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

Le Cordeur, Nathan Seth (2020-03)

Thesis (MScAgric)--Stellenbosch University, 2020.

Thesis

ENGLISH ABSTRACT: Argyrosomus japonicus (dusky kob) is a large sciaenid finfish indigenous to South Africa, and as an emerging aquaculture species, current production practices rely on mass spawning of wild progenitors to produce first filial (F1) - offspring for commercial trade. Economically, this approach can be quite lucrative, as the high fecundity of this species allow for the use of small breeding groups to generate thousands of offspring in a single spawn. In recent years, however, considerable efforts have been initiated to retain such animals with faster growth rate as breeders to the next generation, in order to improve growth related traits through selective breeding. Although mass spawning increases production outputs in the short term, under aquacultural conditions, however, mass spawning complicates the maintenance of pedigree records, thus hindering genetic improvement of the species due to the risk of inbreeding depression in subsequent generations. Therefore, the aim of this study was to genetically and phenotypically characterise commercial cohorts of dusky kob within the context of implementing a selective breeding programme. This aim was accomplished by achieving the following three objectives: to assess the genetic constitution and family structure within dusky kob broodstock and derived offspring cohorts; to estimate phenotypic and genetic parameters for growth traits in dusky kob; and to assess the frequency of genetic polymorphisms associated with growth in a large and small cohort of dusky kob using a candidate gene approach. This was done using 12 microsatellite markers, the genetic properties of a wild population (n = 34) and a commercially used broodstock cohort (n = 23) were compared to an offspring cohort comprised of individuals originating from two spawning events. Despite a heterozygous excess, likely due to the occurrence of a genetic bottleneck, the resulting offspring cohort displayed significantly reduced levels of allelic diversity with respect to both the wild samples and the commercially used broodstock (P < 0.01). This substantial reduction is primarily attributed to the relatively low numbers of breeders utilised in each spawning event (three and four respectively), but also the low participation among breeders, as parentage analysis indicated only two full-sibling families, one from each spawning event respectively. Therefore, the results of this study suggest that hormonal induction of adult breeders may not be sufficient to stimulate effective spawning in dusky kob. The sample size of the study population was subsequently increased by combining pedigree and phenotypic data, for three growth related traits (weight, length and Fulton’s conditioning index), from the current study with that obtained from a relevant study conducted on dusky kob in 2017. Consequently, estimates of narrow-sense heritability (h2) were 0.40 ± 0.25 and 0.39 ± 0.25 for juvenile weight and length respectively, with a strong genetic correlation observed between these traits (1.00 ± 0.01). Although these estimates are likely biased due to detected environmental effects, small sample sizes (i.e. few families) and possible maternal effects, the observed result suggest a moderate to high heritable genetic component to phenotypic expression of growth related traits in dusky kob. Resultantly, a candidate gene approach was employed, with the aim of identifying molecular variants, single nucleotide polymorphisms (SNP’s) in particular, that may be associated with increased growth rate. Sequencing of partial genes and subsequent genotyping via direct sequencing revealed two SNPs, one in the Ladybird homeobox 1 b gene (lbx1b_c.114) and one in the Tankyrase a gene (tnksa_c.69), that display statistical association with the trait of interest. Therefore, lbx1, which reportedly has important functions in neural and muscle development, and tnksa, which have key regulatory roles in glucose transport and insulin stimulated glucose uptake may be considered as putative candidate genes for investigating growth related traits in dusky kob, and may be useful candidates for marker-assisted selection.

