Thesis (M.S.)--Auburn University, 2007. / Abstract. Vita. Includes bibliographic references (ℓ. 107-127)

Thesis (M.Sc.(Agric.)) -- University of Pretoria, 2008. / Abstract in English. Includes bibliographical references.

Assignment (MPhil)--University of Stellenbosch, 2007. / Bibliography. Also available via the Internet.

Thesis (M.S.)--West Virginia University, 1999. / Title from document title page. Document formatted into pages; contains vi, 48 p. : ill. Vita. Includes abstract. Includes bibliographical references (p. 25-47).

Thesis (M.Sc.(Agric)(Animal Science)) -- University of Pretoria, 2001. / Includes bibliographical references.

Thesis (M.S.)--University of Tennessee, Knoxville, 2008. / Title from title page screen (viewed on Sept. 15, 2009). Thesis advisor: Ernest Bazen. Vita. Includes bibliographical references.

Thesis (M.S.)--West Virginia University, 2005. / Title from document title page. Document formatted into pages; contains vii, 73 p. : ill. (some col.). Includes abstract. Includes bibliographical references.

Thesis (MPhil)--University of Stellenbosch, 2005. / Bibliography. Also available via the Internet.

Thesis (MScFoodSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Modern consumers are health conscious and are shifting towards more naturally produced products such as free range chicken. Commercial broiler strains are not suitable for free range rearing and an alternative genotype is needed that will serve the South African market with the acceptable meat quality as a broiler. The objective of this study was to investigate the effect of production system (free range and intensive reared) and genotype (Broiler (COBB™), Ross 308 X Potchefstroom Koekoek hybrid and Potchefstroom Koekoek) on chicken meat quality. This was quantified on the morphological, physical (pH, colour, drip and cooking loss, water holding capacity and tenderness), chemical composition (moisture, protein, fat, ash contents and fatty acid profile), sensory quality and consumer preference of various chicken meat portions. The results of this study indicate that genotype had a more pronounced effect than production system on the morphological and growth properties of chicken meat, as well as on the sensory characteristics and consumer preference. The broilers had the best (P ≤ 0.05) feed conversion ratio (FCR), highest average daily gain (ADG) and European production efficiency factor (EPEF), followed by the Hybrid and then the Potchefstroom Koekoek. For each genotype, the free range chickens produced heavier (P ≤ 0.05) live weights than intensively reared chickens. Despite the poorer growth performance and efficiency of the medium growing Hybrid birds, they had less mortality and fewer leg disorders than the broiler. Additional to these factors, the Hybrid Free Range had higher thigh, drumstick and wing yields (P ≤ 0.05) than the broiler. When investigating the correlation between the chemical and sensory data, it was observed that the Hybrid scored significantly higher (P ≤ 0.05) in both flavour and aroma than the Broiler and Koekoek genotypes for both production systems. For colour, pH and polyunsaturated to saturated fatty acid ratio (PUFA:SFA), the effect of production system was more pronounced than the effect of genotype. Rearing chickens in a free range environment increased the PUFA:SFA ratio (P ≤ 0.05), making it beneficial to human health. Free range rearing resulted in lower muscle pHu (P ≤ 0.05), darker (L* value) (P ≤ 0.05), less red and yellow (a* and b* value) (P ≤ 0.05) chicken meat. It also influenced the chemical composition in different carcass portions; for example, a lower fat content in the thigh and higher protein in the breast of the Broiler. Correlation with the sensory results indicated that juiciness, tenderness, chicken aroma and chicken flavour are the main drivers of liking for consumer’s preference towards chicken meat. The consumers predominantly preferred the Hybrid (P ≤ 0.05) in a blind tasting session, but when information was given on the production system of a chicken product, the consumers lean more towards a free range reared product than an intensive reared product. This indicates that consumer perception plays an immense role in consumer decision making. Cluster analysis was also performed to ascertain whether the consumers differed in their degree of liking of the intrinsic character of the respective chicken samples. Three different clusters of consumers were identified: 1) Consumers that prefer free range reared chicken meat, 2) Consumers that prefer intensively reared chicken meat, 3) Consumers that prefer both free range and intensive reared chicken meat. In conclusion, the Hybrid seems to be a viable option for free range production systems in South Africa, without negatively affecting the overall quality of the meat or consumer acceptance. / AFRIKAANSE OPSOMMING: Moderne verbruikers is baie meer gesonheidsbewus en verkies meer natuurlik geproduseerde produkte soos vrylopende (free range) hoenders. Die kommersiële braaikuiken is nie geskik vir vrylopende produksie nie en `n ander genotipe word benodig wat die Suid-Afrikaanse mark sal kan voorsien met aanvaarbare vleiskwaliteit vergelykbaar met dié van die braaikuiken. Die doel van hierdie navorsing was om die effek van produksiestelsel (vrylopend en intensief) en genotipe (braaikuiken (COBB™), Potchefstroom Koekoek en Ross 308 X Potchefstroom Koekoek kruising) op die morfologiese, fisiese (pH, kleur, drip- en kookverlies, waterhouvermoë en taaiheid), chemiese samestelling (vog-, proteïen-, vet-, asinhoud en vetsuurprofiel), sensoriese kwaliteit en verbruikersaanvaarbaarheid van verskeie hoender vleis porsies te bepaal. Hierdie navorsing het getoon dat genotipe `n groter invloed gehad het as produksiestelsel op die groei en morfologiese eienskappe van die hoenders, asook op die sensoriese eienskappe en verbruikersaanvaarbaarheid. Die braaikuiken, gevolg deur die Ross X Koekoek kruising en dan die Koekoek, het die beste (P ≤ 0.05) voeromsetverhouding (FCR), gemiddelde daaglikse toename (GDT) en Europese produksie effektiwiteitsfaktor (EPEF) getoon. Vir elke genotipe het die vrylopende hoenders swaarder (P ≤ 0.05) lewende massa by slag getoon. Ten spyte daarvan dat die Ross X Koekoek kruising swakker groei en effektiwiteitsresultate getoon het, het hulle laer mortaliteite en minder been breuke en beserings as die braaikuiken gehad. Die Ross X Koekoek kruising wat vrylopend groot gemaak is, het ook swaarder dy, boud en vlerkie massa (P ≤ 0.05) as die braaikuiken getoon. Die navorsing het ook getoon dat kleur, pH en die poli-onversadigde tot versadigde vetsuur verhouding (PUFA:SFA) meer beïnvloed is deur die effek van produksiestelsel as genotipe. Die hoenders wat in ʼn vrylopende omgewing grootgemaak is se PUFA:SFA verhouding is hoër as dié van intensiewe boerdery, wat dit voordelig maak vir menslike gesondheid. Vrylopende hoenders se vleis is donkerder (L*) (P ≤ 0.05) en het ook laer rooi, geel (a* en b*) en pH (P ≤ 0.05) waardes getoon. Produksiestelsel effek het ook variërende chemiese waardes in verskillende karkas porsies tot gevolg gehad: ʼn laer vetinhoud is gevind in die dy en ʼn hoër proteïeninhoud in die borsies van die braaikuikens wat vrylopend grootgemaak is. Korrelasies met die sensoriese data het ook getoon dat sappigheid, taaiheid en hoendervleis geur die grootste dryfvere is in verbruikersaanvaarbaarheid. Tydens die verbruikerstoetse waar die verbruikers die gaar hoendervleis blind geproe het, het die verbruikers oor die algemeen meer gehou van die Ross X Koekoek kruising in vergelyking met die ander hoender genotipes (P ≤ 0.05), maar sodra inligting oor die verskillende produksiestelsels gegee is, het die verbruikers aangedui dat hulle hoenders wat vrylopend groot gemaak is, verkies. Dit dui daarop dat persepsies ʼn baie belangrike rol speel in die verbruiker se finale besluitnemingsproses. Statistiese segmentasietegnieke is ook op die data uitgevoer ten einde te bepaal of verbruikers in groepe verdeel kan word wat betref hul voorkeur van die sensoriese of intrinsieke eienskappe van die hoenderprodukte. Drie verskillende groepe is geïdentifiseer, nl. verbruikers wat 1) vrylopende hoender vleis verkies; 2) intensiewe hoender vleis verkies; 3) beide vrylopende en intensiewe hoender vleis verkies. In die lig van bogenoemde resultate wil dit voorkom of kruisteling tussen die gewone braaikuiken en die Potchefstroom Koekoek ʼn moontlike opsie is vir die Suid-Afrikaanse vryloop hoenderbedryf. Hierdeur word daar van vrylopende produksie stelsels gebruik gemaak sonder om die vleiskwaliteit of gebruikers aanvaarbaarheid negatief te beïnvloed.

