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Browsing by Author "Honaker, C. F."

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    Low-coverage sequencing in a deep intercross of the Virginia body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage
    Ronneburg, T.; Zan, Y.; Honaker, C. F.; Siegel, Paul B.; Carlborg, O. (Elsevier, 2023-05)
    Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experi-mental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experi-mental crosses have targeted major loci using data from a single generation (often the F2) with individuals from later generations being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, bi-directional selection responses for 56-d body weight in the Virginia body weight chicken lines. To achieve this, a strategy was developed to make use of data from all generations (F2-F18) of the advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3% of the chicken genome for >3,300 intercross individuals. In total, 12 genome-wide signifi-cant, and 30 additional suggestive QTL reaching a 10% FDR threshold, were mapped for 56-d body weight. Only 2 of these QTL reached genome-wide significance in earlier analyses of the F2 generation. The minor-effect QTL mapped here were generally due to an overall increase in power by integrating data across generations, with contributions from increased genome-coverage and improved marker information content. The 12 signifi-cant QTL explain >37% of the difference between the parental lines, three times more than 2 previously reported significant QTL. The 42 significant and sugges-tive QTL together explain >80%. Making integrated use of all available samples from multiple generations in experimental crosses are economically feasible using the low-cost, sequencing-based genotyping strategies out-lined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contrib-uting to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-d body weight in the Virginia body weight chicken lines.
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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.