In order to establish a method of assessing the degree of inbreeding within herds of cattle, we constructed a calibration index relating kinship and the degree of DNA band sharing in DNA fingerprints. Firstly, chickens were used as a model system to test the possibility of using microsatellite DNA as a probe for DNA fingerprinting in inbreeding analysis. Six genetic groups of chickens with estimated coefficients of inbreeding ranging from 0.026 to $>$ 0.98 (pedigree analysis) were fingerprinted using the minisatellite probe derived from M13 and the microsatellite probe (CAC)$ sb5$. The degree of band sharing using either probe increased in concert with the known amount of inbreeding and was described by the equation Y = 0.56X ($ pm$0.06) + 0.42 ($ pm$0.03); r = 0.998. Since in-gel hybridization using the microsatellite probes was faster and less labour intensive than using the minisatellite probe, it was used in the subsequent studies. Pedigree analysis in Holstein dairy cattle allowed for the empirical calibration of the association of band sharing with the coefficient of relatedness, (r), defined as the expected proportion of genes in 2 individuals that are identical by descent (i.e. for monozygous twins r = 1; for first order relatives r = 0.5; for half sibs r = 0.25 etc.). The average band sharing between pairs (6 pairs at each r value) of individuals within each class formed the basis for calibration. DNA was digested using RsaI. The relationship between band sharing and relatedness was well represented by a linear approximation Y = 0.51X ($ pm$0.09) + 0.50 ($ pm$0.04); r = 0.992. Using this calibration curve, random samples of animals within herds can be tested to establish the herd variability and to minimize inbreeding.

The effect of composite and descriptive linear type traits on Functional Herd Life in Holstein cows was studied by means of Survival Analysis (Ducrocq and Solkner, 1998a). The original data set contained 331,105 lifetime records from the Programme d'Analyse des Troupeaux Laitiers du Quebec, from January 1980 to March 1995. Only 191,167 records (or cows) had type information. Mixed Weibull models were fitted to analyse the data; the probability of being culled (hazard) was defined as a product of a baseline Weibull hazard function and explanatory variables. The heritability estimates for Functional Herd Life were 0.07 in the log scale and 0.15 in the original scale. Sire Estimated Transmitting Ability for FHL, expressed as relative culling rate, ranged from 0.6 to 1.4 for all models. Solutions for fixed effects (all significant) indicated a higher probability of being culled for primiparous cows calving at older ages, for cows producing below herd average, for first lactation cows in the first and last stage of lactation and for older cows at the end of lactation. The risk of being culled did not change for cows in herds decreasing or increasing in size. Cows classified with a high score for Final Score were less likely to be culled; Final Score seems to be an important selection criteria among Quebec producers. Feet and Legs, Rump and Mammary System are traits that producers consider in their culling policies; cows classified with a high score had more chance of surviving. Among the linear type traits, the 5 traits with the highest impact on productive life, were Rear Attachment Height, Fore Attachment, Bone Quality, Stature and Fore Teat Placement; Quebec producers seem to consider these traits when they make their culling decisions.

Methodologies have been devised to genotype the $ kappa$-casein ($ kappa$-CN) and $ beta$-lactoglobulin ($ beta$-LG) loci using the polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLPs) analysis. A fragment of 432 base pair from the $ kappa$-CN gene which contains the nucleotide substitutions diagnostic of the A- and B-alleles of $ kappa$-CN was amplified. DNA amplified from the A-variant contained a unique HinfI restriction site, whereas DNA amplified from the B-variant contained a unique TaqI site. Thus, the genotype of the animal could be determined by restriction enzyme analysis. A region extending from exon IV to V of the $ beta$-LG gene was also amplified using PCR. In this region, the B-allele contains 2 HaeIII restriction sites which are not present in DNA amplified from the A-allele. The digestion of the PCR product with HaeIII thus allowed discrimination between the A- and B-alleles. Analysis of bulls (n = 68) used by artificial insemination (AI) centres after 1980, bulls (n = 27) used before 1960, a random sample of male calves (n = 102) and cows (n = 123) revealed a frequency of the B allele of $ kappa$-CN as 0.13, 0.37, 0.22 and 0.19 in these populations, respectively. In the populations of bulls (n = 69) used by AI centres after 1980, bulls (n = 27) used before 1960, a random sample of male calves (n = 99), and cows (n = 129), the B-allele of $ beta$-LG was present at frequencies of 0.60, 0.52, 0.67, and 0.65, respectively. Statistical analysis of these data shows the frequency of the B-allele of $ kappa$-CN was significantly higher in sires (n = 27) which were used by the AI centre before 1960 compared to more modern proven sires (n = 68) (P $<$ 0.01).

