Isolation and characterization of 125 microsatellite DNA markers in the blacklip abalone, Haliotis rubra

Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: Effect of null alleles

Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H-W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.

Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data

Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.

Broad-scale genetic patterns of New Zealand abalone, Haliotis iris, across a distribution spanning 13° latitude and major oceanic water masses

The New Zealand black-foot abalone, Haliotis iris, or pāua, is endemic to the rocky reefs surrounding New Zealand, whose main land mass spans 13° of latitude and separates the Tasman Sea from the Pacific Ocean. In this study, we examined the population genetic structure of this important commercial, cultural and recreational species by genotyping nine microsatellite loci in 485 pāua from 27 locations distributed across mainland New Zealand and the Chatham Islands. We found low, but significant, levels of genetic differentiation. Key genetic breaks were identified among the Chatham Islands and mainland samples; patterns that are strongly corroborated by prior work employing mtDNA sequences. AMOVAs indicated that samples from the south of the North Island were more similar to the South Island samples than to other North Island samples, however multivariate analysis and Bayesian clustering could not identify a significant pattern. Differentiation between the Chatham Islands and the mainland is most likely due to isolation by distance, while differentiation of North Island samples corresponds with major components of New Zealand's oceanography, Cook Strait and the East Cape. Despite intense fishing pressure, we detected no signature of genetic bottlenecks in any region suggesting that population sizes have remained relatively stable over recent time or that the census size of this species is much larger than its effective population size.

Molecular genetics to inform spatial management in benthic invertebrate fisheries: a case study using the Australian greenlip abalone

Hierarchical sampling and subsequent microsatellite genotyping of >2300 Haliotis laevigata (greenlip abalone) from 19 locations distributed across five biogeographic regions have substantially advanced our knowledge of population structure and connectivity in this commercially important species. The study has found key differences in stock structure of H. laevigata compared with the sympatric and congeneric Haliotis rubra (blacklip abalone) and yielded valuable insights into the management of fisheries targeting species characterized by spatial structure at small scales (i.e. S-fisheries). As with H. rubra, H. laevigata comprise a series of metapopulations with strong self-recruitment. However, the spatial extent of H. laevigata metapopulations (reefal areas around 30 km(2) ; distances of up to 135 km are effective barriers to larval dispersal) was substantially greater than that identified for H. rubra (Miller et al. 2009). Differences in the dynamics and scale of population processes, even between congeneric haliotids as made evident in this study, imply that for S-fisheries, it is difficult to generalize about the potential consequences of life history commonalities. Consequently, species-specific management reflective of the population structure of the target species remains particularly important. This will likely require integration of information about stock structure and connectivity with data on life history and population dynamics to determine the necessary input (e.g. number of fishers, fishing effort) and output (e.g. minimum legal size, total allowable catch) controls to underpin their sustainable management.

New microsatellite markers for the abalone Haliotis midae developed by 454 pyrosequencing and in silico analyses

Farming of Haliotis midae is the most lucrative aquaculture venture in South Africa. The genome of this species needs to be studied to assist in selective breeding programs aimed at increasing overall yield, and molecular markers will be required to attain this goal. We identified and characterized 82 polymorphic microsatellite loci by using repeat-enriched genomic libraries and high-throughput pyrosequencing technology. The observed number of alleles ranged from 2 to 21, expected heterozygosity from 0.063 to 0.968, observed heterozygosity from 0.000 to 1.000, and polymorphic information content from 0.059 to 0.934. Three loci gave significant hits to other haliotid genes and/or microsatellite loci; hits to genes were always located in the 5'/3'-UTR or intron region. Many of these newly designed markers would be useful for parentage, population and linkage studies.

Population genetic structure and phylogeography of cyprinid fish, Labeo dero (Hamilton, 1822) inferred from allozyme and microsatellite DNA marker analysis

We examined population structure of Labeo dero (Hamilton, 1822) from different riverine locations in India using 10 polymorphic allozyme and eight microsatellite loci. For analysis, 591 different tissue samples were obtained from commercial catches covering a wide geographic range. Allozyme variability (An = 1.28-1.43, Ho = 0.029-0.071) was much lower than for microsatellites (An = 4.625-6.125, Ho = 0.538-0.633). Existence of rare alleles was found at three allozyme (MDH-2, GPI and PGDH) and at two microsatellite loci (R-3 and MFW-15). Deviation from Hardy-Weinberg equilibrium (P < 0.05, after the critical probability levels were adjusted for sequential Bonferroni adjustment) could be detected at three loci (EST-1, -2 and XDH) whereas, after correction for null alleles, two microsatellite loci (MFW-1,-15) deviated from HWE in the river Yamuna. Fst for all the samples combined over all allozyme loci was found to be 0.059 suggesting that 5.9% of the total variation was due to genetic differentiation while microsatellite analysis yielded 0.019 which was concordant to mean Rst (0.02). Hierarchical partition of genetic diversity (AMOVA) showed that greater variability (approx. 95%) was due to within population component than between geographical regions. Based on distribution of genetic differentiation detected by both markers, at least five different genetic stocks of L. dero across its natural distribution could be identified. These results are useful for the evaluation and conservation of L. dero in natural water bodies.

