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Item A study of the phenotypic expression of the lustre gene in sheep and a chromosomal analysis of this abnormality: a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University(Massey University, 1991) Campbell, KarenBlood and skin samples were taken from sheep with both the lustre and normal phenotype for the study of chromosomal banding patterns, follicle density, and cell type distribution. The chromosomal analysis showed no significant difference in the banding pattern, when a comparison was made between normal and Lustre animals. There were however, significant differences in the follicle density analysis. All parameters measured (primary follicle density, secondary follicle density, S/P ration, and total follicle density) showed statistically significant differences between normal and lustre animals (P<0.1). There was also a significant difference in the distribution of the paracortical and orthocortical cells when comparing normal sheep to lustre. In addition to this, there was a significant difference found in proportion of the different types of cells, and the fibre area (P<0.01).Item Genomic selection for traits of economic importance in sheep : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Breeding and Genetics at Massey University, Manawatū, New Zealand(Massey University, 2014) Lepori Honeyman, Alfredo AndresThe main objective of this thesis was to analyse the inclusion of genomic information of production traits into a multitrait sheep breeding programme evaluated for 20 years using deterministic and stochastic simulation models. The breeding objective was to reduce faecal egg score (FES), decrease yearling weight (YW) and increase 160 days lamb carcass weight (CW). The selection criteria included 160 days live weight (instead of CW) plus YW and FES. The first study developed a stochastic model selecting animals based on their individual breeding values estimated using best linear unbiased predictor (BLUP) procedure with a multitrait animal model. The model was validated using a deterministic multitrait selection index; obtaining similar prediction responses for breeding objective and selection criteria traits. The second study deterministically evaluated the inclusion of genomic information explaining different proportions of CW and YW genetic variances into a selection index. Under the same selection scheme a selection index having only genomic information obtained lower accuracies and genetic gains compared to a selection index considering phenotypic information. If shorter generation intervals are implemented, a selection index including phenotypic and genomic information explaining low proportions of the trait's genetic variance could achieve higher genetic and economic gains. The third study evaluated genetic responses of a stochastically modelled breeding flock selecting ewes based on BLUP estimated breeding values and selecting rams based on genomic breeding values (GBV) for CW. The fourth study evaluated accuracy of prediction of CW GBV using the same simulated model. Carcass weight GBVs were calculated in a validation population using single nucleotide polymorphism (SNP) effects from a training population. The further apart the genetic relationship between these two populations, lower the GBV accuracy. Resultant accuracies depended on the proportion of total genetic variance explained by genomic information and also the variance accounted by each SNP, therefore an appropriate GBV estimating method has to be chosen to achieve accuracies as high as possible. Stochastic models proved to be more versatile for managing data, also showing variation of the genetic responses. In contrast, deterministic models were faster regarding computer processing times. The study proved that a breeding programme combining GBV and BLUP estimated breeding values can increase genetic responses by selecting animals at early stages of life.Item Genetic parameters of carcass traits in the New Zealand Romney : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science in Animal Science at Massey Unversity(Massey University, 1976) Mohamed, Abdul MajidThe data used in the present study were collected from wether lambs of a flock of New Zealand Romney sheep started at Massey Agricultural College, Palmerston North, in 1944. The lambs, 474 in number, were the progeny of 12 mixed-age rams born over a period of three years from 1944 to 1947. Altogether, 25 carcass traits were analysed. A linear mathematical model, which included sire, year and type of birth and rearing as the main effects, a sire-year interaction term and age at slaughter as a covariate, was used to describe the data. The estimates of the various terms in the model were derived by least-squares procedures. Preliminary analyses included