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Kotta Raismin - One of the best experts on this subject based on the ideXlab platform.

  • TEKNIK PEMBENIHAN TIRAM MUTIARA (Pinctada maxima)
    Prosiding Seminar Nasional Kemaritiman dan Sumber Daya Pulau-Pulau Kecil, 2018
    Co-Authors: Kotta Raismin
    Abstract:

    Pengamatan terhadap kerang mutiara (Pinctada sp) telah dilakukan terhadap jenis Pinctada maxima dengan tujuan mengetahui teknik pembenihan dan metoda pemeliharaan dari stadium larva hingga ukuran spat di Balai Pengembangan Budidaya Perikanan Pantai (BPBPP) Sekotong Lombok barat. Guna memperoleh anakan kerang mutiara maka dilakukan melalui proses pemijahan. Metoda pemijahan yang digunakan adalah adalah metoda kejut suhu (Thermal shock) dimana terjadi penaikan dan penurunan suhu secara berangsur-angsur dengan tujuan agar seluruh tiram bisa terangsang untuk memijah (spawning) selanjutnya dipindahkan ke bak pemijahan sekaligus bak penetasan dan pemeliharaan larva. Induk tiram yang digunakan pada pengamatan ini adalah tiram mutiara alam (Natural oyster) dengan ukuran panjang induk betina berkisar antara 17.0 – 22.0 cm dan ukuran panjang induk jantan 17.5 – 22.0 cm dengan Tingkat Kematangan Gonad (TKG) stadia IV. Tahapan kegiatan adalah dimulai dari persiapan wadah,seleksi induk,pemijahan,penetasan telur,perawatan larva,sirkulasi air media,kultur pakan alami fitoplankton jenis Nannochloropsis sp,Pavlova lutheri,Isochrysis galbana dengan dosis pemberian meningkat 10% tiap hari dari dosis awal. Selanjutnya untuk menyuburkan pertumbuhan fitoplankton dalam media kultur digunakan pupuk KW 21.Hasil pengamatan menunjukan bahwa pemijahan tiram mutiara berhasil dilakukan dan berdasarkan hasil sampling, jumlah telur yang dihasilkan sebanyak 90.000.000 butir dengan Hatching rate 70% yaitu 63.000.000 ekor serta hasil panen spat dengan waktu pemeliharaan dalam bak pembesaran selama 40 hari sebanyak 2,5% (1.575.000 ekor) dari total larva yang menetas. Stadia larva tiram mutiara terdiri dari D- Shape, Umbo 1,Umbo 2,Umbo 3,Planty grade,Spat. Stadia paling rawan pada fase larva tiram mutiara adalah pada stadia Umbo 2, karena pada stadia ini larva mulai bermetamorfosis menuju fase plantygrade dimana akan membentuk rangkaian menggunakan benang-benang yang disekresikan. Fase terakhir di hatchery, sebelum dipelihara di laut adalah fase spat yang akan dicapai pada hari pemeliharaan ke 20. Spat hampir sepenuhnya seperti tiram muda, hanya bentuk engsel yang membedakan yaitu masih belum rata.Pada fase spat,larva tidak lagi bersifat planktonik tetapi menjadi sesil yaitu menetap pada substrat dengan cara mensekresikan benang-benang bisus dari kelenjar bisus untuk menempel.Kata kunci:Budidaya; Pembenihan tiram mutiara (Pinctada maxima

  • PERTUMBUHAN DAN PERKEMBANGAN SPAT TIRAM MUTIARA (Pinctada maxima) DI PERAIRAN TERNATE SELATAN PULAU TERNATE
    Prosiding Seminar Nasional Kemaritiman dan Sumber Daya Pulau-Pulau Kecil, 2018
    Co-Authors: Kotta Raismin
    Abstract:

