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The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus)
Thesis (MScAgric)--Stellenbosch University, 2023.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2023
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| _version_ | 1867614120363163648 |
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| access_status_str | Open Access |
| author | Sampson, Joshua |
| author2 | Rhode, Clint |
| author_browse | Rhode, Clint Sampson, Joshua |
| author_facet | Rhode, Clint Sampson, Joshua |
| author_sort | Sampson, Joshua |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2023. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/128379 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:46:59.291Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/128379 The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) Sampson, Joshua Rhode, Clint Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics. Argyrosomus japonicus -- Growth Argyrosomus -- Habitat -- South Africa Fishes -- Genetics Aquaculture -- Genetic engineering -- South Africa Single nucleotide polymorphisms - Variation Dusky Kob -- Classification -- Genetic aspects UCTD Thesis (MScAgric)--Stellenbosch University, 2023. ENGLISH ABSTRACT: The misuse of marine resources, and exploitation of global fisheries has led to a severe decline in wild populations of finfish. One such species, dusky kob (Argyrosomus japonicus), has collapsed in South Africa as a direct result of decades of commercial, subsistence and recreational fishing. This has placed initiative to establish dusky kob in aquaculture, with effort focused on characterising the genetic determinants of complex traits such as growth rate, to improve efficiency and production outputs. Current practices for dusky kob have shifted from using wild broodstock, to a combination of wild and fast-growing cultured individuals, in mass spawning to produce offspring for market. This method has significant short-term benefits for production gains in aquaculture, however it places the stock in a genetically disadvantageous position by convoluting pedigree inference and increasing the likelihood of inbreeding in ensuing generations. Furthermore, it distorts population structure by skewing family composition, which can convolute the identification of markers associated with traits of interest (such as growth). The relationship between traits has recently received considerable research, as determination of a biological link between two complex traits may allow for simultaneous improvement, as well as an expanded array of markers for selection. Therefore, this study aimed to identify and characterise SNPs, in neurobehavioral developmental genes, significantly associated with differential growth in a size-graded commercial population of dusky kob. Thirteen microsatellite markers, genetic diversity estimates, and family structure were assessed. Comparisons between broodstock (n = 52) and progeny (n = 96) detected a genetic bottleneck between generations, as a result of a small number of breeders which contributed to the spawning event (n = 9). Broodstock contributions were distorted with a single breeding pair contributing 67% of the total progeny and eight additional low-contributing families identified. No significant differences were detected in growth performance between families. This study indicates that the methods of selective breeding and hormonal induction currently applied to dusky kob are not sufficient. Following a candidate gene approach, five gene regions associated with neurobehavior were selected. A total of 13 novel SNPs in two genes were identified. Case-control analysis identified six SNPs (three in each gene) significantly associated with differential growth, and highlighted family structure as a significant covariate in association analyses. Namely, quantitative correction for family structure using eigenvalues created from microsatellite data outperforms categorical correction using family name. Out of the six SNPs associated with growth, a single non-synonymous SNP was identified, in brain- derived neurotropic factor (BDNF). This mutation results in a significant disruption of protein tertiary structure in small individuals possibly resulting in decreased feeding signals, through the substitution of a serine residue for a proline residue (p. Ser119Pro). The findings of this study therefore suggest a biological link between neurobehavioral development and growth, in dusky kob. Furthermore, it demonstrated the power of utilising a combination of microsatellite and SNP markers: genetic diversity assessment, pedigree inference, marker identification, and family structure correction. AFRIKAANSE OPSOMMING: Die misbruik van mariene hulpbronne en ontginning van visserye het tot 'n ernstige afname in wildvis populasies gelei. Boerkabeljou (Argyrosomus japonicus) het in Suid-Afrika as 'n direkte gevolg van dekade kommersiële, bestaans- en ontspanningsvisvang