Within the last 100 years, commercial chickens have been split into two main groups. Broiler chickens are produced for meat production while layers are produced for egg production. This has caused large phenotypic changes and the genomic signatures of selection may be detectable using statistical techniques. Genomic regions identified by these techniques may include genes associated with production traits, and is therefore of interest to animal breeders. This thesis investigates signatures of selection in a number of commercial chicken lines using several statistical techniques based on population differentiation and levels of genetic diversity. First, signatures of selection were investigated using population differentiation in nine lines of broiler chickens. Weir and Cockerham's pairwise FST was calculated for genome-wide markers between the broiler lines and averaged into overlapping sliding windows to remove stochastic effects. A chromosome bound, circular permutation method was used to generate a null distribution and determine the significance of each window. A total of 51 putative selection signatures were found shared between lines and 87 putative selection signatures were found to be unique to one line. The majority of these regions contain peak positions for broiler QTL found in previous studies and eight regions were significantly enriched for broiler QTL. One region located on chromosome 27 contained 39 broiler QTL and 114 genes, several of which were functional candidates for association with broiler traits. Secondly, areas of low diversity were investigated in three different SNP datasets. All three datasets were taken from the same broiler line at different time points and consisted of different SNP densities, including 12k, 42k and 600k. A number of zero diversity regions were found in each dataset and several were shared between the datasets. The 600k dataset was also analysed using a regression test, which investigates the patterns of diversity as the distance from the selected site increases. This method searches for signatures of selections by fitting a regression to the diversity data to test the fit of the data to the theoretical model. A total of 15 regions were found displaying significant asymptotic regression and diversity values less than 0.005. One of these regions located on chromosome 1 was also found as a fixed region in the 12k and 42k datasets and contained the gene IGF1, which encodes an important protein for growth. Finally, signatures of selection were investigated between broiler and layer datasets by investigating population differentiation and diversity based analysis. Weir and Cockerham's pairwise FST was calculated between the two lines and outliers extracted. A total of 32 regions were found displaying high differentiation. Seven regions of low diversity in the layer dataset were also investigated. Several broiler and layer QTL had been previously identified in these regions. Two genes related to hedgehog proteins were identified within selected regions, which are known to be involved in embryogenesis. Finally seven regions were found to be highly differentiated between the broiler and layer lines, and the nine broiler lines in the first chapter. This may indicate selection which occurred during breed separation. Signatures of selection were identified in four broiler and layer datasets using several statistical techniques. A number of regions were identified in multiple datasets by a number of techniques and are therefore good candidate regions for selection. Other statistical techniques could be used in future studies to further confirm these regions and identify causative genes and variants.