Estimates of genetic and phenotypic parameters of lifetime performance traits and estimates of correlations between these and first lactation traits were obtained using multitrait mixed model and Restricted Maximum Likelihood (REML) methodologies, and accounting for all known additive genetic relationships amongst animals in sires pedigree. Part-lifetime performance traits, i.e. two-, three, and four-parity totals of yield and profit, were also included in the analysis. Data were on 82,835 Holstein cows, daughters of 703 sires, calving first between September 1979 and December 1984 in the herds enrolled in Quebec Dairy Herd Analysis Service (QDHAS). Lifetime performance records, however, continued through December 1989. / Results of analysis indicated low estimates of heritability for lifetime performance traits, e.g., lifetime production and profit (.11$ sim$.13) and longevity (.07$ sim$.09). However, production per day of productive life traits had moderate heritability (.28$ sim$.32). Estimates of genetic and phenotypic parameters decreased from part-lifetime to total lifetime performance because residual variances increased at a greater rate compared to rate of increase in sire variances. Both genetic and phenotypic correlations amongst lifetime production, lifetime profit and longevity traits were very high and approached unity in all cases. / Estimates of genetic and phenotypic correlations of first lactation production and profit traits with all measures of part and total lifetime performance were positive and high. These correlations decrease from part-lifetime to total lifetime performance due to part to whole relationships. / Estimates of parameters of lifetime performance traits were mostly free of the effects of selection on milk production. Positive and high genetic correlation of first lactation milk yield with all lifetime performance traits indicated that selection on first lactation milk yield alone will improve all measures of lifetime performance. However, some consideration should be given to measures of reproduction and health which may help in improving the longevity of dairy cattle. (Abstract shortened by UMI.)

Single-strand conformation polymorphism analysis (SSCP) and restriction fragment length polymorphism analysis (RFLP) were used to determine the genotype of Holsteins at the $ kappa$-casein ($ kappa$-CN) locus. A 432-bp fragment within exon IV containing nucleotide substitutions diagnostic of the A- and B-variants of $ kappa$-CN was amplified using the polymerase chain reaction (PCR). The sires from the earliest years of the AI industry had a significantly higher (p $<$ 0.01) frequency of allele than sires in modern usage. These data indicate that selection or milk production parameters may discriminate against the B-allele. SSCP analysis was also used for detecting polymorphisms within the regulatory region of $ kappa$-CN gene. A 640-bp fragment within the 5$ sp prime$-flanking region of bovine $ kappa$-CN gene which contained the TATA box, CAAT box, and exon I was amplified using PCR. The SSCP analysis of this fragment revealed no variation, possibly due to the lower detection efficiency of SSCP with large fragment size. Nested primers were, therefore, designed to amplify fragments of 234- and 486-bp. Polymorphism was detected only in the 486-bp fragment and the two variants were designated M$ sb1$ and M$ sb2.$ The allelic frequencies of M$ sb1$ and M$ sb2$ in bulls used by AI industry before 1970 were 0.67 and 0.33, and in bulls used by AI industry after 1980 the frequencies were 0.68 and 0.32, respectively. The frequency of these alleles were not significantly different in Holsteins used by AI industry before 1970 and after 1980. Unlike the apparent change in frequency of the A- and B-variants noted within exon IV, this polymorphism seems to have not responded to selection. However, a higher frequency of M$ sb1$ allele appeared to be associated with B-variant (exon IV) genotypes. The presence of these variants within the regulatory region may possibly be involved in the quantitative expression of $ kappa$-CN gene. (Abstract shortened by UMI.)

Zugl.: Berlin, Humboldt-Univ., Diss., 2006

Thesis (M.S.)--Virginia Polytechnic Institute and State University, 1994. / Vita. Abstract. Includes bibliographical references (leaves 93-104). Also available via the Internet.

Thesis (Ph.D.)--University of Nebraska-Lincoln, 2009. / Title from title screen (site viewed June 26, 2009). PDF text: v, 114 p. : ill. ; 1.05 Mb. UMI publication number: AAT 3352316. Includes bibliographical references. Also available in microfilm and microfiche formats.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1959. / Typescript. Abstracted in Dissertation abstracts, v. 19 (1959) no. 7, p. 1496-1497. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 60-63).

Thesis--Wisconsin. / Vita. Includes bibliographical references.