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Browsing by Author "Burke, Joan M."

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    Association between FAMACHA scores and fecal egg counts in Katahdin lambs
    Notter, David R.; Burke, Joan M.; Miller, James E.; Morgan, James L. M. (2017-03)
    The FAMACHA system was introduced to the U.S. just over 10 yr ago to allow selective deworming of lambs with anemia associated with Haemonchus contortus and retard the development of anthelmintic resistance. The FAMACHA system was initially developed as a predictor of packed cell volume (PCV), but correlations between FAMACHA and fecal egg counts (FEC) have also been reported. It is important to understand factors that influence FAMACHA scores among farms to improve management of gastrointestinal nematodes. The objectives of this study were therefore to quantify associations between FAMACHA scores, FEC, BW, and age in Katahdin lambs at 2 different measurement times in 8 flocks in the eastern U.S., and to assess consistency of relationships between FAMACHA and FEC among flocks. Data came from 1,644 Katahdin lambs from 7 flocks sampled at approximately 90 d of age, and 1,295 lambs from 6 flocks sampled at approximately 120 d of age over a 5 yr period. Residual correlations among log-transformed FEC (LFEC), FAMACHA scores, BW, and lamb ages at each measurement time were determined. Repeatability of each variable was also determined as residual correlations among repeated measures. At both 90 and 120 d of age, correlations of FAMACHA scores with LFEC and BW were significant (P < 0.001), but numerically modest (0.25 and -0.16, respectively at 90 d; 0.31 and -0.16, respectively at 120 d), demonstrating that higher FAMACHA scores were associated with higher FEC and more likely to be observed in lighter lambs. A small negative correlation was observed between FAMACHA score and lamb age (r = -0.05, P = 0.05, 90 d; r = -0.11, P < 0.001, 120 d) indicating that younger lambs were more likely to have elevated FAMACHA scores. Thus, younger and lighter lambs will likely be more susceptible to parasitism and may need to be managed more diligently than older or heavier lambs. In addition, FAMACHA scores have potential to improve breeding value estimates in programs designed to genetically improve parasite resistance.
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    Factors affecting fecal egg counts in periparturient Katahdin ewes and their lambs
    Notter, David R.; Burke, Joan M.; Miller, James E.; Morgan, James L. M. (2017-01)
    Selection for low fecal egg counts (FEC) can be used to genetically enhance resistance to gastrointestinal nematode parasites in growing lambs, thereby reducing the frequency of use of anthelmintics, facilitating marketing of organic lamb, and reducing the risk of development of anthelmintic resistance by the parasite. Recording of FEC in lambs has, therefore, been incorporated into several national sheep genetic evaluation programs. Ewes in late gestation and early lactation are also vulnerable to parasite infection and commonly experience a periparturient rise in FEC. This study was designed to assess factors associated with the periparturient rise in FEC in Katahdin ewes and associated changes in FEC in their lambs. Data came from 1,487 lambings by 931 Katahdin ewes from 11 farms in the Eastern United States. Fecal egg counts were measured in ewes at approximately 0, 30, and 60 d postpartum and in their lambs at approximately 60, 90, and 120 d of age. Approximately 1,400 lambs were evaluated at each measurement age. Data were analyzed separately for ewes and lambs and also initially analyzed separately for each measurement time. Repeated-measures analyses were then used to evaluate responses across measurement times. In ewes, FEC peaked at approximately 28 d postpartum, and we concluded that informative periparturient FEC could be obtained from 1 wk before until approximately 5 wk after lambing. Yearling ewes had higher FEC than adult ewes (P < 0.01), and ewes that nursed twin or triplet lambs had higher FEC than ewes that nursed single lambs (P < 0.01). In lambs, FEC increased through approximately 120 d of age. Lambs from yearling ewes and lambs nursed in larger litters were, like their dams, at greater risk of parasitism (P < 0.05). Ewes and lambs in these groups would benefit from enhanced monitoring of parasite loads at lambing and in early lactation. Correlations (r) between FEC in lambs at 90 d of age and FEC in ewes at 0, 30, and 60 d postpartum of 0.05 to 0.09 (P <= 0.05) support the presence of a genetic relationship between these 2 indicators of parasite resistance.
