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Altered phosphorylation, electrophysiology, and behavior on attenuation of PDE4B action in hippocampus
Campbell, Susan L.; van Groen, Thomas; Kadish, Inga; Smoot, Lisa High Mitchell; Bolger, Graeme B. (BMC, 2017)
Background: PDE4 cyclic nucleotide phosphodiesterases regulate 3′, 5′ cAMP abundance in the CNS and thereby regulate PKA activity and phosphorylation of CREB, which has been implicated in learning and memory, depression and other functions. The PDE4 isoform PDE4B1 also interacts with the DISC1 protein, implicated in neural development and behavioral disorders. The cellular functions of PDE4B1 have been investigated extensively, but its function(s) in the intact organism remained unexplored. Results: To specifically disrupt PDE4B1, we developed mice that express a PDE4B1-D564A transgene in the hippocampus and forebrain. The transgenic mice showed enhanced phosphorylation of CREB and ERK1/2 in hippocampus. Hippocampal neurogenesis was increased in the transgenic mice. Hippocampal electrophysiological studies showed increased baseline synaptic transmission and enhanced LTP in male transgenic mice. Behaviorally, male transgenic mice showed increased activity in prolonged open field testing, but neither male nor female transgenic mice showed detectable anxiety-like behavior or antidepressant effects in the elevated plus-maze, tail-suspension or forced-swim tests. Neither sex showed any significant differences in associative fear conditioning or showed any demonstrable abnormalities in pre-pulse inhibition. Conclusions: These data support the use of an isoform-selective approach to the study of PDE4B1 function in the CNS and suggest a probable role of PDE4B1 in synaptic plasticity and behavior. They also provide additional rationale and a refined approach to the development of small-molecule PDE4B1-selective inhibitors, which have potential functions in disorders of cognition, memory, mood and affect.
Beef heifer fertility: importance of management practices and technological advancements
Moorey, Sarah E.; Biase, Fernando H. (2020-10-01)
The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA, National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under development for cow replacement. A compilation of data from several studies indicate that between 85% and 95% of these heifers will become pregnant in their first breeding season. Several thousands of heifers being raised for replacement may not deliver a calf on their first breeding season and result in economic losses to cow-calf producers. Many management procedures have been developed to maximize the reproductive potential of beef heifers. Such approaches include, but are not limited to the following: nutritional management for controlled weight gain, identification of reproductive maturity by physiological and morphological indicators, and the implementation of an estrous synchronization program. The implementation of management strategies has important positive impact(s) on the reproductive efficiency of heifers. There are limitations, however, because some heifers deemed ready to enter their first breeding season do not become pregnant. In parallel, genetic selection for fertility-related traits in beef heifers have not promoted major genetic gains on this particular area, most likely due to low heritability of female fertility traits in cattle. Technologies such as antral follicle counting, DNA genotyping and RNA profiling are being investigated as a means to aid in the identification of heifers of low fertility potential. To date, many polymorphisms have been associated with heifer fertility, but no DNA markers have been identified across herds. Antral follicle count is an indication of the ovarian reserve and is an indicator of the reproductive health of a heifer. We have been working on the identification of transcriptome profiles in heifers associated with pregnancy outcome. Our current investigations integrating protein-coding transcript abundance and artificial intelligence have identified the potential for bloodborne transcript abundance to be used as indicators of fertility potential in beef heifers. In summary, there is an ongoing pressure for reducing costs and increasing efficiency in cow-calf production systems, and new technologies can help reduce the long-standing limitations in beef heifer fertility.
