Genetic and phenotypic characterisation of commercial dusky kob (Argyrosomus japonicus) cohorts

Jenkins, Stephan Francois (2018-03)

Thesis (MSc)--Stellenbosch University, 2018.

Thesis

ENGLISH ABSTRACT: Dusky kob, Argyrosomus japonicus, is a large Sciaenid finfish that has been identified as an emergent aquaculture species in South Africa. Current production practices for dusky kob are based on mass spawning of genetically unimproved (wild-caught) broodstock. In recent years, considerable efforts have been initiated to retain first filial (F1)-generation animals with fast growth rate as potential broodstock for a selective breeding programme. Although a few studies have been conducted on the species, previous studies have not addressed fundamental questions related to the effects of mass spawning production practices for the development of a selective breeding programme for dusky kob. This study aimed not only to bridge this gap, but also to investigate, for the first time, the potential for selection for increased growth rate in dusky kob. By using 14 microsatellite markers, the genetic properties of a wild population (n = 34) were compared to an F1 cohort that represents three temporal groups that were sampled throughout the production cycle (i.e. from weaning to market size). Despite a heterozygote excess, likely as a result of a genetic bottleneck, the F1 cohort displayed comparatively low levels of allelic diversity with respect to the wild population (P < 0.01). This was attributed primarily to the establishment of a small founder breeding population (n = 12), but also to low participation amongst females during the spawning event. Parentage analyses indicated only five (full-sib) F1 families. Families with low starting contributions were not eliminated following removal of the smallest animals by culling. Culling, however, did contribute to a significant increase in genetic relatedness and a single family represented 88% of the market-sized group, suggesting that these practices may have the potential to further complicate the selection of unrelated broodstock in commercial mass spawning species. Pedigree relations were inferred for an additional three F1 cohorts each produced from a breeding population comprising no more than five wild captive broodstock. Averaged relatedness amongst the three F1 cohorts was comparatively higher than that detected for the F1 animals of the first spawning event analysed. Furthermore, estimates of direct heritability (h2) were 0.34±0.25 and 0.36±0.27 for juvenile weight and length, respectively, and the genetic correlation between the traits was 0.98±0.03. Although estimates of h2 are likely biased due to small sample sizes, and possibly maternal and/or competition effects, it is concluded that selective breeding for increased growth rate can be successful in juvenile dusky kob. However, the current analysis indicates that F1 broodstock candidates are likely to be related and when bred will lead to excessive inbreeding. As this could have grave consequences for the profitability of dusky kob production, it is advisable that a selection programme for the species will need to consider both individual growth performance and genetic relatedness, e.g. using walk-back selection. Continued monitoring is therefore advised.

AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse kabeljou, Argyrosomus japonicus, algemeen bekend as “dusky kob”, is 'n groot Sciaenied vinvis wat as 'n opkomende akwakultuurspesie geïdentifiseer is. Huidige produksiepraktyke vir kabeljou is gebaseer op die massa-teling van onverbeterde (wild gevang) populasies. Die afgelope jare is aansienlike pogings egter aangewend om F1-generasie diere met 'n vinnige groeikoers as potensiële broeidiere te behou, met die spesifieke doel om 'n selektiewe teelprogram te begin. Vorige studies het nie fundamentele vrae wat verband hou met die uitwerking van massaproduksiepraktyke op die ontwikkeling van 'n teelprogram vir dusky kob aangespreek nie. Hierdie studie het gemik om nie net hierdie gaping te oorbrug nie, maar ook om vir die eerste keer die potensiaal vir seleksie vir verhoogde groeikoers in kabeljou te ondersoek. Deur 14 mikrosatelliet-merkers te gebruik, is die genetiese eienskappe van 'n wilde populasie (van 34 individue) met dié van drie temporale F1-kohorte wat gedurende die produksiesiklus (dit wil sê van speen tot markgrootte) gemonster is, vergelyk. Algeheel het die F1 diere 'n aansienlike hoeveelheid alleliese diversiteit verloor in vergelyking met die wilde individue (P < 0.01). Dit is hoofsaaklik toegeskryf aan die totstandkoming van ʼn klein stammende broeipopulase (van 12 individue), maar ook tot 'n lae deelname onder vroulike broeivisse tydens die broeigeleenthied. Slegs vyf nageslagfamilies is aangedui. Families met 'n lae aanvangsbydrae is nie uitgeskakel na die verwydering van die kleinste diere deur uitdunning nie. Uitdunning het egter bygedrae tot ʼn beduidende toename in genetiese verwantskap en in enkele nageslagfamilie het 88% van die markgrootte groep verteenwoordig. Dit dui daarop dat hierdie praktyke die potensiaal kan hê om die seleksie van onverwante broeiviskandidate in kommersiële massa broeispesies verder te bemoeilik. Stamboomverhoudings is afgelei vir 'n addisionele drie F1-kohorte wat elk geproduseer was van 'n broeipopulasie van nie meer as vyf wild-gevange diere nie. Die genetiese verwantskap tussen die drie F1-kohorte was aansienlik hoër as dié wat vir die vorige broeigeleentheid bespeur is. Verder is genetiese parameters vir liggaamsgewig en standaardlengte bereken. Oorerflikheid (h2) was 0.34±0.25 en 0.36±0.27 vir die twee groeiverwante eienskappe, respektiewelik, en die genetiese korrelasie tussen die twee eienskappe was 0.98±0.03. Alhoewel ramings van h2 waarskynlik bevooroordeel is as gevolg van klein steekproefgroottes, en moontlik moederlike- en/of kompetisie effekte, word daar tot die gevolgtrekking gekom dat selektiewe teling vir verhoogde groeikoers suksesvol kan wees in kabeljou. Uit die resultate in die huidige studie is dit egter duidelik dat F1-broeiviskandidate verwant sal wees en dus sal inteel. Aangesien dit ernstige gevolge kan hê vir die produktiwiteit van akwakultuur, is dit raadsaam dat 'n seleksieprogram vir die spesie beide individuele groeiprestasie en genetiese verwantskap in ag moet neem, bv. deur van terugloop seleksie gebruik te maak. Voortgesette monitering word dus aangeraai.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/103687
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