Quantitative trait loci (QTL) mapping of blush skin and flowering time in a European pear (Pyrus communis) progeny of ‘Flamingo’ × ‘Abate Fetel’
Ntladi, Solomon M. ; Human, Jan P. ; Bester, Cecilia ; Vervalle, Jessica ; Roodt-Wilding, Rouvay ; Tobutt, Kenneth R. - \ 2018
Tree Genetics and Genomes 14 (2018)5. - ISSN 1614-2942
Blush skin - Candidate genes - European pear - Flowering time - QTLs - SSRs
Blush skin and flowering time are agronomic traits of interest to the Agricultural Research Council (ARC) Infruitec-Nietvoorbij pear breeding programme. The genetic control of these traits was investigated in the pear progeny derived from ‘Flamingo’ (blush cultivar) × ‘Abate Fetel’ (slightly blush) made up of 121 seedlings. Blush skin was scored phenotypically over three seasons and flowering time was scored over two seasons. A total of 160 loci from 137 simple sequence repeat (SSR) markers were scored in the progeny and used to construct parental genetic linkage maps. Quantitative trait loci (QTL) analysis revealed two QTLs for blush skin, a major QTL on linkage group (LG) 5 in ‘Flamingo’, and a major QTL on LG9 in ‘Abate Fetel’. Two SSR markers, NB101a and SAmsCO865954, were closely linked with the major QTL on LG5 in ‘Flamingo’, with alleles 139 bp and 462 bp in coupling, respectively. These markers were present in approximately 90% of the seedlings scored as good blush (class 4) based on the average data set. These two markers were used to genotype other pear accessions to validate the QTL on LG5 with the view of marker-assisted selection. Two candidate genes, MYB86 and UDP-glucosyl transferase, were associated with the QTL on LG5 and MYB21 and MYB39 were associated with the QTL on LG9. QTL analysis for flowering time revealed a major QTL located on LG9 in both parents. Marker GD142 with allele 161 bp from ‘Flamingo’ was present in approximately 88% of the seedlings that flowered earlier than either parent, based on the average data set. The QTLs and linked markers will facilitate marker-assisted selection for the improvement of these complex traits.
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.
Detection of molecular signatures of selection at microsatellite loci in the South African abalone (Haliotis midae) using a population genomic approach
Rhode, Clint ; Vervalle, Jessica ; Bester-van der Merwe, Aletta E. ; Roodt-Wilding, Rouvay - \ 2013
Marine Genomics 10 (2013). - ISSN 1874-7787 - p. 27 - 36.
Adaptation - F-outlier - Linkage disequilibrium - Neutrality - Population genomics - Selection
Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in order to identify loci that may be candidates for selection amongst six populations (three cultured and three wild) of the South African abalone, Haliotis midae. Approximately 9% of the genome-wide microsatellite markers were putatively subject to directional selection, whilst 6-18% of the genome is thought to be influenced by balancing selection. Genetic diversity estimates for candidate loci under directional selection was significantly reduced in comparison to candidate neutral loci, whilst candidate balancing selection loci demonstrated significantly higher levels of genetic diversity (Kruskal-Wallis test, P<0.05). Pairwise Fst estimates based on candidate directional selection loci also demonstrated increased levels of differentiation between study populations. Various candidate loci under selection showed significant inter-chromosomal linkage disequilibrium, suggesting possible gene-networks underling adaptive phenotypes. Furthermore, several loci had significant hits to known genes when performing BLAST searches to NCBI's non-redundant databases, whilst others are known to be derived from expressed sequences even though homology to a known gene could not be established. A number of loci also demonstrated relatively high similarity to transposable elements. The association of these loci to functional and genomically active sequences could in part explain the observed signatures of selection.
Isolation and validation of microsatellite markers from a depleted South African sciaenid species, the dusky kob (Argyrosomus japonicus), by means of the FIASCO/454 approach
Mirimin, L. ; Ruiz Guajardo, J.C. ; Vervalle, J. ; Bester-Van der Merwe, Aletta ; Kerwath, S. ; Macey, B. ; Bloomer, P. ; Roodt-Wilding, R. - \ 2013
Conservation Genetics Resources 5 (2013)3. - ISSN 1877-7252 - p. 841 - 844.
454 GS-FLX - Argyrosomus spp - FIASCO - Microsatellites - Sciaenid
The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild population structure, assist the effectiveness of broodstock and breeding programmes, and ensure monitoring of potential interactions between wild and farmed fish. The present study uses a recently tested approach that combines the FIASCO enrichment protocol with 454 GS-FLX Next Generation Sequencing, to identify large numbers of microsatellite-containing sequences at a low cost and high discovery rate from the dusky kob genome. Following the FIASCO enrichment (targeting specifically tetranucleotide repeats), 2,355 potential tetranucleotide microsatellites (perfect repeat motifs including eight or more repeat units flanked by regions for primer design) were identified from 1/5th of a single 454 lane. From these sequences, a test panel of 60 potential markers was selected for validation. A total of eight (13 %) markers were successfully amplified from a test sample of wild dusky kob individuals and showed high levels of polymorphism (observed heterozygosity per locus ranging between 0.375 and 0.905). Cross-species amplification of seven of these markers was also successfully carried out in another closely related and commercially important South African sciaenid species, the silver kob (A. inodorus). The microsatellite markers developed in the present study are readily available tools suitable to address genetic variability of Argyrosomus species of southern Africa.
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.