Biallelic modification of IL2RG leads to severe combined immunodeficiency in pigs
Clark-Deener, Sherrie; Kang, Jung-Taek; Cho, Bumrae; Ryu, Junghyun; Ray, Caitlin; Lee, Eun-Jin; Ahn, SunMi; Lee, JinSeok; Ji, Dal-Young; Jue, Nathaniel; Lee, Kiho; Park, Kwang-Wook (2016-11-03)
Background: Pigs with SCID can be a useful model in regenerative medicine, xenotransplantation, and cancer cell transplantation studies. Utilizing genome editing technologies such as CRISPR/Cas9 system allows us to generate genetically engineered pigs at a higher efficiency. In this study, we report generation and phenotypic characterization of IL2RG knockout female pigs produced through combination of CRISPR/Cas9 system and SCNT. As expected, pigs lacking IL2RG presented SCID phenotype. Methods: First, specific CRISPR/Cas9 systems targeting IL2RG were introduced into developing pig embryos then the embryos were transferred into surrogates. A total of six fetuses were obtained from the embryo transfer and fetal fibroblast cell lines were established. Then IL2RG knockout female cells carrying biallelic genetic modification were used as donor cells for SCNT, followed by embryo transfer. Results: Three live cloned female piglets carrying biallelic mutations in IL2RG were produced. All cloned piglets completely lacked thymus and they had a significantly reduced level of mature T, B and NK cells in their blood and spleen. Conclusions: Here, we generated IL2RG knockout female pigs showing phenotypic characterization of SCID. This IL2RG knockout female pigs will be a promising model for biomedical and translational research.
Central administration of dipeptides, beta-alanyl-BCAAs, induces hyperactivity in chicks
Tsuneyoshi, Yousuke; Tomonaga, Shozo; Asechi, Mari; Morishita, Koji; Denbow, D. Michael; Furuse, Mitsuhiro (2007-05-31)
Background Carnosine (β-alanyl-L-histidine) is a putative neurotransmitter and has a possible role in neuron-glia cell interactions. Previously, we reported that carnosine induced hyperactivity in chicks when intracerebroventricularly (i.c.v.) administered. In the present study, we focused on other β-alanyl dipeptides to determine if they have novel functions. Results In Experiment 1, i.c.v. injection of β-alanyl-L-leucine, but not β-alanyl-glycine, induced hyperactivity behavior as observed with carnosine. Both carnosine and β-alanyl-L-leucine stimulated corticosterone release. Thus, dipeptides of β-alanyl-branched chain amino acids were compared in Experiment 2. The i.c.v. injection of β-alanyl-L-isoleucine caused a similar response as β-alanyl-L-leucine, but β-alanyl-L-valine was somewhat less effective than the other two dipeptides. β-Alanyl-L-leucine strongly stimulated, and the other two dipeptides tended to stimulate, corticosterone release. Conclusion These results suggest that central β-alanyl-branched chain amino acid stimulates activity in chicks through the hypothalamus-pituitary-adrenal axis. We named β-alanyl-L-leucine, β-alanyl-L-isoleucine and β-alanyl-L-valine as Excitin-1, Excitin-2 and Excitin-3, respectively.
Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken
Li, Jingyi; Davis, Brian W.; Jern, Patric; Dorshorst, Benjamin J.; Siegel, Paul B.; Andersson, Leif (2019-08-28)
Background Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of CYP19A1 encoding aromatase that converts androgens to estrogen and thereby inhibits the development of male-specific plumage. A long terminal repeat (LTR) from an uncharacterized endogenous retrovirus (ERV) insertion was found in an isoform of the CYP19A1 transcript from henny feathering chicken. However, the complete sequence and the genomic position of the insertion were not determined. Results We used publicly available whole genome sequence data to determine the flanking sequences of the ERV, and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region, was detected partially in an aromatase transcript, which present a plausible explanation for ectopic expression of aromatase in non-ovarian tissues underlying the henny feathering phenotype. Conclusions We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5’end of CYP19A1. The presence of this ERV showed complete concordance with the henny feathering phenotype both within a pedigree segregating for this phenotype and across breeds.
Combination of probiotics and coccidiosis vaccine enhances protection against an Eimeria challenge
Ritzi, Miranda M.; Abdelrahman, Wael; van-Heerden, Kobus; Mohnl, Michaela; Barrett, Nathaniel W.; Dalloul, Rami A. (BMC, 2016-11-08)
Coccidiosis is endemic in the commercial broiler industry capable of inflicting devastating economic losses to poultry operations. Vaccines are relatively effective in controlling the disease; their efficacy could potentially be improved with concurrent use of probiotics as evaluated in this study using an Eimeria challenge. Day of hatch 400 Cobb-500 male broilers were assigned to one of four treatment groups including control (CON), vaccine-only gel application (VNC), probiotic-only gel application (NPC), and vaccine-plus-probiotic gel application (VPC). Birds were placed in floor pens (6 replicate pens/treatment, 16–17 birds/pen). NPC and VPC birds received the probiotics in the water on days 2–4, 8, 14–20, 22, 29, and 34–36. On day 15, birds were mildly challenged with 0.5 mL of a mixed oral inoculum of Eimeria sp. prepared with the coccidiosis vaccine at 10× the vaccination dose. Performance measurements were recorded on first day and weekly afterwards, and lesion scores were evaluated 6 days post-challenge. Overall, the probiotics and coccidiosis vaccine resulted in an enhanced protective effect against the challenge, with VPC birds exhibiting lower lesion scores in the duodenum than VNC or NPC birds. Birds in the VPC treatment also demonstrated higher weight gains during days 1–15, days 7–15, and days 21–28 when compared to the VNC birds. These results suggest that the combination of probiotics and coccidiosis vaccines could enhance performance and provide an additional protective effect against a mixed Eimeria challenge.