determining the significance of the sire-year interaction in each of the 25 traits. In traits where the sire-year interaction were found not significant, the main effects and regression term were estimated. Variance components were estimated using Henderson's Method III. Heritability was estimated by paternal half-sib correlation. The procedures used in the estimation of covariance components were, in many ways, similar to those used in the analysis of variance components. In the former, the sums of crossproducts for the appropriate effects were computed from the difference between two reductions in sums of crossproducts. Sire-year interaction was found to be significant in four traits, namely width of gigot (G) and the ratio of the weight of the forequarter to the hindquarter (FQ/HQ) at the 1% level of probability and, carcass grade and cannon bone weight at the 5% level of probability. Estimates of heritability of carcass traits are as follows: Internal measurements: A, 1.11 ± 0.27; B, 0.20 ± 0.12; C, 0.31 ± 0.14; D, 0.27 ± 0.13; X, 0.09 ± 0.08; Y, 0.28 ± 0.14; J, 0.35 ± 0.15. Measurements indicative of bone length and weight: F, 0.73 ± 0.22; T, 0.62 ± 0.20; R, 0.55 ± 0.19; P, 0.70 ± 0.22; Cannon bone length, 0.80 ± 0.23; cannon bone weight, 1.01 ± 0.26. Measurements indicative of width or depth of body: G, 0.41 ± 0.17; WR, 0.14 ± 0.10; WF, 0.09 ± 0.08; WTh, 0.37 ± 0.16; Th, 0.67 ± 0.21. Measurements indicative of length of body: K, 0.34 ± 0.15; L, 0.55 ± 0.19; H, 0.20 ± 0.12. "Other" carcass traits: carcass weight, 0.03 ± 0.04; carcass grade, -0.04; carcass total, 0.34 ± 0.15; FQ/HQ, 0.00. Estimates of genetic correlations showed large sampling errors. The correlations between the ratio of the weight of the forequarter to the hindquarter (FQ/HQ) and the other carcass traits were not included because the sampling errors were very large. In the majority of cases, the genetic correlations were of the same sign as the phenotypic correlationsItem Estimation of genetic and phenotypic parameters in New Zealand Romney sheep : a thesis presented in partial fulfilment of the requirements for the degree of Masterate of Agricultural Science in Animal Science at Massey University(Massey University, 1983) Tait, Susan JaneGenetic and phenotypic parameters were estimated from liveweight and fleece data recorded on 1604 New Zealand Romney lambs between 1970 and 1972. The flock into which the lambs were born is located at Woodlands Research Station near Invercargill. The data analysed are from the establishment phase of a long-term selection experiment; the flock was closed for selection in 1973. The traits studied were birthweight (BWT), docking weight (DWT), weaning weight (WWT), April liveweight (APR), June liveweight (JUN), August liveweight (AUG), November liveweight (NOV), 2-tooth liveweight (2TH), lamb fleece weight (LFW), hogget fleece weight (HFW), staple length (STL), quality number (QNO), character (CHR), fleece colour (COL) and break severity (BRS). Restricted maximum likelihood (REML) estimates of the variance components were obtained. These were used in the generation of paternal half-sib estimates of the heritabilities (h2), the inter-trait genetic (rg) and phenotypic (rp) correlations, and the best linear unbiased estimates (BLUE) of the non-genetic (fixed) effects. The estimates of the h2's for the liveweights ranged from 0.08 for BWT, increasing through to 0.13 for 2TH. These estimates are lower than most of the values previously published (generally, from 0.2-0.A, respectively), although they are comparable with many of the more recent h2 estimates for liveweight. The estimates of h2 for the fleece traits were generally similar to the estimates of previous studies. Estimates of 0.19 and 0.30 were obtained for LFW and HFW, respectively, and 0.37 for STL. The fleece quality traits were found to have h2 estimates ranging from 0.07 for BRS to 0.56 for QNO. The estimates of the genetic and phenotypic correlations between the traits studied were comparable with estimates from previous studies in most cases. Important exceptions include the low genetic correlations of WWT with the liveweights from JUN (of 0.38) through to 2TH (of 0.50). The BLUE's of the fixed effects generally agree well with the estimates of previous studies. Year-of-birth, birth-rearing rank and date-of-birth effects were significant for all the traits studied. In addition, age-of-dam effects were significant for all the liveweights, and sex effects were significant for BWT, DWT and WWT.Item A study of the inheritance of some productive traits in Perendale sheep : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science at Massey University(Massey University, 1975) Elliott, Kenneth HamiltonGenetic parameters were estimated using 3,313 half-sib records from 62 sires and .1720 daughter-dam pairs. The