Bioinformatic survey of Haliotis midae microsatellites reveals a non-random distribution of repeat motifs

Recent studies have shown the non-random distribution of microsatellite motifs between genomic regions within a particular species. This study investigates such microsatellite distributions in the genome of the economically important abalone Haliotis midae, via a bioinformatic survey. In particular, the association of specific repeat motifs to coding regions and transposable elements is investigated. An understanding of microsatellite genomic distribution will facilitate more efficient use and development of this popular molecular marker. A bias toward di- and tetranucleotide repeats was found in the H. midae genome. CA microsatellite units were the most abundant repeat motif, but were notably underrepresented in genic regions where GAGT repeats predominate. Approximately 17.5% and 21% of the microsatellites showed gene and/or transposable element associations, respectively. This could explain the high genomic frequencies of particular motifs across the genome and may allude to a possible functional role. The data presented in this study are the first to demonstrate such non-random dispersal of microsatellites in abalone and support previous findings arguing in favor of non-random distribution of repeat motifs.

Development and characterization of 60 microsatellite markers in the abalone Haliotis diversicolor

The abalone, Haliotis diversicolor, is one of the most important mariculture species in southern China. We developed 60 new polymorphic microsatellite markers for H. diversicolor and characterized them in 30 individuals from a cultured population in Sanya, China. All 60 markers were found to be polymorphic. The number of alleles ranged from two to nine per locus, with an average of 4.12/locus. The expected and observed heterozygosities ranged from 0.10 to 0.88 and from 0.07 to 0.87, respectively. Forty-four loci were in Hardy-Weinberg equilibrium. These 44 microsatellite markers should be useful for genome mapping and population genetic studies.

Genetic diversity and gene flow in collapsed and healthy abalone fisheries

Overexploitation of marine species invariably results in population decline but can also have indirect effects on ecological processes such as larval dispersal and recruitment that ultimately affect genetic diversity and population resilience. We compared microsatellite DNA variation among depleted and healthy populations of the black-lip abalone Haliotis rubra from Tasmania, Australia, to determine if over-fishing had affected genetic diversity. We also used genetic data to assess whether variation in the scale and frequency of larval dispersal was linked to greater population decline in some regions than in others, and if larval dispersal was sufficient to facilitate natural recovery of depleted populations. Surprisingly, allelic diversity was higher in depleted populations than in healthy populations (P < 0.05). Significant subdivision across hundreds of metres among our sampling sites (F(ST) = 0.026, P < 0.01), coupled with assignment tests, indicated that larval dispersal is restricted in all regions studied, and that abalone populations across Tasmania are largely self-recruiting. Low levels of larval exchange appear to occur at the meso-scale (7-20 km), but age estimates based on shell size indicated that successful migration of larvae between any two sites may happen only once every few years. We suggest that genetic diversity may be higher in depleted populations due to the higher relative ratio of migrant to self-recruiting larvae. In addition, we expect that recovery of depleted abalone populations will be reliant on sources of larvae at the meso-scale (tens of km), but that natural recovery is only likely to occur on a timescale unacceptable to fishers and resource managers.

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling

The objective of this study was to identify QTL for growth rate in the blacklip abalone Haliotis rubra using selective DNA pooling. Three full-sibling families of H. rubra derived from crosses of wild broodstock were used. DNA was extracted from the largest and smallest 10% of progeny and combined into two pools for each phenotypic tail. The DNA pools were typed with 139 microsatellites, and markers showing significant differences between the peak height ratios of alleles inherited from the parents were individually genotyped and analysed by interval mapping. A strong correlation (r = 0.94, P < 0.001) was found between the t-values from the analysis of pools and the t-values from the analysis of individual genotypes. Based on the interval mapping analysis, QTL were detected on nine linkage groups at a chromosome-wide P < 0.01 and one linkage group at a chromosome-wide P < 0.05. The study demonstrated that selective DNA pooling is efficient and effective as a first-pass screen for the discovery of QTL in an aquaculture species.

A microsatellite linkage map of the blacklip abalone, Haliotis rubra

There is considerable scope for genetic improvement of cultured blacklip abalone Haliotis rubra in Australia using molecular marker-assisted, selective-breeding practices. Such improvement is dependent on the availability of primary genetic resources, such as a genetic linkage map. This study presents a first-generation linkage map of H. rubra, containing 122 microsatellite markers typed in a single full-sib family. These loci mapped to 17 and 20 linkage groups for the male and female respectively, and when aligned, the consensus map represented 18 linkage groups. The male linkage map contained 102 markers (one unlinked) covering 621 cM with an average intermarker spacing of 7.3 cM, and the female map contained 98 markers (eight unlinked) covering 766 cM with an average intermarker spacing of 9.8 cM. Analysis of markers informative in both parents showed a significantly higher recombination rate in the female parent, with an average male-to-female recombination ratio of 1:1.45 between linked pairs of markers. This linkage map represents a significant advancement in the genetic resource available for H. rubra and provides a framework for future quantitative trait loci mapping and eventual implementation of marker-assisted selection.