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    Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep
    Becker, Gabrielle M.; Thorne, Jacob W.; Burke, Joan M.; Lewis, Ronald M.; Notter, David R.; Morgan, James L. M.; Schauer, Christopher S.; Stewart, Whit C.; Redden, R. R.; Murdoch, Brenda M. (2024-07-30)
    Background: Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright’s fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). Results: Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. Conclusions: In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
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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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    Single Nucleotide Polymorphism Effects on Lamb Fecal Egg Count Estimated Breeding Values in Progeny-Tested Katahdin Sires
    Notter, David R.; Heidaritabar, Marzieh; Burke, Joan M.; Shirali, Masoud; Murdoch, Brenda M.; Morgan, James L. M.; Morota, Gota; Sonstegard, Tad S.; Becker, Gabrielle M.; Spangler, Gordon L.; MacNeil, Michael D.; Miller, James E. (Frontiers, 2022-05-03)
    Estimated breeding values (EBV) for fecal egg counts (FEC) at 42-90 days of age (WFEC) and 91-150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000 SNP with minor-allele frequencies >= 0.10 on an Illumina high-density ovine array. Associations between markers and FEC EBV were initially quantified by single-SNP linear regression. Effects of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those SNP achieved chromosome-wide significance after Bonferroni correction based on the 14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance. The largest SNP effects were at 63, 67, and 70 Mb, with LD among these SNP of r(2) <= 0.2. Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that one 500-SNP window between 65.9 and 69.9 Mb accounted for significant variation in PFEC EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p < 0.10) significance for PFEC EBV. Although previous studies rarely identified markers for parasite resistance on chromosome 5, the IL12B gene at 68.5 Mb codes for the p40 subunit of both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of chromosome 5, providing opportunity for additive or associative effects.
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    Variance components for direct and maternal effects on body weights of Katahdin lambs
    Ngere, L.; Burke, Joan M.; Notter, David R.; Morgan, James L. M. (2017-08)
    The aim of this study was to estimate genetic parameters for BW in Katahdin lambs. Six animal models were used to study direct and maternal effects on birth weight (BWT), weaning weight (WWT), and postweaning weight (PWWT) using 41,066 BWT, 33,980 WWT, and 22,793 PWWT records collected over 17 yr in 100 flocks. Models included fixed effects of management group, dam age, type of birth (for BWT) or birth and rearing (for WWT and PWWT), and lamb age at weighing (fitted as a covariate for WWT and PWWT; all P < 0.05). Variance components for random effects were estimated in sequentially more complex models and tested for significance with likelihood-ratio tests. A model that fitted only an additive animal effect overestimated additive variance for all BW, resulting in larger estimates of direct heritability than models that included maternal effects. Maternal effects explained variation (P < 0.05) in all BW. Heritability estimates for optimal models were 0.15 +/- 0.01 for BWT, 0.18 +/- 0.02 for WWT, and 0.20 +/- 0.02 for PWWT. Estimates of maternal heritabilities were 0.14 for BWT, 0.10 for WWT, and 0.06 for PWWT, with SE = 0.01. Permanent environmental maternal effects explained 4 to 6% (+/- 1%) of total phenotypic variances for these BW. Litter effects included temporary environmental effects common to littermates and a proportion of the dominance genetic variance and accounted for 16 to 19% (+/- 1%) of phenotypic variance. Correlations between additive direct and maternal genetic effects were -0.14 for BWT, -0.23 for WWT, and -0.04 for PWWT but differed from 0 (P < 0.05) only for WWT. The total heritability predicted the total response in direct and maternal genetic effects from mass selection and was 0.23 for BWT, 0.20 for WWT, and 0.23 for PWWT. Direct and maternal additive, maternal permanent environmental, residual, and phenotypic correlations between BWT and WWT were 0.53 +/- 0.05, 0.58 +/- 0.06, 0.51 +/- 0.06, 0.39 +/- 0.01, and 0.44 +/- 0.01, respectively; those between BWT and PWWT were 0.45 +/- 0.06, 0.58 +/- 0.08, 0.36 +/- 0.08, 0.33 +/- 0.01, and 0.37 +/- 0.01 respectively; and those between WWT and PWWT were 0.85, 0.99, 0.92, 0.77, and 0.81, respectively, with SE = 0.02. Therefore, both direct and maternal effects had an important impact on BW in Katahdin lambs. Models that included both additive and permanent environmental maternal effects as well as a temporary environmental litter effect should result in more accurate estimates of breeding values and better selection decisions.