data used were obtained over the period 1957 to 1972. The estimates of heritability by paternal half-sib and daughter-dam regression analysis were respectively:- weaning weight (0.20 and 0.16); hogget body weight (0.27 and 0.44); fleece weight (0.32 and 0.30); quality number (0.26 and O.31); fibre diameter (0.54 and 0.47); staple length (0.49 and 0.35); character (0.23 and 0.23). An estimate of 0.03 was obtained for lambs weaned/ewe lambing (Lw/EL) by the daughter-dam regression analysis from 665 daughter-dam pairs. Estimates of genetic correlations were in the following ranges;- Medium negative (-0.4 to -0.6) Low negative (-02. to -0.4) Low positive (0.2 to 0.4) Medium positive (0.4 to 0.6) High positive (0.6 and over) Hogget body weight with character. Quality number with staple length. Weaning weight with quality number, fibre diameter and character. Quality number with fleece weight and fibre diameter. Hogget body weight with weaning weight and quality number. Staple length with character. Fleece weight with fibre diameter and character. Fleece weight with staple length. Phenotypic and environmental correlations were also estimated. Phenotypic correlations generally agreed with the genetic correlations. Important exceptions were hogget body weight with fleece weight, staple length and fibre diameter. Among the environmental factors studied, age of dam and rearing rank effects for the wool traits were generally small. These effects had a marked influence on weaning weight and hogget body weight. At weaning, singles were 4.2 kg heavier than twins, while at 14 months, this difference had been reduced to 2.1 kg. When comparing a two-year-old and mature age of dam effects, a 1.44 kg difference at weaning in favour of the mature age of dam reared animals, was reduced to a 1.11 kg difference at 14 months. The estimated parameters and environmental effects were discussed with reference to their implications in selection programmes. Relationships between hogget traits and the ewes lifetime production (four consecutive years) were analysed. Records from 458 sheep were used. Correlation coefficients indicated that hogget fleece weight, quality number, fibre diameter and staple length were good indicators of lifetime ewe performance for these traits. The results indicated that a poor relation exists between hogget body weight and number of lambs weaned by the ewe over four lambings. A regression analysis of hogget traits on life-time economic value of the ewe indicated that fleece weight and hogget body weight were the most important variables influencing life-time economic value. Implications of the results were discussed with reference to selection and culling programmes at the hogget age in ram breeding and non-ram breeding flocks.Item Genetics of flystrike, dagginess and associated traits in New Zealand dual-purpose sheep : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2013) Pickering, Natalie KathleenA literature review identified breech bareness, dagginess and fibre traits as potential indirect indicator traits for flystrike. Dagginess (faecal accumulation) had the greatest potential as an indirect indicator, and has been identified as an important trait itself. Therefore flystrike and dagginess were investigated for their associations with fibre and production traits. A genome-wide association study (GWAS) was performed to identify regions under selection and associated with these traits. Finally, a genomic selection (GS) analysis was performed for dagginess and dual-purpose production traits to estimate molecular breeding values (MBVs) and to determine their impact on the New Zealand dual-purpose selection index. Heritability, genetic and phenotypic parameter estimations were performed on a flystrike case-control dataset collected over 2 years. Flystrike had a heritability of 0.37, and high genetic and phenotypic correlations with dag score and a high genetic correlation with the coefficient of variation of fibre diameter. A similar analysis was performed on an existing New Zealand sheep industry dataset of about 2 million pedigree-recorded animals born between 1990 and 2008. The heritability for dag score at 3 and 8 months (DAG3, DAG8) was 0.34 and 0.31 respectively. There were low or nil genetic and phenotypic correlations of DAG3 and DAG8 with the other standard live weight, fleece weight, reproduction and faecal egg count production traits or breech bareness, fibre and wool traits. A GWAS performed on an industry dataset of 8,705 genotyped animals, using phenotype information on about 3 million pedigree-recorded animals, identified regions on chromosome 6 and 15 associated with DAG3 and DAG8. The lambs from the flystrike case-control dataset with SNPs imputed from 5K to 50K identified a number of immune, diarrhoea and wool/hair growth genes