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 Andrea; Vervalle, Jessica; Merwe, Aletta E. Bester‐van der; Roodt‐Wilding, Rouvay

doi:10.1016/j.aquaculture.2012.05.012

Cited by 22 publications

(21 citation statements)

References 87 publications

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“…Population analysis indicated that allele fixation (increasing F ST ) was evident between cultured and wild populations, but was most striking between the three cultured full-sib families. The differentiation between wild and cultured abalone was in accordance with what has recently been found in H. midae based on microsatellite markers [3], while the unusually high variation observed between the cultured populations (pairwise F ST > 0.15) could be attributed to the highly heterozygous nature of the wild-caught parents, leading to an increase in the probability of the resulting F1 progenies receiving two different alleles at each locus, inflating the genetic distinctness of the respective families. With regards to the wild populations that included abalone from the West (Saldanha Bay), South (Witsand) and East coast (Riet Point) of South Africa, FCA results corroborated the summary statistics in that the only statistically unsupported pairwise F ST value was found between the wild populations of Witsand and Saldanha Bay.…”

Section: Resultssupporting

confidence: 86%

“…These SNPs can ultimately be applied in conjunction with microsatellite markers in various applications, such as genetic diversity studies, population structure analyses, linkage mapping, quantitative trait locus (QTL) analysis and parentage assignment. A further objective of this study was therefore to test the utility of the successfully genotyped SNPs in determining genetic diversity, population differentiation and family informativeness in H. midae , since previously, these types of applications were addressed mainly using microsatellite markers [3,5,55,70]. In this study, transcriptome characterization with the aid of NGS technologies proved to be adequate for the use of marker development in H. midae .…”

Section: Discussionmentioning

confidence: 97%

“…The South African abalone industry, the largest outside Asia, currently has a total output of 1015.44 metric tons, valued at 355 million South African Rand (ZAR) [2]. In order to supply the growing international market and to ensure the sustainability of the industry, effective farm management practices, including the employment of molecular markers in genetic management programs, are vital [3]. To date, mainly microsatellite markers (274) have been developed for H. midae using various enrichment and in silico techniques [4–7].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

Merwe

Blaauw

Plessis

et al. 2013

IJMS

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Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular markers, such as microsatellites and single nucleotide (SNPs). Transcriptome sequences generated through sequencing-by-synthesis technology were utilized for the in vitro and in silico identification of 505 putative SNPs from a total of 316 selected contigs. A subset of 234 SNPs were further validated and characterized in wild and cultured abalone using two Illumina GoldenGate genotyping assays. Combined with VeraCode technology, this genotyping platform yielded a 65%–69% conversion rate (percentage polymorphic markers) with a global genotyping success rate of 76%–85% and provided a viable means for validating SNP markers in a non-model species. The utility of 31 of the validated SNPs in population structure analysis was confirmed, while a large number of SNPs (174) were shown to be informative and are, thus, good candidates for linkage map construction. The non-synonymous SNPs (50) located in coding regions of genes that showed similarities with known proteins will also be useful for genetic applications, such as the marker-assisted selection of genes of relevance to abalone aquaculture.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

Merwe

Blaauw

Plessis

et al. 2013

IJMS

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“…Rhode et al 2012). Removal of these loci did not change the outcome of analyses; therefore, results based on all loci are reported.…”

mentioning

confidence: 99%

Comparison of population genetic estimates amongst wild, F1 and F2 cultured abalone (Haliotis midae)

et al. 2014

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Haliotis midae is South Africa's most important aquaculture species. The reproduction cycle is currently not closed as many farms rely on wild-caught broodstock for seed production. However, there is an increasing interest in genetic improvement in commercial stocks, with a growing number of producers implementing selective breeding strategies. High throughput commercial production and mass spawning make it difficult to maintain breeding records; therefore, mostly mass selection is practised. The high fecundity and unequal parental contributions also often lead to increased levels of inbreeding. This study therefore aimed to assess the genetic effects of such breeding practices on commercial populations of H. midae. Using microsatellite loci, the genetic properties of a wild, an F1 and an F2 population were estimated and compared. Although there was no significant loss of genetic diversity amongst the cultured populations in comparison with the wild progenitor population, there was low-to-moderate genetic differentiation between populations. Relatedness amongst the F2 population was significant, and the rate of inbreeding was high. The effective population size for the F2 (±50) was also comparatively small with respect to the wild (∞) and F1 (±470) populations. These results suggest that farms need to give caution to breeding practices beyond the first (F1) generation and aim to increase effective population sizes and minimise inbreeding to ensure long-term genetic gain and productivity. This study also confirms the usefulness of population genetic analyses for commercial breeding and stock management in the absence of extensive pedigree records.

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“…The broodstock animals in each hatchery were all wild individuals collected from the “native” geographical region to establish a base population that encapsulates most of the available natural variation (Roodt‐Wilding and Brink ; Bester‐van der Merwe et al ); thus the cohorts under investigation are F1 generation (first generation under culture). Only broodstock that have previously spawned successfully are retained by the hatchery; despite this, unequal parental contributions are expected to occur (van den Bergh and Roodt‐Wilding ; Slabbert et al ) and could lead to genetic differentiation between stocks (Rhode et al ).…”

Section: Methodsmentioning

confidence: 99%

An Assessment of Hatchery Cohort Growth Rates of South African Abalone, Haliotis midae, Across Four Commercial Environments

Vlok

Difford

Rhode

et al. 2016

J World Aquaculture Soc

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The abalone, Haliotis midae (commonly referred to as “perlemoen”), is an important aquaculture species in South Africa, accounting for the highest percentage of total aquaculture production revenue. The industry largely makes use of wild, undomesticated broodstock and thus a consortium of top producers was formed to develop a genetic improvement program to increase efficiency and sustainability of the industry. As such, the current study aimed to evaluate growth trait performance (wet weight and shell length) of four hatchery‐derived cohorts of South African abalone, across four differing production environments. No significant cohort‐by‐location effects were found for weight and length traits; however, differences were detected between respective cohorts and locations. It is concluded that a single synthetic population comprised of all hatchery cohorts under a single breeding goal is suitable for production at all test locations. Furthermore, advances in artificial reproductive technologies, genetic markers, and individual identification hold promise for genetic improvement of the species.

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A population genetic analysis of abalone domestication events in South Africa: Implications for the management of the abalone resource

Cited by 22 publications

References 87 publications

Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

Comparison of population genetic estimates amongst wild, F1 and F2 cultured abalone (Haliotis midae)

An Assessment of Hatchery Cohort Growth Rates of South African Abalone, Haliotis midae, Across Four Commercial Environments

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