AFRIKAANSE OPSOMMING: Argyrosomus japonicus (kabeljou) is ‘n groot Sciaenied vinvis, en wat as ʼn opkomende akwakultuur spesie, huidiglik staatmaak op die massa-teling van wilde ouers om die eerste nageslag (F1) vir kommersiële handel te produseer. Ekonomies gesien, kan hierdie benadering winsgewend wees, aangesien die hoë vrugbaarheid van hierdie spesie toelaat dat duisende individue in ʼn enkele kuit van ʼn klein telingsgroep geproduseer kan word. Daar is onlangs ʼn aansienlike poging aangewend om diere met ʼn vinniger groeitempo as telers vir die volgende generasie te behou, om sodoende groeiverwante eienskappe deur selektiewe teling te verbeter. Alhoewel massa-teling produksie-uitsette op korttermyn verhoog, bemoeilik dit die instandhouding van stamboekrekords, en belemmer dit daardeur genetiese verbetering van die spesie, as gevolg van die verhoogte risiko vir intelingsdepressie in die daaropvolgende generasies. Daarom was die doel van hierdie studie om kommersiële kabeljou geneties en fenotipies te karakteriseer, binne die konteks vir die implementering van ʼn genetiese verbeteringsprogram. Hierdie doelwit is bereik deur die volgende drie doelstellings: om die genetiese samestelling en familiestruktuur binne die teelstoet en afgeleide nageslagkohorte te evalueer; om fenotipiese en genetiese parameters vir groeienskappe in kabeljou te skat; en om die frekwensie van genetiese polimorfismes geassosieer met groei in 'n groot en klein kohort van kabeljou met behulp van 'n kandidaatgenbenadering te bepaal. Twaalf mikrosatelliet merkers was gebruik om die genetiese eienskappe van ʼn wilde populasie (n = 34) en kommersiëel geproduseerde teeldiere (n = 23) te vergelyk met nageslag wat afkomstig is van twee broeigeleenthede (kuite). Ondanks ʼn oormaat van heterosigositeit, wat heel waarskynlik veroorsaak is deur ʼn genetiese bottelnek, het die nageslag betekenisvolle verlaagde vlakke van alleliese diversiteit getoon in vergelyking met beide die wilde populasie en die kommersiëel geproduseerde teeldiere (P < 0.01). Hierdie aansienlike afname word hoofsaaklik toegeskryf aan die relatief lae getal telers wat gebruik is in elke broeigeleentheid (drie en vier onderskeidelik), maar ook as gevolg van die lae deelname van hierdie telers, aangesien slegs twee volsib-families waargeneem is, een afkomstig van elke broeigeleentheid. Die resultate van hierdie studie dui dus daarop dat hormonale induksie van volwasse kabeljoutelers moontlik nie voldoende is om effektiewe deelname binne broeigeleenthede te stimuleer nie. Die steekproefgrootte van hierdie studiepopulasie is vervolgens verhoog, deur die stamboek- en fenotipiese data vir drie groeiverwante eienskappe (gewig, lengte en Fulton se kondisioneringsindeks) van die huidige studie, sowel as ʼn verwante studie op kabeljou, wat in 2017 uitgevoer is, te kombineer. Gevolglik, was die nou-sin oorerflikheid (h2) bereken op 0.40 ±0.25 en 0.39 ±0.25 onderskeidelik vir gewig en lengte, met ‘n sterk genetiese korrelasie tussen hierdie eienskappe (1.00 ±0.01). Alhoewel die huidige oorerflikheidsberekeninge moontlik beïnvloed is deur waargenome omgewingseffekte, klein steekproefgroottes (min families) en moontlike moederlike effekte, dui die waargenome resultate op ʼn gematigde tot hoë erflike genetiese komponent van die fenotipiese uitdrukking van groeiverwante eienskappe binne kabeljou. Gevolglik was ʼn kandidaatgeenbenadering toegepas met die oog om molekulêre variante, meer spesifiek enkel nukleotied polifmorfismes (ENPs), te identifseer wat kan bydra tot verhoogde groeitempo. Die gedeeltelike volgordebepaling van kandidaatgene en gevolglike genotipering het twee ENPs, een binne die “Ladybird homeobox 1 b” geen ((lbx1b_c.114), en een binne die “tankyrase a” geen (tnksa_c.69), geïdentifseer wat statistiese assosiasie getoon het met groei. Daarom kan hierdie twee gene, lbx1 wat volgens vorige studies ʼn belangrike funksie in neurale en spierontwikkeling het, en tnksa met ʼn regulatoriese rol in glukose-vervo en insulien gestimuleerde glukose opname, oorweeg word as moontlike kandidaatgene om groeiverwante eienskappe binne kabeljou verder te ondersoek, met toepassing vir merker bemiddelde seleksie.

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