    Perairan Pulau Ternate bagian selatan merupakan salah satu lokasi yang potensial untuk melakukan kegiatan budidaya biota laut termasuk tiram mutiara (Pinctada maxima) . Hal ini disebabkan karena ketersediaan pakan alami (Phitoplankton) serta kondisi perairan termasuk arus yang ideal merupakan faktor utama dalam mendukung keberlanjutan usaha tersebut. Penelitian ini dilaksanakan di perairan ternate selatan (Stasiun Penelitian Lapangan LIPI Kecamatan Sasa Kota Ternate Selatan) selama dua (2) bulan yaitu dari bulan Mei – Juni 2017. Tujuan penelitian ini adalah untuk mengetahui laju pertumbuhan spat tiram mutiara (Pinctada maxima) pada berbagai tingkat kedalaman serta presentase kelangsungan hidup spat yang dipelihara menggunakan metoda tali rentang (Long line) di perairan ternate selatan pada. Tiram mutiara yang dipelihara dari ukuran spat yang masih menempel pada media kolektor yang terbuat dari serat monofilament sampai dengan ukuran kira-kira 4-5 mm dan ditebar pada kemudian ditebar pada poket spiral dengan kepadatan 75-100 ekor, dibungkus waring dan digantung pada long line, Pengukuran panjang cangkang dilakukan menggunakan penggaris dengan ketelitian 1 mm. Hasil Penelitian menunjukan bahwa selama masa pemeliharaan dua (2) bulan, Laju pertumbuhan spesifik rata-rata panjang cangkang 19,74 mm,sedangkan faktor kualitas air yaitu Suhu berkisar 29,6-30,3 0C,salinitas 33-35 ppt,pH 7,1-7,2 serta kecerahan 10-13 m, serta tingkat mortalitas yang rendah. Dari hasil penelitian ini diperoleh laju pertumbuhan cukup baik pada kedalaman pemeliharaan 2 meter dan diikuti oleh kedalama 6,4 dan 8. Hal ini didukung oleh kondisi perairan yang memadai,Pola arus yang baik dimana msh terdapat terumbu karang dan lamun yang melimpah. maka dapatlah diprediksikan bahwa Perairan ternate selatan masih produktif untuk pemeliharaan tiram mutiara (Pinctada maxima) dan dapat di tingkatkan pemeliharaannya sampai ukuran siap di adakan penyuntikan/Insersi (size 10 – 12 cm) untuk dilakukan tahapan selanjutnya yakni penyuntikan/insersi guna menghasilkan butiran mutiara. Melihat kondisi riel di lokasi penelitian tentang pertumbuhan dan perkembangan tiram mutiara (Pinctada maxima) yang di pelihara memberikan indikasi bahwa budidaya tiram mutiara di perairan ternate selatan harus di dorong dan dapat dijadikan salah satu bidang usaha bagi masyarakat pesisir di wilayah ternate selatan khususnya dan Maluku utara pada umumnya dengan melibatkan pengusaha lokal, pemerintah daerah (Dinas Perikanan Kelautan) serta Lembaga riset (LIPI dan Universitas) dalam rangka meningkatkan Pendapatan Asli Daerah dari subsektor budidaya laut.Kata kunci: Budidaya, kerang mutiara, pertumbuhan, Pinctada maxima

  • PEMBERIAN KALSIUM KARBONAT (CaC03) PADA MEDIA BUDIDAYA UNTUK PERTUMBUHAN LARVA KERANG MUTIARA Pinctada maxima STADIA VELIGER-PEDIVELIGER
    Program Studi Budidaya Perairan, 2015
    Co-Authors: Asrori, Ahmad Zuli, Hilyana Sitti, Kotta Raismin
    Abstract:

    Kerang mutiara Pinetada maxima merupakan kerang penghasil mutiara "South Sea Pearl"  salah satu komoditas hasil laut Indonesia yang bemilai ekonomis dan sangat digemari di pasaran dunia. Banyaknya per­ mintaan mutiara jenis Pinetada maxima dan semakin berkembangnya budidaya mutiara saat ini menjadi pemicu meningkatnya permintaan spat dan kerang siap operasi. Kendala utama pada produksi kerang mutiara saat ini adalah pertumbuhan yang lambat dan sintasan rendah dalam pemeliharaan larva dan spat. Faktor biofisik-kim­ ia lingkungan sangat berperan dalam pertumbuhan kerang mutiara antara lain suhu perairan, salinitas, makanan dan unsur kimia dalam air laut. Unsur kimia air laut berupa mineral kalsium (Ca) merupakan makro mineral terdapat dalam tubuh yang dibutuhkan dalam jumlah yang relatif besar. Salah satu upaya yang dapat dilaku­ kan untuk mengatasi tersebut adalah dengan penambahan kapur (CaCO)  dengan konsentrasi yang sesuai di dalam media budidaya saat stadia veliger-pediveliger. Penelitian ini bertujuan  untuk mengetahui pengaruh pem­ berian kalsium karbonat (CaCO) terhadap tingkat pertumbuhan dan kelangsungan hidup larva kerang mutiara (Pinetada maxima). Penelitian ini dilaksanakan pada tanggal 3-22 September 2014 di PT Autore Pearl Culture, Malaka, Kecamatan Pemenang Kabupaten Lombok Utara Provinsi Nusa Tenggara Barat. Pemeliharaan dilaku­ kan pada toples plastik volume 10 L dengan kepadatan 1.000 individu/l (8.000 indi/wadah). Kalsium karbonat (CaC03) yang digunakan  dari cangkang kerang (Pinctada maxima). Metode yang digunakan dalam penelitian ini adalah metode eksperimental Rancangan Acak Lengkap(RAL) yang terdiri dari 4 perlakuan dan 4 ulangan. A kontrol (tanpa pemberian CaCO), B (CaC03 25mg/l), C (CaC0350 mg/l) dan D(CaC0375mg/l). Hasil men­ unjukkan pertumbuhan panjang mutlak tertinggi pada perlakuan B (CaC03  25 mg/l)  189 urn ± 7,39 dan  ter­ endah pada perlakuan A (kontrol tanpa pemberian CaC03)  98,5 um ± 8,02. Nilai kelangsungan hidup tertinggi pada perlakuan B (CaC03 25 mg/l) 48,75 ± 33,7 dan terendah pada perlakuan D (CaC03  75 rng/l) 4,7% ± 2,

Shane Raidal - One of the best experts on this subject based on the ideXlab platform.

  • intracellular ciliated protozoal infection in silverlip pearl oysters Pinctada maxima jameson 1901
    Journal of Invertebrate Pathology, 2008
    Co-Authors: Zoe Spiers, Douglas Bearham, J B Jones, A J Ohara, Shane Raidal
    Abstract:

    The pathology associated with an intracellular ciliate infection in the digestive gland of pearl oysters Pinctada maxima (Jameson, 1901) is described. Histopathological and transmission electron microscopic examination were used to characterise the organism and its location within host cells. The parasite is tear-drop shaped measuring 5.53 μm (range of 2.73–7.47 μm, n = 9) in width and 11.15 μm (range of 9.02–16.2 μm) in length with a centrally located lobulated nucleus and a large nucleus:cytoplasmic ratio. The ciliate has nine evenly spaced rows of cilia running obliquely along the length of cell, converging on the pointed end. Infected digestive glands typically had a moderate to severe infiltration with mononuclear hemocyte. A strong correlation existed between the burden of ciliates and the host response; (p < 0.001, C = 0.315 Pearson Correlation). The use of a single tissue section upon microscopic examination was found to detect only 38–50% of the infections. However, examination of serial haematoxylin and eosin stained sections improved the reliability of detecting infection.

Robert A Rose - One of the best experts on this subject based on the ideXlab platform.