ineengestort.Dit het inisiatief om boerkabeljou in akwakultuur te vestig geplaas. Daar is fokus aan die karakterisering van die genetiese oorsake van komplekse eienskappe geplaas, soos groeitempo, om doeltreffendheid en produksie-uitsette te verbeter. Huidige praktyke vir boerkabeljou het na die gebruik van wilde broei aan 'n kombinasie van wilde en vinnig groeiende gekweekte individue geskuif, in massakaai om nageslag vir mark te produseer. Hierdie metode hou aansienlike korttermynvoordele vir produksiewinste in akwakultuur, maar dit plaas die vee in 'n geneties nadelige posisie deur stamboomafleiding te verdraai. Die waarskynlikheid van inteling in opvolgende generasies is daarom verhoog. Verder verwring dit bevolkingstruktuur deur gesinsamestelling te verskeef, Dit kon die identifikasie van merkers wat eienskappe met belang (soos groei) geassosieer word verwikkel. Die verwantskap tussen eienskappe het onlangs aansienlike navorsing ontvang, aangesien die bepaling van 'n biologiese verband tussen twee komplekse eienskappe gelyktydige verbetering, sowel as 'n uitgebreide reeks merkers vir seleksie kon moontlik maak. Daarom het hierdie bestudeer ten doel gehad om ENPs te identifiseer en te karakteriseer, in neurogedragsontwikkelings gene, wat met differensiële groei in 'n grootte-gegradeerde kommersiële populasie van boerkabeljoi betekenisvol geassosieer kan word. Dertien mikrosatellietmerkers is gebruik om genetiese diversiteitskattings en familiestruktuur te assesseer. Vergelykings tussen broeistok (n = 52) en nageslag generasie (n = 96) het 'n genetiese bottelnek tussen generasies opgespoor, as gevolg van 'n klein aantal telers (n = 9) wat tot die paaigebeurtenis bygedra het. Broeibydraes is verwring met 'n enkele broeipaar wat 67% van die totale nageslag bygedra het en agt bykomende lae-bydraende families is ook geïdentifiseer. Geen beduidende verskille tussen gesinne is in groeiprestasie bespeur nie. Hierdie studie dui aan dat die metodes van selektiewe teling en hormonale induksie wat tans op dusky kob toegepas word nie voldoende is nie. Na aanleiding van 'n kandidaat-geenbenadering is vyf geenstreke wat met neurogedrag geassosieer word geselekteer. 'n Totaal van 13 nuwe ENP's in twee gene is geïdentifiseer. Gevalle-kontrole-analise het ses ENP's (drie in elke geen) wat beduidend met differensiële groei geassosieer word geïdentifiseer, en het gesinstruktuur as 'n beduidende kovariaat in assosiasie-ontledings uitgelig. Kwantitatiewe regstelling vir familiestruktuur deur gebruik van eiewaardes wat uit mikrosatellietdata geskep is, presteer naamlik beter as kategoriese regstelling deur familienaam te gebruik. Uit die ses ENP wat met groei geassosieer word is 'n enkele nie-sinonieme ENP, wat binne brein-afgeleide neurotropiese faktor (BDNF) is, geïdentifiseer. Hierdie mutasie lei tot 'n beduidende ontwrigting van proteïen tersiêre struktuur in klein individue wat moontlik lei tot verminderde voedingsseine, deur die vervanging van 'n serienresidu vir 'n prolienresidu (p. Ser119Pro). Die bevindinge van hierdie studie dui dus op 'n biologiese verband tussen neurogedragsontwikkeling en groei in boerkabeljou. Verder het dit die krag van die gebruik van 'n kombinasie van mikrosatelliet- en ENP-merkers vir genetiese diversiteitsbepaling, stamboomafleiding, merker identifikasie en familiestruktuurkorreksie gedemonstreer. Masters 2023-03-06T08:59:22Z 2023-08-30T13:05:53Z 2023-03-06 2023-03-06T08:59:22Z 2023-08-31T09:18:32Z 2023-03-06T08:59:22Z 2023-08-31T09:18:32Z 2023-03 Thesis https://scholar.sun.ac.za/handle/10019.1/128379 en_ZA Stellenbosch University application/pdf xvii, 125 pages : illustrations, maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Argyrosomus japonicus -- Growth Argyrosomus -- Habitat -- South Africa Fishes -- Genetics Aquaculture -- Genetic engineering -- South Africa Single nucleotide polymorphisms - Variation Dusky Kob -- Classification -- Genetic aspects UCTD Sampson, Joshua The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) |
| title | The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) |
| title_full | The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) |
| title_fullStr | The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) |
| title_full_unstemmed | The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) |
| title_short | The relationship between genetic variation in neurobehavioral developmental genes, and growth rate, in dusky kob (Argyrosomus japonicus) |
| title_sort | relationship between genetic variation in neurobehavioral developmental genes and growth rate in dusky kob argyrosomus japonicus |
| topic | Argyrosomus japonicus -- Growth Argyrosomus -- Habitat -- South Africa Fishes -- Genetics Aquaculture -- Genetic engineering -- South Africa Single nucleotide polymorphisms - Variation Dusky Kob -- Classification -- Genetic aspects UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/128379 |
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