Association analysis of coat colour in blue wildebeest (Connochaetes taurinus taurinus)

Van Deventer, Riana (2019-12)

Thesis (MScAgric)--Stellenbosch University, 2019.

Thesis

ENGLISH ABSTRACT: The blue wildebeest (Connochaetes taurinus taurinus) is an economically important African antelope species that is regularly sold on game auctions and is widely utilised in commercial hunting in South Africa. A colour variant of the blue wildebeest, known as the golden wildebeest, has become one of the most common colour variant animals that wildlife ranchers breed with. Despite the economic importance of blue wildebeest, very few genomic resources are currently available for this species that can be used for management and research. This study aimed to use a genotyping-by-sequencing (GBS) approach to discover and genotype single nucleotide polymorphisms (SNPs) in blue wildebeest, and to use these SNPs in a case-control genome-wide association study (GWAS) to identify putative candidate genes involved in blue wildebeest pigmentation. The sample population consisted of 94 blue wildebeest, which included 35 blue wildebeest with the golden coat colour variation. The DArTseq genotyping platform was used for SNP discovery and a total of 20 563 SNPs, each located in a 69 bp marker sequence, were identified. The generated SNP markers were of high quality with a high average reproducibility (>99%) and a low percentage (~9.21%) missing data. In addition, the DArTseq platform was able to generate a large number of informative SNPs for blue wildebeest, exhibiting high heterozygosity and resolving power among the population samples. Furthermore, the Bos taurus genome was used for the in silico mapping of the marker sequences to estimate the distribution of the generated SNPs throughout the genome and to identify putative orthologous genes. A total of 6 020 (29.28%) SNP sequences were successfully mapped against the bovine genome of which 3 907 mapped to putative gene orthologues. The SNP sequences mapped to all of the bovine chromosomes establishing their genome-wide distribution. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions. The GWAS identified 377 SNPs that were significantly associated with coat colour in blue wildebeest. Eight of these DArTseq SNP markers mapped to seven different genes that were considered as putative candidate genes for coat colour determination based on previous literature reports. Based on their reported biological function, the putative candidate genes for coat colour determination in blue wildebeest are myosin VC (MYO5C), myosin VIIA (MYO7A), solute carrier family 6 member 3 (SLC6A3), solute carrier family 28 member 2 (SLC28A2), dopamine receptor D2 (DRD2), frizzled class receptor 4 (FZD4) and tyrosinase (TYR). The established mode of inheritance for the majority of the SNPs located in these candidate genes were additive. This observation, together with the limited gene-gene interaction observed between the candidate SNPs, suggest that coat colour in blue wildebeest could be a quantitative threshold trait rather than a simple autosomal recessive trait as originally suspected. This study represents the first large genetic polymorphism discovery performed in an African antelope species that is farmed commercially. The generated DArTseq markers could be a useful resource for the genetic management of ranched blue wildebeest, and could also be used to facilitate research in this species. Furthermore, this study provides a foundation to further investigate the genetic underpinning of coat colour in blue wildebeest.

AFRIKAANSE OPSOMMING: Die blou wildebees (Connochaetes taurinus taurinus) is ‘n wildsbokspesie van Afrika wat gereeld op wildsveilings verkoop word en van kommersiële belang is in die Suid-Afrikaanse jagbedryf. ‘n Kleurvariant van die blou wildebees, bekend as die goue wildebees, het onlangs een van die mees algemene kleurvariante geword waarmee wildsboere teël. Ten spyte van die ekonomiese belang van die blou wildebees, is die genomiese hulpbronne beskikbaar vir populasiebestuur en navorsing baie beperk vir hierdie spesie. Hierdie studie het gepoog om ‘n genotipering-deur-volgordebepaling (GBS) benadering te gebruik om enkel nukleotied polimorfismes (SNPs) te identifiseer en te genotipeer in die genoom van die blou wildebees. Verder, is hierdie SNPs gebruik in ‘n genoom-wye assosiasie studie (GWAS) om kandidaatgene te identifiseer wat betrokke is by pigmentasie in blou wildebeeste. Die steekproefpopulasie het bestaan uit 94 blou wildebeeste, wat 35 individue met die goue pelskleur ingesluit het. Die DArTseq platform is gebruik vir SNP identifikasie. ‘n Totaal van 20 563 SNPs, elkeen geleë in ‘n 69 bp merkervolgorde, is geЇdentifiseer. Die geЇdentifiseerde SNPs was van ‘n hoë kwaliteit, aangesien die SNPs hoogs reproduseerbaar was (>99%) en die persentasie ontbrekende data in die datastel laag was (~9.21%). Verder, was die DArTseq platform in staat om ‘n groot aantal informatiewe SNPs te genereer wat hoë heterosigositeit en diskriminasievermoë getoon het tussen die individue van die steekproefpopulasie. Die Bos taurus genoom is gebruik vir die in silico kartering van die merkervolgordes om, sodoende, die verspreiding van die SNPs deur die genoom te beraam en om ortoloë-gene te identifiseer. ‘n Totaal van 6 020 (29.28%) van die SNP merkervolgordes was suksesvol karteer teen die beesgenoom, waarvan 3 907 karteer is teen ortoloë-gene. Die merkervolgordes is karteer oor al die chromosome van die bees, wat die genoom-wye verspreiding van die SNPs bevestig het. Verder, het funksionele annotasie van die merkervolgordes ‘n wye verskeidenheid funksies onthul. Die GWAS het 377 SNPs identifiseer wat beduidend geassosieer was met pelskleur in die blou wildebees. Agt van hierdie DArTseq SNPs was gekarteer teen sewe verskillende gene wat oorweeg was as kandidaatgene vir die bepaling van pelskleur gebaseer op vorige literatuurverslae. Hierdie kandidaat gene is miosien VC (MYO5C), miosien VIIA (MYO7A), oplossingsdraer famile 6 lid 3 (SLC6A3), oplossingsdraer 28 lid 2 (SLC28A2), dopamien reseptor D2 (DRD2), frizzel-klas reseptor 4 (FZD4) and tirosinase (TYR). Die meeste van die SNPs geleë in die kandidaatgene het ‘n additatiewe oorerwingsmodel getoon. Hierdie bevinding, tesame met die beperkte geen-geen interaksie wat waargeneem is tussen die kandidaat SNPs, stel voor dat pelskleur in die blou wildebees moontlik ‘n kwantitatiewe drumpel-eienskap is eerder as ‘n outosomaal resessiewe eienskap soos oorspronklik vermoed. Hierdie studie verteenwoordig die eerste grootskaalse polimorfisme identifikasie wat uitgevoer is in ‘n wildsbokspesie waarmee kommersieël geboer word. Hierdie nuwe SNP merkers kan ‘n nuttige hulpbron wees vir die genetiese bestuur van blou wildebees populasies en kan ook gebruik word om navorsing in hierdie spesie te fasiliteer. Laastens, dien hierdie studie as ‘n fondasie vir verdere ondersoek in verband met die onderliggende genetiese basis van pelskleur in die blou wildebees.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/106929
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