  • parallel evolution of nacre building gene sets in molluscs
    Molecular Biology and Evolution, 2010
    Co-Authors: Patrick Moase, Robert A Rose, Daniel S Rokhsar, Carmel Mcdougall, Daniel J. Jackson, Michael Kube, Richard Reinhardt, Benjamin J. Woodcroft
    Abstract:

    The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently and in parallel in at least some groups. To test this proposition and gain insight into the evolution of structural genes that contribute to shell fabrication, we compared genes expressed in nacre (mother-of-pearl) forming cells in the mantle of the bivalve Pinctada maxima and the gastropod Haliotis asinina. Despite both species having highly lustrous nacre, we find extensive differences in these expressed gene sets. Following the removal of housekeeping genes, less than 10% of all gene clusters are shared between these molluscs, with some being conserved biomineralization genes that are also found in deuterostomes. These differences extend to secreted proteins that may localize to the organic shell matrix, with less than 15% of this secretome being shared. Despite these differences, H. asinina and P. maxima both secrete proteins with repetitive low-complexity domains (RLCDs). Pinctada maxima RLCD proteins—for example, the shematrins—are predominated by silk/fibroin-like domains, which are absent from the H. asinina data set. Comparisons of shematrin genes across three species of Pinctada indicate that this gene family has undergone extensive divergent evolution within pearl oysters. We also detect fundamental bivalve– gastropod differences in extracellular matrix proteins involved in mollusc-shell formation. Pinctada maxima expresses a chitin synthase at high levels and several chitin deacetylation genes, whereas only one protein involved in chitin interactions is present in the H. asinina data set, suggesting that the organic matrix on which calcification proceeds differs fundamentally between these species. Large-scale differences in genes expressed in nacre-forming cells of Pinctada and Haliotis are compatible with the hypothesis that gastropod and bivalve nacre is the result of convergent evolution. The expression of novel biomineralizing RLCD proteins in each of these two molluscs and, interestingly, sea urchins suggests that the evolution of such structural proteins has occurred independently multiple times in the Metazoa.

  • The Nutritional Value of Five Species of Microalgae for Spat of the Silver-Lip Pearl Oyster, Pinctada maxima (Jameson) (Mollusca: Pteriidae)
    Asian fisheries science, 1997
    Co-Authors: Joseph J. Taylor, Paul C Southgate, M S Wing, Robert A Rose
    Abstract:

    A feeding trial was conducted to assess the nutritional value of five monospecific microalgal diets for spat of the silver-lip (or gold-lip) pearl oyster, Pinctada maxima. The five species tested were Isochrysis aff. Galbana (T-ISO), Pavlova lutheri, Chaetoceros muelleri, Chaetoceros calcitrans and Tetraselmis suecica. Spat were 75-d okod at the start of the growth trial which ran for 21 d. Pearl oyster spat fed C. muelleri showed the largest increase in ash-free dry weight (organic content), which was significantly greater (P 0.05). The final AFDW of spat fed P. lutheri was not significantly different from that on unfed spat (P>0.05). Differences in the food value of the five species of algae could not be explained by their reported nutrient composition alone. The results illustrate the importance of experimental testing of algal diets for bivalve spat rather than sole reliance on published nutritional values.; ;

  • larval and spat culture of the western australian silver or goldlip pearl oyster Pinctada maxima jameson mollusca pteriidae
    Aquaculture, 1994
    Co-Authors: Robert A Rose, Shane B Baker
    Abstract:

    The larvae of Pinctada maxima were fed Tahitian Isochrysis galbana, Chaetoceros calcitrans, C. gracilis and Nannochloropsis oculata. Food concentrations for larvae were increased gradually from 0.2–2 algal cells·μl−1 on day 1 to 20–40 cells·μl−1 on day 30. Initial stocking densities of 1–8 larvae·ml−1 were reduced to 0.5–1 larvae·ml−1 at settlement. For 70% of the population, settlement began on day 24 and lasted up to 7 days. Ten to 15% of the population failed to grow appreciably and another 10–15% grew comparatively rapidly, reaching settlement by days 15–17. The smallest spat observed on day 28 was 331 μm shell length (SL)×305 μm shell height (SH). Spat were fed the same phytoplankton as the larvae, as well as Tetraselmis chuii twice daily at 40–285 cells μl−1 over 5 months. Spat reared in downwellers at densities of 4 and 25 individuals·100 cm−2 grew 9.6 and 6 mm·mth−1 SH, respectively. Those reared in plastic cages at sea at densities of 3 and 7 individuals·100 cm−2 grew 9.2 and 7.3 mm mth−1 SH, respectively. Mortality 5 months after settlement was 1–2% for those reared in the hatchery and 9–12% for those reared at sea. Hatchery-propagated spat were similar in appearance to natural spat and 20–25% were suitable for pearl culture 19 months after fertilization, or when they were 120 mm SH.

