Novel genomic microsatellite markers for genetic population and diversity studies of tropical scalloped spiny lobster (Panulirus homarus) and their potential application in related Panulirus species

Delghandi, Madjid; Goddard, Stephen; Jerry, Dean R.; Dao, Hoc Tan; Hinai, Manal Saif Nasser Al; Al-Amry, Wahida; Al-Marzouqi, Abdulaziz

doi:10.4238/gmr.15027846

Cited by 3 publications

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“…This approach has been successfully applied in several marine fish species for assignment of individuals to groups of families or to estimate the relationship among individuals (Herlin, Delghandi, Wesmajervi, Taggart, McAndrew & Penman ; Vandeputte & Haffray ; Zhang, Ma, Wang, Gui & Mei ). Recently, we have isolated several microsatellite markers for tropical spiny lobster (Delghandi, Goddard, Jerry, Dao, Afzal & Al‐Jardani ; Delghandi, Afzal, Al Hinai, Al‐Breiki, Jerry & Dao ; Delghandi, Goddard, Jerry, Dao, Al Hinai, Al‐Amry & Al‐Marzouqi ). Based on genetic diversity, allelic size and polymerase chain reaction (PCR) conditions, seven loci were selected and multiplexed to assess the power of the markers for parentage assignment studies.…”

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confidence: 99%

Parentage analysis of tropical spiny lobster (Panulirus homarus) by microsatellite markers

et al. 2017

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have contributed equally to the work. AbstractParentage analysis is of vital importance for hatchery production and breeding programmes. Two multiplex PCR protocols including seven tropical spiny lobster (Panulirus homarus) microsatellites (Pho-G06, Pho-G25, Pho-G53, Pho-G62, Pho-G74, Pho-G89 and Pho-G100) were introduced for parentage assignment. All loci were polymorphic with allele sizes from 113 to 337 base pairs (bp), observed alleles (k) from two to seven and polymorphic information content (PIC) of 0.25 to 0.73. Twenty-four stage-3 phyllosoma larvae (39 days posthatching) were collected for paternity exclusion study using selected microsatellites. Exclusion-based parentage analysis unambiguously assigned 83% of fry (20 of 24) to a single female parent. Of ten putative female parents, five have contributed to the 20 allocated offspring, with one being true parent of 11. Four others were assigned to two or more potential female parents, probably due to genotyping error or the presence of null allele. The exclusion power (EP) for the seven loci varied between 13% and 54% with known genotypes of one parent (P1) and 19% and 71% for given the genotypes of both parents (P2). The theoretical combined parentage exclusion (cEP) power for all seven microsatellites was P1 = 95% and P2 = 99%. The power of discrimination for each locus varied between 0.18 and 0.86. This report presents the first study to utilize microsatellite markers for successful parentage assignment of P. homarus. The selected microsatellites provide a practical tool for parentage analysis in hatchery production of juveniles as well as in future commercial breeding programme of tropical spiny lobsters.

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Section: Introductionmentioning

confidence: 99%

Parentage analysis of tropical spiny lobster (Panulirus homarus) by microsatellite markers

et al. 2017

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The Significance of PCR Primer Design in Genetic Diversity Studies: Exemplified by Recent Research into the Genetic Structure of Marine Species

Delghandi

Goddard²

2021

Methods in Molecular Biology

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Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

et al. 2018

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BackgroundThe scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species.ResultsAfter stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = − 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288–0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus.ConclusionsFindings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5044-8) contains supplementary material, which is available to authorized users.

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Novel genomic microsatellite markers for genetic population and diversity studies of tropical scalloped spiny lobster (Panulirus homarus) and their potential application in related Panulirus species

Cited by 3 publications

References 14 publications

Parentage analysis of tropical spiny lobster (Panulirus homarus) by microsatellite markers

Parentage analysis of tropical spiny lobster (Panulirus homarus) by microsatellite markers

The Significance of PCR Primer Design in Genetic Diversity Studies: Exemplified by Recent Research into the Genetic Structure of Marine Species

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

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