associated with flystrike, dag score and fibre traits in a GWAS. There were no similarities in the genes identified in the industry or case-control GWAS; however, the SNP on chromosome 15 was re-identified in the GS analysis for DAG8. The GS analysis showed that genomic predictions can be Genetics of flystrike and dagginess in New Zealand dual-purpose sheep performed for DAG3 and DAG8 and that using MBVs and modifying generation interval can increase the rate of the genetic gain of the dual-purpose index by 84% per year.Item A silver-staining study of the nucleolus organizer regions of the chromosomes of domestic sheep (Ovis aries) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University(Massey University, 1979) Henderson, Leigh MarianA study was made of various aspects of the nucleolus organizer regions (NORs) on sheep mitotic chromosomes, using the Ag-AS and Ag-I techniques. The sheep used in this study were carriers of the t1, t2 and t3 Robertsonian translocations in various heterozygous and homozygous combinations. The locations of the NORs were determined to be at the telomeres on the metacentric chromosomes 1p, 2q and 3q and on the acrocentric chromosomes 4 and 25. The identity of the NO-chromosome was confirmed by a duplicate G-banding and Ag-I technique. The terminal location of the NORs indicates that they do not have a causative role in acrocentric association or Robertsonian translocation in domestic sheep. They also do not coincide with the regions in which secondary constrictions are sometimes seen. Individual animals were found to have a characteristic silver-staining pattern. The chromosomal distribution of the Ag-staining NORs (Ag-NORs), the frequency and size of the Ag-NORs were fairly constant in different cells of an individual and in replicate cultures of an animal. Differences between cells and replicates in Ag-staining involved variation in the frequency of staining of Ag-NORs with small Ag-deposits. Overall, the metacentrics had the highest frequency of Ag-NORs followed by chromosome 25 and then chromosome 4. The association frequency of individual NO-chromosomes was found to be positively correlated with the frequency of Ag-NORs and the size of the Ag-deposit. The frequency of each pairwise combination of associating chromosomes was determined solely by the frequency of Ag-NORs of the component chromosomes. No evidence was found for a non-random fusion of NORs. These observations provide an explanation of the reports of non-random participation of acrocentric chromosomes in satellite association in man. The increased association of NO-chromosomes with large deposits could be due to an increased chance of fusion of larger nucleoli or to differences in the disintegration rate of different sized nucleoli. The presence of a NOR. on the chromosome 25 / t3 polymorphism was utilized in inheritance studies of Ag-stainability. Five pedigree groups in which this chromosome was segregating were studied and in all cases the size of the Ag-deposits and frequency of staining was consistent between consecutive generations. The value of Ag-staining in genetic mapping studies is discussed. In 3 animals, the Ag-staining patterns of transformed lymphocytes and fibroblasts were compared and found to be similar. A comparative study was made of 5 species of the Bovidae: domestic sheep (Ovis aries), domestic goat (Capra hircus), aoudad (Ammotragus lervia),bharal (Pseudois nayaur) and cattle (Bos taurus). Five NO-chromosome pairs were found in sheep, goat, aoudad and cattle and these chromosomes have homologous banding patterns. The bharal has at least four NO-chromosome pairs homologous to sheep. These results indicate a conservation of the NORs during evolution in this family. Based on the results of the frequency of Ag-staining of NORs, the heritability of Ag-stainability and the constancy of Ag-staining patterns found in the tissue studies, the nature of the Ag-staining is discussed and a model on the basis of the Ag-stainability of individual chromosomes is presented.Item A study of genetic and environmental variation and covariation in productive traits of a flock of Perendale sheep : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University(Massey University, 1978) Lewer, Roger PaulPerformance records on 1724 two-year, 1160 three-year, 726 four-year and 449 five-year Perendale sheep from the Massey University flock were analysed. These records were collected between birth-years 1961 and 1974 inclusive, and therefore different numbers of years were involved at each age. The data comprised 97, 82, 65 and 56 sire groups for the respective ages. There were 403 ewes in 56 sire groups which had four consecutive records between two- and five-years of age. There were 922 two-year, 584 three-year, 296 four-year and 125 five-year dam-daughter pairs, but the