Zenger, Kyall R - One of the best experts on this subject based on the ideXlab platform.

  • Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima)
    'Elsevier BV', 2016
    Co-Authors: Nayfa, Maria G., Zenger, Kyall R
    Abstract:

    Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G × E effects) among populations in this region. Global F(st) values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise F(st) comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAF(avg) = 0.144, H(o) = 0.238 and MAF(avg) = 0.232, H(o) = 0.369, respectively) compared to Aru (MAF(avg) = 0.292, H(o) = 0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and F(st) analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure

  • Determining genetic contributions to host oyster shell growth: quantitative trait loci and genetic association analysis for the silver-lipped pearl oyster, Pinctada maxima
    'Elsevier BV', 2014
    Co-Authors: Jones, David B, Jerry, Dean R, Khatkar, Mehar S., Moser Gerhard, Raadsma, Herman W., Taylor, Joseph J., Zenger, Kyall R
    Abstract:

    The silver-lipped pearl oyster, Pinctada maxima, is of high economic importance to the global pearling industry. However, pearling industries worldwide have reported declines in gross pearl production values over the last decade, leading to the establishment of several genetic breeding programmes aiming to improve commercially important pearl production traits within pearl oyster stock. Even though the value of a pearl is directly determined by its graded quality, production traits such as host oyster shell growth and shell width define the timing of seeding operations and the size of the implanted nuclei, and therefore have considerable influence on the production of a pearl. In this study, the genetic architecture of complex oyster growth traits (i.e. shell height, length, width and weight) is explored and putative QTL and marker associations are identified.Heritability estimates for pearl oyster shell growth traits ranged from 0.18 to 0.33 indicating the potential for moderate response to genetic selection. A total of six QTL and four genetic associations were detected for four oyster shell growth traits (shell height, length, width and weight). These QTL are estimated to explain a minimum of 32.5%, 20.7% and 30.1% of the phenotypic variation observed in shell height (2 QTL), width (3 QTL) and weight (1 QTL) respectively within the 11 half-sib families (n= 342). In addition, three of the four genetic associations detected for shell length (effect sizes from 3.3 to 4.3) are co-localised on LG4 near the mapped biomineralisation genes PFMG1, Pif177 and CS1.This study confirms previous quantitative genetic studies that oyster growth traits are polygenic, and provides additional evidence that these traits have sufficient genetic basis for improvement in animal selective breeding programmes. The preliminary QTL and genetic associations identified here also serve as prime candidates for ongoing analysis aiming to unravel the complex biological processes involved in pearl oyster growth and shell formation (i.e. biomineralisation). Furthermore, selection programmes incorporating marker information for growth traits with large QTL effects should further accelerate genetic gains within the P. maxima pearling industry

  • Determining genetic contributions to host oyster shell growth : quantitative trait loci and genetic association analysis for the silver-lipped pearl oyster, Pinctada maxima
    'Elsevier BV', 2014
    Co-Authors: Jones, David B, Jerry, Dean R, Khatkar, Mehar S., Moser Gerhard, Raadsma, Herman W., Taylor, Joseph J., Zenger, Kyall R
    Abstract:

    The silver-lipped pearl oyster, Pinctada maxima, is of high economic importance to the global pearling industry. However, pearling industries worldwide have reported declines in gross pearl production values over the last decade, leading to the establishment of several genetic breeding programmes aiming to improve commercially important pearl production traits within pearl oyster stock. Even though the value of a pearl is directly determined by its graded quality, production traits such as host oyster shell growth and shell width define the timing of seeding operations and the size of the implanted nuclei, and therefore have considerable influence on the production of a pearl. In this study, the genetic architecture of complex oyster growth traits (i.e. shell height, length, width and weight) is explored and putative QTL and marker associations are identified. Heritability estimates for pearl oyster shell growth traits ranged from 0.18 to 0.33 indicating the potential for moderate response to genetic selection. A total of six QTL and four genetic associations were detected for four oyster shell growth traits (shell height, length, width and weight). These QTL are estimated to explain a minimum of 32.5%, 20.7% and 30.1% of the phenotypic variation observed in shell height (2 QTL), width (3 QTL) and weight (1 QTL) respectively within the 11 half-sib families (n = 342). In addition, three of the four genetic associations detected for shell length (effect sizes from 3.3 to 4.3) are co-localised on LG4 near the mapped biomineralisation genes PFMG1, Pif177 and CS1. This study confirms previous quantitative genetic studies that oyster growth traits are polygenic, and provides additional evidence that these traits have sufficient genetic basis for improvement in animal selective breeding programmes. The preliminary QTL and genetic associations identified here also serve as prime candidates for ongoing analysis aiming to unravel the complex biological processes involved in pearl oyster growth and shell formation (i.e. biomineralisation). Furthermore, selection programmes incorporating marker information for growth traits with large QTL effects should further accelerate genetic gains within the P. maxima pearling industry.9 page(s

  • A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection
    BioMed Central, 2013
    Co-Authors: Jones, David B, Jerry, Dean R, Khatkar, Mehar S., Raadsma, Herman W., Zenger, Kyall R
    Abstract:

    Background: The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters.\ud \ud Results: A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes.\ud \ud Conclusions: This high-density SNP genetic map is the first comprehensive linkage map for any pearl oyster species. It provides an essential genomic tool facilitating studies investigating the genomic architecture of complex trait variation and identifying quantitative trait loci for economically important traits useful in genetic selection programs within the P. maxima pearling industry. Furthermore, this map provides a foundation for further research aiming to improve our understanding of the dynamic process of biomineralization, and pearl oyster evolution and synteny

  • Genome-Wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima
    'Springer Science and Business Media LLC', 2013
    Co-Authors: Jones, David B, Jerry, Dean R, Foret Sylvain, Konovalov, Dmitry A, Zenger, Kyall R
    Abstract:

    Pearl oysters are not only farmed for their gemstone quality pearls worldwide, but they are also becoming important model organisms for investigating genetic mechanisms of biomineralisation. Despite their economic and scientific significance, limited genomic resources are available for this important group of bivalves, hampering investigations into identifying genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). The silver-lipped pearl oyster, Pinctada maxima, is one species where there is interest in understanding genes that regulate commercially important pearl traits, but presently, there is a dearth of genomic information. The objective of this study was to develop and validate a large number of type I genome-wide single nucleotide polymorphisms (SNPs) for P. maxima suitable for high-throughput genotyping. In addition, sequence annotations and Gene Ontology terms were assigned to a large mantle tissue 454 expressed sequence tag assembly (96,794 contigs) and information on known bivalve biomineralisation genes was incorporated into SNP discovery. The SNP discovery effort resulted in the de novo identification of 172,625 SNPs, of which 9,108 were identified as high value [minor allele frequency (MAF) ≥ 0.15, read depth ≥ 8]. Validation of 2,782 of these SNPs using Illumina iSelect Infinium genotyping technology returned some of the highest assay conversion (86.6 %) and validation (59.9 %; mean MAF 0.28) rates observed in aquaculture species to date. Genomic resources presented here will be pivotal to future research investigating the biological mechanisms behind biomineralisation and will form a strong foundation for genetic selective breeding programs in the P. maxima pearling industry.12 page(s

Dean R. Jerry - One of the best experts on this subject based on the ideXlab platform.

