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Browsing by Author "Lewis, R. M."

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    Genome-wide association study to identify genetic loci associated with gastrointestinal nematode resistance in Katahdin sheep
    Becker, G. M.; Davenport, K. M.; Burke, Joan M.; Lewis, R. M.; Miller, James E.; Morgan, James L. M.; Notter, David R.; Murdoch, Brenda M. (2020-01-03)
    Resistance to gastrointestinal nematodes has previously been shown to be a moderately heritable trait in some breeds of sheep, but the mechanisms of resistance are not well understood. Selection for resistance currently relies upon faecal egg counts (FEC), blood packed cell volumes and FAMACHA visual indicator scores of anaemia. Identifying genomic markers associated with disease resistance would potentially improve the selection process and provide a more reliable means of classifying and understanding the biology behind resistant and susceptible sheep. A GWAS was conducted to identify possible genetic loci associated with resistance to Haemonchus contortus in Katahdin sheep. Forty animals were selected from the top and bottom 10% of estimated breeding values for FEC from a total pool of 641 sires and ram lambs. Samples were genotyped using Applied Biosystems (TM) Axiom (TM) Ovine Genotyping Array (50K) consisting of 51 572 SNPs. Following quality control, 46 268 SNPs were included in subsequent analyses. Analyses were conducted using a linear regression model in plink v1.90 and a single-locus mixed model in snp and variation suite. Genome-wide significance was determined by a Bonferroni correction for multiple testing. Using linear regression, loci on chromosomes 2, 3, 16, 23 and 24 were significantly associated at the genome level with FEC estimated breeding values, and we identified a region on chromosome 2 that was significant using both statistical analyses. We suggest a potential role for the gene DIS3L2 for gastrointestinal nematode resistance in Katahdin sheep, although further research is needed to validate these findings.
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    Population dynamics of a long-term selection experiment in White Plymouth Rock chickens selected for low or high body weight
    Harrison, S. J.; Siegel, Paul B.; Honaker, C. F.; Lewis, R. M. (Elsevier, 2023-05)
    The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selec-tion horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 indi-viduals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was avail-able. Inbreeding (F) and average relatedness (AR) coef-ficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective num-ber of founders was 17 and 15, effective number of ances-tors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders con-tributed to both lines. Moderately high levels of inbreed-ing and low effective population sizes were inevitable, as this was a closed population. However, effects on the fit-ness of the population were expected to be less substan-tial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were rela-tively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selec-tion responses in the 2 lines therefore should be reliable.