Model definition for genetic evaluation of purebred and crossbred lambs including heterosis

Crossbreeding is a common practice among commercial sheep producers to improve animal performance. However, genetic evaluation of U.S. sheep is performed within breed type (terminal sire, semi-prolific, and western range). While incorporating crossbred records may improve assessment of purebreds, it requires accounting for heterotic and breed effects in the evaluation. The objectives of this study were to: 1) describe the development of a paternal composite (PC) line, 2) determine the effect of direct and maternal heterosis on growth traits of crossbred lambs, 3) estimate (co)variance components for direct and maternal additive, and uncorrelated maternal environmental, effects, and 4) provide an interpretation of the estimates of random effects of genetic groups, and to use those solutions to compare the genetic merit of founding breed subpopulations. Data included purebred and crossbred records on birth weight (BN; n = 14,536), pre-weaning weight measured at 39 or 84 d (WN; n = 9,362) depending on year, weaning weight measured at 123 d (WW; n = 9,297), and post-weaning weight measured at 252 d (PW; n = 1,614). Mean (SD) body weights were 5.3 (1.1), 16.8 (3.9) and 28.0 (7.6), 39.1 (7.2), and 54.2 (8.7) kg for BN, WN (at the two ages), WW, and PW, respectively. In designed experiments, the Siremax, Suffolk, Texel, Polypay, Columbia, Rambouillet, and Targhee breeds were compared within the same environment. Estimates of heterotic effects and covariance components were obtained using a multiple trait animal model. Genetic effects based on founders’ breeds were significant and included in the model. Percent estimates of direct heterosis were 2.89 ± 0.61, 2.60 ± 0.65, 4.24 ± 0.56, and 6.09 ± 0.86, and estimates of maternal heterosis were 1.92 ± 0.87, 4.64 ± 0.80, 3.95 ± 0.66, and 4.04 ± 0.91, for BN, WN, WW, and PW, respectively. Correspondingly, direct heritability estimates were 0.17 ± 0.02, 0.13 ± 0.02, 0.17 ± 0.02, and 0.46 ± 0.04 for BN, WN, WW, and PW. Additive maternal effects accounted for trivial variation in PW. For BN, WN, and WW, respectively, maternal heritability estimates were 0.16 ± 0.02, 0.10 ± 0.02, and 0.07 ± 0.01. Uncorrelated maternal environmental effects accounted for little variation in any trait. Direct and maternal heterosis had considerable impact on growth traits, emphasizing the value of crossbreeding and the need to account for heterosis, in addition to breed effects, if crossbred lamb information is included in genetic evaluation. Lay Summary Crossbreeding is common in commercial sheep enterprises. It allows breeds with different attributes to be combined to generate crossbred progeny tailored to production environments and customer preferences. Additionally, crossbreds often benefit from heterosis, performing at levels above the average of their parental breeds. Over two decades, body weights were collected at birth and at pre-weaning, weaning, and post-weaning ages on purebred and crossbred lambs from semi-prolific (Polypay), western range (Columbia, Rambouillet, Targhee), and terminal sire (Siremax, Suffolk, Texel) breeds at the U.S. Sheep Experiment Station. When combined, the value of direct heterosis—that due to a lamb being crossbred—and maternal heterosis—that due to the lamb’s dam being crossbred—increased birth (5%) and post-natal (up to 10%) weights in crossbred lambs. This highlights the value of crossbreeding to the U.S. sheep industry, especially in western range production systems. Genetic variation between and within breeds also was detected for the purebred parental breeds. Such heterotic and breed effects must be accounted for if crossbred performance is to be incorporated in genetic evaluation of purebreds. Therefore, these results provide the foundation for utilizing crossbred information in the evaluation and selection of purebred sheep in the United States

Combined purebred and crossbred genetic evaluation of Columbia, Suffolk, and crossbred lamb birth and weaning weights: systematic effects and heterogeneous variances