last age group of records was considered too few to justify analysis. The dependent variables examined were quality number (QN), wool character (WC), staple length (SL), greasy fleece weight (GFW), fibre diameter (FD), and number of lambs weaned per ewe joined and present at lambing (NLW). Fibre diameter had been recorded in fewer years than the other traits and there were consequently less [i.e. fewer] observations available. The effects of the environmental factors of year, age of the dam of the ewe, rearing rank, NLW (wool traits only), and all interactions among them were assessed by computing the percentage of the total variance contributed by each factor for each variable. Quadratic components for these fixed effects were temporarily considered to be variance components for this purpose. Year effects were the most important source of enviromental variation in wool characteristics, but were less important for NLW. None of the other main effects were consistently important (i.e. contributed greater than two percent of the total variation) in explaining the observed variability. Year x NLW was the only interaction which contributed more than two percent of the total variance in any wool trait. The affected characteristics were two- and three-year QN, three-year FD and five-year SL. NLW (five-year-old ewes only) was affected by dam age x rearing rank and year x rearing rank interaction. Heritability estimates calculated by paternal half-sib method (daughter-dam regression estimates in brackets) were in the range of 0.22 - 0.28 (0.39 - 0.66), 0.16 - 0.39 (0.12 - 0.25), 0.32 - 0.71 (0.25 - 0.36), 0.24 - 0.53 (0.43 - 0.62), 0.38 - 0.68 (0.45 - 0.50) and 0.02 - 0.24 (-0.02 - 0.03) for QN, WC, SL, GFW, FD and NLW respectively. Differences between ages were seldom significant and the relevance of such a comparison was discussed. Paternal half-sib heritability estimates for the average of four mature (two- to five-years) production records were 0.50, 0.61, 0.84, 0.44, 0.49 and -0.01 for the same respective characteristics. Binomial analysis methods resulted in heritability estimates for fertility (twinning in brackets) of 0.06 (0.12), 0.02 (0.15), -0.01 (0.13), and -0.15 (0.01 for two-, three-, four- and five-year-old ewes respectively. Repeatability was estimated by averaging the regression of later on earlier record for all pairs of ages for wool traits and mature ages for reproductive characteristics and resulted in values of 0.46 (QN), 0.18 (WC), 0.50 (SL), 0.62 (GFW), 0.71 (FD), and 0.09 (NLW). Similar methods gave computed values for the repeatability of the difference between zero and one lamb weaned of 0.01, and between one and two lambs weaned of 0.13. Genetic and phenotypic correlations between all variables were calculated separately at each age by paternal half-sib and daughter-dam methods. The correlations were positive for GFW - FD, GFW - SL, GFW - WC, QN - WC and FD - SL, negative for GFW - QN, QN - FD and QN - SL, and mixed for FD - WC and SL - WC although the last of these were mostly positive. The phenotypic correlations between wool traits and reproduction were negative for NLW - GFW and NLW - SL and approximately zero for the remainder. Genetic correlations were negative for NLW - GFW, NLW - FD and NLW - SL, positive for NLW - QN and mainly positive for NLW - WC. Many of the genetic correlations involving NLW had large standard errors. Application of the results was discussed in terms of the selection indices which were constructed.Item Genetic improvement in a Texel breeding operation : a case study & Maximising pedigree accuracy for genetic gain : a comparison of DNA-assigned parentage and lambing-book assigned parentage : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agriscience in Animal Breeding and Genetics at Massey University, Manawatu, New Zealand(Massey University, 2011) Andrews, Nicole FayThere were two main aims to this research. The first was to carry out an investigation of the genetic gain of Landcorp Farming Limited's Waikite Texel breeding operation. This was in order to identify factors that may have been limiting ΔG and the financial return of the system and make recommendations for improvement. It was found that the achieved mean ΔG of 33¢/ewe/year was less (P<0.05) than that predicted for the Innervalue Fat Index at 97¢/ewe/year. Financially the system was found to have made a net return over the course of the studied period; however, this was less than what was predicted as possible. The main cause of this shortfall was the majority of genetic selection being imposed on live-weight BVs rather than Index values. This investigation also found that there was little room for improvement in the ewe and ram generation intervals with hogget mating and maintenance of current levels being recommended for L. While the ram selection