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    Variants Within Genes EDIL3 and ADGRB3 are Associated With Divergent Fecal Egg Counts in Katahdin Sheep at Weaning
    Becker, Gabrielle M.; Burke, Joan M.; Lewis, Ronald M.; Miller, James E.; Morgan, James L. M.; Rosen, Benjamin D.; Van Tassell, Curtis P.; Notter, David R.; Murdoch, Brenda M. (Frontiers, 2022-03-10)
    Gastrointestinal nematodes (GIN) pose a severe threat to sheep production worldwide. Anthelmintic drug resistance coupled with growing concern regarding potential environmental effects of drug use have demonstrated the necessity of implementing other methods of GIN control. The aim of this study was to test for genetic variants associated with resistance or susceptibility to GIN in Katahdin sheep to improve the current understanding of the genetic mechanisms responsible for host response to GIN. Linear regression and case-control genome-wide association studies were conducted with high-density genotype data and cube-root transformed weaning fecal egg counts (tFEC) of 583 Katahdin sheep. The case-control GWAS identified two significant SNPs (P-values 1.49e-08 to 1.01e-08) within introns of the gene adhesion G protein-coupled receptor B3 (ADGRB3) associated with lower fecal egg counts. With linear regression, four significant SNPs (P-values 7.82e-08 to 3.34e-08) were identified within the first intron of the gene EGF-like repeats and discoidin domains 3 (EDIL3). These identified SNPs were in very high linkage disequilibrium (r(2) of 0.996-1), and animals with alternate homozygous genotypes had significantly higher median weaning tFEC phenotypes compared to all other genotypes. Significant SNPs were queried through public databases to identify putative transcription factor binding site (TFBS) and potential lncRNA differences between reference and alternate alleles. Changes in TFBS were predicted at two SNPs, and one significant SNP was found to be within a predicted lncRNA sequence with greater than 90% similarity to a known lncRNA in the bovine genome. The gene EDIL3 has been described in other species for its roles in the inhibition and resolution of inflammation. Potential changes of EDIL3 expression mediated through lncRNA expression and/or transcription factor binding may impact the overall immune response and reduce the ability of Katahdin sheep to control GIN infection. This study lays the foundation for further research of EDIL3 and ADGRB3 towards understanding genetic mechanisms of susceptibility to GIN, and suggests these SNPs may contribute to genetic strategies for improving parasite resistance traits in sheep.
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    Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry
    Spangler, Gordon L.; Rosen, Benjamin D.; Ilori, Moses Babatunde; Hanotte, Olivier; Kim, Eui-Soo; Sonstegard, Tad S.; Burke, Joan M.; Morgan, James L. M.; Notter, David R.; Van Tassell, Curtis P. (PLOS, 2017-06-29)
    Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Their lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust production performance even in the presence of drug-resistant gastrointestinal nematodes, a rising concern to the industry. Despite the growing importance of hair sheep in the Americas their genetic origins have remained speculative. Prior to this report no genetic studies were able to identify a unique geographical origin of hair sheep in the New World. Our study clarifies the African and European ancestry of Caribbean hair sheep. Whole-genome structural analysis was conducted on four established breeds of hair sheep from the Caribbean region. Using breeds representing Africa and Europe we establish an objective measure indicating Caribbean hair sheep are derived from Iberian and West African origins. Caribbean hair sheep result from West African introgression into established ecotypes of Iberian descent. Genotypes from 47,750 autosomal single nucleotide polymorphism markers scored in 290 animals were used to characterize the population structure of the St. Croix, Barbados Blackbelly, Morada Nova, and Santa Ines. Principal components, admixture, and phylogenetic analyses results correlate with historical patterns of colonization and trade. These patterns support co-migration of these sheep with humans.