Despite the benefits of crossbreeding on animal performance, genetic evaluation of sheep in the U.S. does not directly incorporate records from crossbred lambs. Crossbred animals may be raised in different environments as compared to purebreds. Systemic factors such as age of dam and birth and rearing type may, therefore, affect purebred and crossbred performance differently. Furthermore, crossbred performance may benefit from heterozygosity, and genetic and environmental variances may be heterogeneous in different breeds and their crosses. Such issues must be accounted for in a combined (purebred and crossbred) genetic evaluation. The objectives of this study were to i) determine the effect of dam age and birth type on birth weight, and dam age and birth-rearing type on weaning weight, in purebred and crossbred lambs, ii) test for heterogeneous genetic and environmental variances in those weights, and iii) assess the impact of including weights on crossbred progeny on sire estimated breeding values (EBV). Performance records were available on purebred Columbia and Suffolk lambs. Crossbred information was available on lambs sired by Suffolk, Columbia or Texel rams mated to Columbia, Suffolk, or crossbred ewes. A multiple-trait animal model was fitted in which weights from Columbia, Suffolk, or crossbred lambs were considered different traits. At birth, there were 4,160, 2,356, and 5,273 Columbia, Suffolk, and crossbred records, respectively, with means (SD) of 5.14 (1.04), 5.32 (1.14), and 5.43 (1.23) kg, respectively. At weaning, on average at 122 (12) d, there were 2,557, 980, and 3,876 Columbia, Suffolk, and crossbred records, respectively, with corresponding means of 39.8 (7.2), 40.3 (7.9), and 39.6 (8.0) kg. Dam age had a large positive effect on birth and weaning weight in pure and crossbred lambs. At birth, however, the predicted effect was larger in crossbred and Suffolk lambs. While an increase in a number of lambs born and reared had a strong and negative influence on birth and weaning weight, the size of the effect did not differ across-breed types. Environmental variances were similar at birth and weaning, but additive variances differed among breed types for both weights. Combining purebred and crossbred information in the evaluation not only improved predictions of genetic merit in purebred sires but also allowed for direct comparisons of sires of different breeds. Breeders thus can benefit from an additional tool for making selection decisions

Spring Clipping, Fire, and Simulated Increased Atmospheric Nitrogen Deposition Effects on Tallgrass Prairie Vegetation

Defoliation aimed at introduced cool-season grasses, which uses similar resources of native grasses, could substantially reduce their competitiveness and improve the quality of the northern tallgrass prairie. The objective was to evaluate the use of early season clipping and fire in conjunction with simulated increased levels of atmospheric nitrogen deposition on foliar canopy cover of tallgrass prairie vegetation. This study was conducted from 2009 to 2012 at two locations in eastern South Dakota. Small plots arranged in a split-plot treatment design were randomized in four complete blocks on a warm-season grass interseeded and a native prairie site in east-central South Dakota. The whole plot consisted of seven treatments: annual clip, biennial clip, triennial clip, annual fire, biennial fire, triennial fire, and undefoliated control. The clip plots consisted of weekly clipping in May to simulate heavy grazing. Fire was applied in late April or early May. The subplot consisted of nitrogen applied at 0 or 15 kg N · ha−1 in early June. All treatments were initially applied in 2009. Biennial and triennial treatments were reapplied in 2011 and 2012, respectively. Canopy cover of species/major plant functional groups was estimated in late August/early September. Annual clipping was just as effective as annual fire in increasing native warm-season grass and decreasing introduced cool-season grass cover. Annual defoliation resulted in greater native warm-season grass cover, less introduced cool-season grass cover, and less native cool-season grass cover than biennial or triennial defoliation applications. Low levels of nitrogen did not affect native warm-season grass or introduced cool-season cover for any of the defoliation treatments, but it increased introduced cool-season grass cover in the undefoliated control at the native prairie site. This study supports the hypothesis that appropriately applied management results in consistent desired outcomes regardless of increased simulated atmospheric nitrogen depositions

