRD WA staff as part of a fisheries independent survey, while the Esperance samples were collected by DPIRD WA staff from commercial catch for a former population genetics project (see Gardner et al, 2014Gardner et al, , 2017Gardner & Chaplin, 2011).…”

“…Recent mark‐recapture work on the lower west coast of WA indicated that adult movement is largely limited to spatial scales of <20 km, although this estimate is probably influenced by spatial variability in fishing effort (Crisafulli et al, 2019). Microsatellite DNA analyses have suggested that snapper in WA are characterized by an isolation by distance pattern of population structure, rather than genetically distinct subpopulations (Gardner & Chaplin, 2011). Otolith microchemistry studies have reported different patterns of mixing during different life stages as well as a range of patterns of spatial differentiation using different chemical tags (Edmonds et al, 1999; Fairclough et al, 2013).…”

Pelagic early life stages promote connectivity in the demersal labrid Choerodon rubescens

“…The PCR protocols, primer sequences and locus characteristics are as described by Gardner et al (2011).…”

Isolation and characterisation of novel microsatellite markers from Pagrus auratus and cross amplification in Acanthopagrus butcheri

“…Unless otherwise stated, methods were as described in Gardner et al (2011). Four partial genomic libraries, enriched for TAGA, CAGA, CA and ATG motifs, were constructed.…”

“…Primer pairs were designed for 35 loci. The PCR mixtures were as per Gardner et al (2011) except for different concentrations of Taqpolymerase (0.25 U), dNTPs (0.1 mM), and primers (0.02 µM for the forward and M13A or M13B primers and 0.04 µM for the reverse).…”