Identification of SNPs associated with robustness and greater reproductive success in the South African merino sheep using SNP chip technology

Sandenbergh, Lise (2015-04)

Thesis (PhD)--Stellenbosch University, 2015.

Thesis

ENGLISH ABSTRACT: Reproduction and robustness traits are integral in ensuring sustainable, efficient and profitable sheep farming. Increases in genetic gain of reproduction and robustness traits are however, hampered by low heritability coupled with the difficulty in quantification of these traits for traditional selective breeding strategies. The aim of the current study was therefore to identify genomic regions underlying variation in reproduction traits and elucidate quantitative trait loci (QTL) and/or genes associated with reproductive traits. The Elsenburg Merino flock has been divergently selected for the ability to raise multiple offspring and has resulted in a High and a Low line that differ markedly with regard to reproductive output and other robustness traits. The flock thus served as an ideal platform to identify genomic regions subject to selection for reproductive traits. To pinpoint genomic regions subject to selection, a whole-genome genotyping platform, the OvineSNP50 chip, was selected to determine the genotype of more than 50 000 SNPs spread evenly across the ovine genome. The utility of the OvineSNP50 chip was determined for the Elsenburg Merino flock as well as additional South African Merino samples and three other important South African sheep breeds, the Blackheaded Dorper, South African Mutton Merino (SAMM) and the Namaqua Afrikaner. Although genotyping analysis of the Elsenburg Merino flock indicated some signs of poor genotype quality, the overall utility of the genotype data were successfully demonstrated for the South African Merino and the other two commercial breeds, the Dorper and SAMM. Genotyping results of the Namaqua Afrikaner and possibly other indigenous African breeds may be influenced by SNP ascertainment bias due to the limited number of indigenous African breeds used during SNP discovery. Analysis of pedigree, phenotypic records and SNP genotype data of the Elsenburg Merino cohort used in the current study, confirmed that the lines are phenotypically as well as genetically distinct. Numerous putative genomic regions subject to selection were identified by either an FST outlier approach or a genomic scan for regions of homozygosity (ROH) in the High and Low lines. Although annotated genes with putative roles in reproduction were identified, the exact mechanism of involvement with variation in reproduction traits could not be determined for all regions and genes. Putative ROH overlapped with QTL for several reproduction, milk, production and parasite resistance traits, and sheds some light on the possible function of these regions. The overlap between QTL for production and parasite resistance with putative ROH may indicate that several, seemingly unrelated traits add to the net-reproduction and may have been indirectly selected in the Elsenburg Merino flock. A SNP genotyping panel based solely on reproduction traits may therefore be ineffective to capture the variation in all traits influencing reproduction and robustness traits. A holistic selection strategy taking several important traits, such as robustness, reproduction and production into account may as such be a more effective strategy to breed animals with the ability to produce and reproduce more efficiently and thereby ensure profitable and sustainable sheep farming in South Africa.

AFRIKAANSE OPSOMMING: Reproduksie- en gehardheids-eienskappe is noodsaaklik om volhoubare, doeltreffende en winsgewende skaapboerdery te verseker. ‘n Toename in genetiese vordering in reproduksie- en gehardheids-eienskappe word egter bemoeilik deur lae oorerflikhede tesame met die probleme in kwantifisering van hierdie eienskappe vir tradisionele selektiewe diereteelt strategieë. Die doel van die huidige studie was dus om gebiede in die genoom onderliggend tot variasie in reproduksie-eienskappe te identifiseer en die rol van verwante kwantitatiewe eienskap loki (KEL) en/of gene met reproduktiewe eienskappe te bepaal. Die Elsenburg Merinokudde is uiteenlopend geselekteer vir die vermoë om meerlinge groot te maak en het gelei tot 'n Hoë en 'n Lae lyn wat merkbaar verskil ten opsigte van reproduksie-uitsette en ander gehardheids-eienskappe. Die kudde het dus gedien as 'n ideale platform om genomiese areas onderhewig aan seleksie vir reproduksie-eienskappe te identifiseer. Om vas te stel waar genomiese areas onderhewig aan seleksie gevind kan word, is ‘n heel-genoom genotiperingsplatform, die OvineSNP50 skyfie, gekies om die genotipes van meer as 50 000 enkel nukleotied polimorfismes (ENPs) eweredig versprei oor die skaap genoom, te bepaal. Die nut van die OvineSNP50 skyfie is bepaal vir die Elsenburg Merinokudde sowel as addisionele Suid-Afrikaanse Merinos en drie ander belangrike Suid-Afrikaanse skaaprasse, die Swartkop Dorper, Suid-Afrikaanse Vleismerino (SAVM) en die Namakwa Afrikaner. Hoewel genotipe resultate van die Elsenburg Merino kudde sommige tekens van swak genotipe gehalte getoon het, kon die algehele nut van die genotipering resultate vir die Suid-Afrikaanse Merino en die ander twee kommersiële rasse, die Dorper en SAVM, bevestig word. Genotipering resultate van die Namakwa Afrikaner en moontlik ook ander inheemse Afrika rasse kan deur ENP vasstellingspartydigheid beïnvloed word as gevolg van die beperkte aantal inheemse Afrika rasse gebruik tydens ENP ontdekking. Ontleding van stamboom inligting, fenotipe rekords en ENP genotipe data van die Elsenburg Merino-kohort gebruik in die huidige studie, het bevestig dat die lyne fenotipies asook geneties verskil. Talle vermeende genomiese areas onderhewig aan seleksie is geïdentifiseer deur 'n FST uitskieter benadering of deur ‘n genomiese skandering vir gebiede van homogositeit (GVH) in die Hoë en Lae lyne. Hoewel geannoteerde gene met potensiële rolle in reproduksie geïdentifiseer is, kan die presiese meganisme van betrokkenheid by variasie in reproduksie-eienskappe nie bevestig word vir al die gebiede en gene nie. Vermeende GVH oorvleuel met KEL vir 'n paar reproduksie-, melk-, produksie- en parasietweerstand-eienskappe, en werp daarom lig op die moontlike funksie van hierdie gebiede. Die oorvleueling tussen KEL vir produksie en parasietweerstand met vermeende GVH kan daarop dui dat 'n hele paar, skynbaar onverwante, eienskappe bydrae tot net-reproduksie, wat indirek geselekteer mag wees in die Elsenburg Merino-kudde. ‘n ENP genotiperingspaneel uitsluitlik gebaseer op reproduksie-eienskappe mag daarom onvoldoende wees om die variasie in alle eienskappe wat betrekking het op reproduksie- en gehardheids-eienskappe, in te sluit. ‘n Holistiese seleksie strategie wat verskeie belangrike eienskappe, soos gehardheid, reproduksie en produksie in ag neem, mag ‘n meer effektiewe strategie wees om diere te teel met die vermoë om in 'n meer doeltreffende manier te produseer en reproduseer en om daardeur winsgewende en volhoubare skaapboerdery in Suid-Afrika te verseker.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/97093
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