Classical scrapie prions are associated with peripheral blood monocytes and T-lymphocytes from naturally infected sheep

BACKGROUND: Classical scrapie is a transmissible spongiform encephalopathy (TSE) that affects sheep and goats. Our previous bioassay studies in lambs revealed that scrapie prions could be detected in association with peripheral blood monocular cells (PBMC), B lymphocytes and platelet-rich plasma fractions. In the present study, bioassay in lambs was again used to determine if scrapie prions are associated with the other two subsets of PBMC, monocytes and T lymphocytes. RESULTS: PBMC, monocytes and T lymphocytes were isolated from two preclinically affected VRQ/VRQ sheep naturally infected with classical ovine scrapie and intravenously transfused into VRQ/VRQ lambs post-weaning. As determined using standard immunohistochemistry for scrapie, abnormal isoforms of prion protein were detected in lymphoid tissues of lambs inoculated with PBMC (4/4 recipient lambs), monocytes (2/5) and T lymphocytes (1/4). Prion protein misfolding activity was detected by serial protein misfolding cyclic amplification (sPMCA) in PBMC from monocyte and T lymphocyte recipient sheep in agreement with antemortem rectal biopsy results, but such prion protein misfolding activity was not detected from other recipients. CONCLUSIONS: These findings show that scrapie prions are associated with monocytes and T lymphocytes circulating in the peripheral blood of sheep naturally infected with classical scrapie. Combined with our previous findings, we can now conclude that all three major subsets of PBMC can harbor prions during preclinical disease and thus, present logical targets for development of a sensitive assay to detect scrapie prions. In this regard, we have also demonstrated that sPMCA can be used to detect scrapie prions associated with PBMC

Increased Risk of Chronic Wasting Disease in Rocky Mountain Elk Associated With Decreased Magnesium and Increased Manganese in Brain Tissue

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) of Rocky Mountain elk in North America. Recent studies suggest that tissue and blood mineral levels may be valuable in assessing TSE infection in sheep and cattle. The objectives of this study were to examine baseline levels of copper, manganese, magnesium, zinc, selenium, and molybdenum in the brains of Rocky Mountain elk with differing prion genotypes and to assess the association of mineral levels with CWD infection. Elk with leucine at prion position 132 had significantly lower magnesium levels than elk with 2 copies of methionine. Chronic wasting disease-positive elk had significantly lower magnesium than control elk. The incorporation of manganese levels in addition to magnesium significantly refined explanatory ability, even though manganese alone was not significantly associated with CWD. This study demonstrated that mineral analysis may provide an additional disease correlate for assessing CWD risk, particularly in conjunction with genotype

Genome-wide associations with longevity and reproductive traits in U.S. rangeland ewes

Introduction: Improving ewe longevity is an important breeding and management goal, as death loss and early culling of mature ewes are economic burdens in the sheep industry. Ewe longevity can be improved by selecting for positive reproductive outcomes. However, the breeding approaches for accomplishing this come with the challenge of recording a lifetime trait. Characterizing genetic factors underpinning ewe longevity and related traits could result in the development of genomic selection strategies to improve the stayability of sheep through early, informed selection of replacement ewes.Methods: Towards this aim, a genome-wide association study (GWAS) was performed to identify genetic markers associated with ewe longevity, reproductive, and production traits. Traits evaluated included longevity (i.e., length of time in the flock), parity and the lifetime number of lambs born, lambs born alive, lambs weaned, and weight of lambs weaned. Ewe records from previous studies were used. Specifically, Rambouillet (n = 480), Polypay (n = 404), Suffolk (n = 182), and Columbia (n = 64) breed ewes (N = 1,130) were analyzed against 503,617 SNPs in across-breed and within-breed GWAS conducted with the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model in R.Results: The across-breed GWAS identified 25 significant SNPs and the within-breed GWAS for Rambouillet, Polypay, and Suffolk ewes identified an additional 19 significant SNPs. The most significant markers were rs411309094 (13:22,467,143) associated with longevity in across-breed GWAS (p-value = 8.3E-13) and rs429525276 (2:148,398,336) associated with both longevity (p-value = 6.4E-15) and parity (p-value = 4.8E-15) in Rambouillet GWAS. Significant SNPs were identified within or in proximity (±50 kb) of genes with known or proposed roles in reproduction, dentition, and the immune system. These genes include ALPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, CEP89, DISC1, ITGB6, KCNH8, MBNL3, MINDY4, MTSS1, PLEKHA7, PRIM2, RNF43, ROBO2, SLCO1A2, TMEM266, TNFRSF21, and ZNF804B.Discussion: This study proposes multiple SNPs as candidates for use in selection indices and suggests genes for further research towards improving understanding of the genetic factors contributing to longevity, reproductive, and production traits of ewes

Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations

Visna/Maedi, or ovine progressive pneumonia (OPP) as it is known in the United States, is an incurable slow-acting disease of sheep caused by persistent lentivirus infection. This disease affects multiple tissues, including those of the respiratory and central nervous systems. Our aim was to identify ovine genetic risk factors for lentivirus infection. Sixty-nine matched pairs of infected cases and uninfected controls were identified among 736 naturally exposed sheep older than five years of age. These pairs were used in a genome-wide association study with 50,614 markers. A single SNP was identified in the ovine transmembrane protein (TMEM154) that exceeded genome-wide significance (unadjusted p-value 3×10−9). Sanger sequencing of the ovine TMEM154 coding region identified six missense and two frameshift deletion mutations in the predicted signal peptide and extracellular domain. Two TMEM154 haplotypes encoding glutamate (E) at position 35 were associated with infection while a third haplotype with lysine (K) at position 35 was not. Haplotypes encoding full-length E35 isoforms were analyzed together as genetic risk factors in a multi-breed, matched case-control design, with 61 pairs of 4-year-old ewes. The odds of infection for ewes with one copy of a full-length TMEM154 E35 allele were 28 times greater than the odds for those without (p-value<0.0001, 95% CI 5–1,100). In a combined analysis of nine cohorts with 2,705 sheep from Nebraska, Idaho, and Iowa, the relative risk of infection was 2.85 times greater for sheep with a full-length TMEM154 E35 allele (p-value<0.0001, 95% CI 2.36–3.43). Although rare, some sheep were homozygous for TMEM154 deletion mutations and remained uninfected despite a lifetime of significant exposure. Together, these findings indicate that TMEM154 may play a central role in ovine lentivirus infection and removing sheep with the most susceptible genotypes may help eradicate OPP and protect flocks from reinfection

Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep.

Supplementary data for publication: Lifan Zhang, Michelle R. Mousel, Xiaolin Wu, Jennifer J. Michal, Xiang Zhou, Bo Ding, Gregory S. Lewis and Zhihua Jiang. (2013). Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep. PLoS ONE, 2013 Jun 10;8(6):e65942. doi: 10.1371

Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep.

Supplementary data for publication: Lifan Zhang, Michelle R. Mousel, Xiaolin Wu, Jennifer J. Michal, Xiang Zhou, Bo Ding, Gregory S. Lewis and Zhihua Jiang. (2013). Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep. PLoS ONE, 2013 Jun 10;8(6):e65942. doi: 10.1371

Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent

Supplementary data for publication: Michelle R. Mousel, Stephen N White, David R. Herndon, James O. Reynolds, Michael V. Gonzalez, Wendell C. Johnson, Massaro W. Ueti, J. Bret Taylor, Donald P. Knowles (2015). Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent Anim Genet. 2016 Feb;47(1):136-7. doi: 10.1111/age.1238