intensity had little room for improvement, the ewe selection intensity did and this is achievable by imposing less selection pressure on structural traits and more on genetic merit. The second aim of this research was to compare lambing-book dam records and DNA-assigned dam records in order to identify management practices that would target the minimisation of pedigree identification error. Triplets and lambs born to older dams were found to be the groups most at risk of having incorrect lambing-book data, while singles had a lower mean probability that the DNA identified dam was correct. Although DNA parentage testing was not found to financially benefit a system, it did offer the opportunity to reduce pedigree error through the use of a variety of practices. These practices include: single sire mating of ewes, lambing ewes in mobs of equal or near equal proportions from each sire group, lambing in mobs based on scanning rank, carrying out two or more checks per day on ewes during lambing, and increase the number of markers used in the DNA parentage assignments of groups most at risk from incorrect parentage assignment if financially feasible.Item A study of meiosis in rams carrying multiple Robertsonian translocations : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University(Massey University, 1982) Scott, Ian StewartA study was made of meiotic chromosomes in air-dried preparations from 30 genitally sound rams (Ovis aries). Three of the rams had a normal mitotic karyotype (2n = 54) and the remainder were carriers of the t1, t2 and t3 Robertsonian translocations in various heterozygous and homozygous combinations. The studies on the primary spermatocytes showed that the normal rams had a modal number of 27 chromosomal elements and the translocation-carrying rams were recorded with a modal number of either 24 or 25. The translocation in the heterozygous state was characterized by the presence of a trivalent in cells at the diplotene, diakinesis and metaphase I stages, while in the homozygous state it was characterized by the presence of a bivalent. The modal number of chromosomal elements was recorded in 90.5 to 97.3 percent of the cells at diakinesis and metaphase I in the translocation-carrying rams. The modal number of chromosomal elements was recorded in 88.3 percent of the cells in the normal rams. An association between the sex bivalent and a small autosomal bivalent was recorded in 3.5 to 5.3 percent of the cells at diakinesis and metaphase I in the translocation-carrying rams. Eight percent of the cells in the normal rams were seen with a sex bivalent association. The sex chromosomes were separated in 0.0 to 1.1 percent of the cells at diakinesis and metaphase I in the translocation-carrying rams, while 0.7 percent of the cells in the normal rams had separated sex chromosomes. However, aneuploidy involving the sex chromosomes was not observed in the secondary spermatocytes from the normal and translocation-carrying rams. A total of 1,757 secondary spermatocytes were counted from 27 translocation-carrying rams and 103 secondary spermatocytes from 3 normal rams. The studies on the secondary spermatocytes showed that the modal number of 30 chromosome arms was recorded in 87.3 to 96.0 percent of the non-polyploid cells in the translocation-carrying rams and 95.2 percent of the cells in the normal rams. No hypermodal cells were found in the normal rams. Hypermodal cells were recorded in 0.0 to 3.6 per cent of the non-polyploid cells in the translocation-carrying rams. There were individual variations in the percentage of hypermodal cells recorded in rams with identical karyotypes. There were also significantly greater numbers of cells with 29 chromosome arms than with 31 chromosome arms in the translocation-carrying rams. This suggested that chromosome loss due to lagging at anaphase I or technical manipulation, must have occurred in addition to non-disjunction. A significant surplus of secondary spermatocytes of normal karyotype and a deficit of 25, t1 t3 were found in the metaphase II figures from the triple heterozygous rams. Significantly uneven distributions of segregation products were also found in the multiple translocation-carrying rams with karyotypes of 50,xy,t1t2t2t3 and 49,xy,t1t2t2t3tx. The translocation-carrying sheep have been shown to have good conception rates and an average breeding performance. This would suggest that only balanced (euploid) spermatozoa are involved in fertilization and the unbalanced (aneuploid) spermatocytes fail to mature into spermatozoa and are selected against or degenerate during spermatogenesis. The evidence indicates that the fertility of the ram is unaffected by the presence of the translocation chromosomes and consequently these sheep should not be eliminated arbitrarily from our animal populations.