  • Using Image Processing to Automatically Measure Pearl Oyster Size for Selective Breeding
    2019 Digital Image Computing: Techniques and Applications (DICTA), 2019
    Co-Authors: Adrian Lapico, Mangalam Sankupellay, Louis Cianciullo, Trina Myers, Preston Toole, Dean R. Jerry, Dmitry A. Konovalov, David B. Jones, Kyall R. Zenger
    Abstract:

    The growth rate is a genetic trait that is often recorded in pearl oyster farming for use in selective breeding programs. By tracking the growth rate of a pearl oyster, farmers can make better decisions on which oysters to breed or manage in order to produce healthier offspring and higher quality pearls. However, the current practice of measurement by hand results in measurement inaccuracies, slow processing, and unnecessary employee costs. To rectify this, we propose automating the workflow via computer vision techniques, which can be used to capture images of pearl oysters and process the images to obtain the absolute measurements of each oyster. Specifically, we utilise and compare a set of edge detection algorithms to produce an image-processing algorithm that automatically segments an image containing multiple oysters and returns the height and width of the oyster shell. Our final algorithm was tested on images containing 2523 oysters (Pinctada maxima) captured on farming boats in Indonesia. This algorithm achieved reliability (of identifying at least one required oyster measurement correctly) equal to 92.1%.

  • Genome-Wide SNP Validation and Mantle Tissue Transcriptome Analysis in the Silver-Lipped Pearl Oyster, Pinctada maxima
    Marine Biotechnology, 2013
    Co-Authors: David B. Jones, Sylvain Forêt, Dean R. Jerry, Dmitry A. Konovalov, Kyall R. Zenger
    Abstract:

    Pearl oysters are not only farmed for their gemstone quality pearls worldwide, but they are also becoming important model organisms for investigating genetic mechanisms of biomineralisation. Despite their economic and scientific significance, limited genomic resources are available for this important group of bivalves, hampering investigations into identifying genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). The silver-lipped pearl oyster, Pinctada maxima , is one species where there is interest in understanding genes that regulate commercially important pearl traits, but presently, there is a dearth of genomic information. The objective of this study was to develop and validate a large number of type I genome-wide single nucleotide polymorphisms (SNPs) for P. maxima suitable for high-throughput genotyping. In addition, sequence annotations and Gene Ontology terms were assigned to a large mantle tissue 454 expressed sequence tag assembly (96,794 contigs) and information on known bivalve biomineralisation genes was incorporated into SNP discovery. The SNP discovery effort resulted in the de novo identification of 172,625 SNPs, of which 9,108 were identified as high value [minor allele frequency (MAF) ≥ 0.15, read depth ≥ 8]. Validation of 2,782 of these SNPs using Illumina iSelect Infinium genotyping technology returned some of the highest assay conversion (86.6 %) and validation (59.9 %; mean MAF 0.28) rates observed in aquaculture species to date. Genomic resources presented here will be pivotal to future research investigating the biological mechanisms behind biomineralisation and will form a strong foundation for genetic selective breeding programs in the P. maxima pearling industry.

  • donor oyster derived heritability estimates and the effect of genotype environment interaction on the production of pearl quality traits in the silver lip pearl oyster Pinctada maxima
    Aquaculture, 2012
    Co-Authors: Dean R. Jerry, Renate Kvingedal, Joseph J. Taylor, Brad S Evans, Curtis E Lind, Alex Safari
    Abstract:

    The silver-lip pearl oyster, Pinctada maxima, produces the largest and most valuable pearls in the world. Despite the importance of this species very little is known about genetic parameters of commercially important pearl traits. As an initial step towards developing a selective breeding program, site selection effects, donor oyster derived genetic parameters and genotype by environment (G × E)interactions were estimated for pearl quality traits of P. maxima, originating from three populations (Aru, Bali, West Papua), reared at two commercial grow-out locations in Indonesia (Bali and Lombok). Microsatellite-based DNA parentage analyses were used to assign oysters to families and population of origin. Six pearl traits that are together the major determinants of pearl value (pearl weight (g), size (mm), shape, colour, complexion and lustre) were recorded at harvest. Pearls produced at the Lombok site were bigger and more valuable compared to pearls produced at the Bali site (P < 0.05). G × E interactions were present for size (rg = − 0.22), colour (rg = 0.28), weight (rg = 0.38), shape (rg = 0.56) and lustre (rg = 0.59) due to re-ranking of relative family performances at the two sites, although there were large standard errors associated with these estimates. Complexion was the only trait that showed little evidence for re-ranking (rg = 0.85). Donor related-heritability estimates for size (h2 = 0.13), lustre (h2 = 0.14), weight (h2 = 0.15), colour (h2 = 0.15) and shape (h2 = 0.06) were low, while for complexion estimates were moderate (h2 = 0.25). A positive and high genetic correlation was found between pearl size and weight (rg = 0.99), shape and complexion (rg = 0.65) and shape and colour (rg = 0.62); however, interestingly pearl weight was negatively genetically correlated with shape (rg = − 0.46), complexion (rg = − 0.11), colour (rg = − 0.03) and lustre (rg = − 0.15). Given the complex relationship amongst pearl quality traits and the likelihood for G × E interaction effects care should be executed when designing breeding objectives for the genetic improvement of these traits in P. maxima.

