Genetic association analysis of candidate loci under selection with size in the South African abalone
Dale-Kuys, Ruth ; Vervalle, Jessica ; Roodt-Wilding, Rouvay ; Rhode, Clint - \ 2017
Aquaculture International 25 (2017)3. - ISSN 0967-6120 - p. 1197 - 1214.
Association studies - Domestication - Growth rate - Haliotis midae - Marker assisted selection - Quantitative trait loci - Signatures of selection
The abalone, Haliotis midae, is an important aquaculture species in South Africa and the largest generator of revenue for the mariculture sector. Despite domestication of this species still being in the initial stages, significant differentiation has been observed between wild and cultured populations. The genetic consequences of founder effects have been well documented in many aquaculture species; however, the effects of selection remain under-investigated. Previous studies in this species identified several loci thought to be under divergent selection between wild and cultured populations. The aim of this study was therefore to investigate the influence of artificial selection on genetic variation by determining whether these candidate loci are associated with larger size (primary production trait) in a commercial F1 population. Thirteen microsatellite markers, putatively identified as being under directional selection, were chosen for association analysis. Various statistical tests were used to detect significant genotype-phenotype associations within a family-bias corrected population cohort and two family cohorts. Two loci demonstrated significant evidence for association with size, with both loci possessing alleles that correlated significantly with either increased or decreased size. As size is currently the only trait actively selected for in terms of production, the current results suggest that natural selection for adaptation to the novel aquaculture environment is the predominant selective force shaping genetic variation during the initial stages of domestication in abalone. Furthermore, whilst it is currently unclear as to whether these loci represent causative variants for size traits, they may be useful in future molecular-assisted breeding programmes for H. midae.
Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers
Vervalle, Jessica ; Hepple, Juli Ann ; Jansen, Suzaan ; Plessis, Jana Du ; Wang, Peizheng ; Rhode, Clint ; Roodt-Wilding, Rouvay - \ 2013
Journal of Shellfish Research 32 (2013)1. - ISSN 0730-8000 - p. 89 - 103.
abalone - Haliotis midae - linkage map - microsatellites - single nucleotide polymorphisms
The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.
A population genetic analysis of abalone domestication events in South Africa : Implications for the management of the abalone resource
Rhode, Clint ; Hepple, Juli-Ann ; Jansen, Suzaan ; Davis, Tanja ; Vervalle, Jessica ; Bester-van der Merwe, Aletta Elizabeth ; Roodt-Wilding, Rouvay - \ 2012
Aquaculture 356-357 (2012). - ISSN 0044-8486 - p. 235 - 242.
Abalone - Aquaculture - Conservation - Domestication - Genetic diversity - Haliotis midae
Abalone culture is South Africa's largest aquaculture sector in terms of revenue. Nonetheless, the industry is in its formative years and much scope remains for refinement and regulation of production practices. It is important to manage genetic diversity in terms of the particular breeding objectives pursued by respective facilities: selective breeding vs. ranching; whilst conserving the genetic integrity of wild populations remains a national imperative. The present study found no significant decrease in genetic diversity between wild and cultured populations as based on heterozygosity and allelic content of genomic- and EST-microsatellite loci. However, estimates for pairwise genotypic differentiation, F st, AMOVA and Factorial correspondence analysis suggest the genetic heterogeneity of cultured populations and their significant differentiation from the wild progenitor populations. As expected, the cultured population showed reduced effective population sizes, but relatedness remained low. It is postulated that both neutral and selective evolutionary forces are responsible for the observed patterns of genetic variability within and amongst populations. The implications of the results are discussed in terms of broad managerial objectives for the South African abalone and continued monitoring is advised.