  • population and family growth response to different rearing location heritability estimates and genotype environment interaction in the silver lip pearl oyster Pinctada maxima
    Aquaculture, 2010
    Co-Authors: Renate Kvingedal, Joseph J. Taylor, Brad S Evans, Curtis E Lind, Mathilde Dupontnivet, Dean R. Jerry
    Abstract:

    Genetic parameters and genotype by environment interactions were estimated from the growth responses of silver-lip pearl oyster (Pinctada maxima) families originating from three populations (Aru, Bali, West Papua) reared at two Indonesian commercial sites (Bali and Lombok). Microsatellite-based DNA parentage analyses were used to assign oysters to their family and population of origin and four shell growth traits (anterior–posterior measurement (APM), dorsal–ventral measurement (DVM), shell width (SW) and wet weight (WW)) recorded at 14 and 18 months of age. Significant size differences were observed in all shell growth traits between oyster populations, and between oysters cultured at the different locations. Oysters from Bali and West Papua grew faster than those sourced from Aru at both culture sites, whilst the Lombok site produced the fastest growing oysters overall. Significant size differences were also present in shell traits among families, indicating a large amount of genetic variability present for potential breeding programs. Although there were significant familial size differences for shell traits, genetic correlation analyses showed little evidence for re-ranking of family performance among the two culture sites (rg = 0.89–0.99), suggesting low genotype by environment deviations among sites. Heritability of the shell traits DVM, APM and WW was moderate (0.15 ± 0.003 (DVM), 0.23 ± 0.030 (APM)) and as a consequence should respond to targeted selection.

  • decreased genetic diversity and a reduced effective population size in cultured silver lipped pearl oysters Pinctada maxima
    Aquaculture, 2009
    Co-Authors: Curtis E Lind, Brad S Evans, Joseph J. Taylor, Jens Knauer, Dean R. Jerry
    Abstract:

    Before selection programmes for aquaculture species can commence, a fundamental knowledge of how the culture process affects genetic diversity is requisite. “South Sea” pearl production, through the culture of the silver-lipped pearl oyster, Pinctada maxima, stands to gain substantially from genetic selection. Aquaculture techniques for P. maxima have progressed vastly, to a point where the majority of current operations are based on hatchery-propagated stock; however, there has been no investigation on how the culture process is affecting the genetic diversity of this species. To address this deficiency, we investigated the genetic diversity and effective population sizes (Ne) in three wild and five hatchery-produced P. maxima populations. Using six microsatellite DNA markers, cultured populations exhibited low Ne (3.5–9.2) and reduced allelic richness (29–44%) compared with their wild progenitors. Observed heterozygosities were not affected greatly, however, an increased mean pairwise genetic relatedness was observed in all cultured populations. The practice of mass spawning was identified as a major factor in the reduction of diversity, although diversity was not necessarily maintained when a more controlled spawning approach was utilised. Pedigree reconstructions revealed genetic diversity and Ne is affected by large skews in full-sib family representations (up to 40% from a single family, in a cohort using 28 broodstock), and could be due to differential survival rates amongst communally reared families. In order to maximise future selective breeding efforts, further research should be directed towards identifying critical stages of the culture process in which genetic diversity is lost