Development and validation of a house finch interleukin-1β (HfIL-1β) ELISA system
Kim, Sungwon; Park, Myeongseon; Leon, Ariel E.; Adelman, James S.; Hawley, Dana M.; Dalloul, Rami A. (2017-08-30)
Background A unique clade of the bacterium Mycoplasma gallisepticum (MG), which causes chronic respiratory disease in poultry, has resulted in annual epidemics of conjunctivitis in North American house finches since the 1990s. Currently, few immunological tools have been validated for this songbird species. Interleukin-1β (IL-1β) is a prototypic multifunctional cytokine and can affect almost every cell type during Mycoplasma infection. The overall goal of this study was to develop and validate a direct ELISA assay for house finch IL-1β (HfIL-1β) using a cross-reactive chicken antibody. Methods A direct ELISA approach was used to develop this system using two different coating methods, carbonate and dehydration. In both methods, antigens (recombinant HfIL-1b or house finch plasma) were serially diluted in carbonate-bicarbonate coating buffer and either incubated at 4 °C overnight or at 60 °C on a heating block for 2 hr. To generate the standard curve, rHfIL-1b protein was serially diluted at 0, 3, 6, 9, 12, 15, 18, 21, and 24 ng/mL. Following blocking and washing, anti-chicken IL-1b polyclonal antibody was added, plates were later incubated with detecting antibodies, and reactions developed with tetramethylbenzidine solution. Results A commercially available anti-chicken IL-1β (ChIL-1β) polyclonal antibody (pAb) cross-reacted with house finch plasma IL-1β as well as bacterially expressed recombinant house finch IL-1β (rHfIL-1β) in immunoblotting assays. In a direct ELISA system, rHfIL-1β could not be detected by an anti-ChIL-1β pAb when the antigen was coated with carbonate-bicarbonate buffer at 4°C overnight. However, rHfIL-1β was detected by the anti-ChIL-1β pAb when the antigen was coated using a dehydration method by heat (60°C). Using the developed direct ELISA for HfIL-1β with commercial anti-ChIL-1β pAb, we were able to measure plasma IL-1β levels from house finches. Conclusions Based on high amino acid sequence homology, we hypothesized and demonstrated cross-reactivity of anti-ChIL-1β pAb and HfIL-1β. Then, we developed and validated a direct ELISA system for HfIL-1β using a commercial anti-ChIL-1β pAb by measuring plasma HfIL-1β in house finches.
Direct and correlated responses to selection for autumn lambing in sheep
Asadi-Fozi, Masood; Bradford, Heather L.; Notter, David R. (2020-10-02)
Background Seasonal reproduction limits productivity, flexibility, and profitability in commercial sheep production. Hormonal and (or) photoperiodic manipulation can be used to control estrous cycles in sheep and reduce limitations that are imposed by the seasonal anestrous but are often impractical or incompatible with the extensive management systems preferred for ruminant livestock. Thus, the current study investigated the use of selection to improve realized fertility (i.e., the proportion of ewes that lambed) following an out-of-season spring joining period (May and June) in a crossbred sheep population. Results Over 17 years, estimated breeding values (EBV) for fertility in selected (S) ewes increased by 0.175 (0.01 per year). The mean EBV for fertility of S ewes was greater than that of control ewes by year 10 (P = 0.02), and the fertility of adult (≥ 3 years old) ewes reached 0.88 ± 0.05 by year 17. Lambing began approximately 140 days after the introduction of rams, and 64% of the S ewes that lambed did so in the first 17 days of the potential lambing season, which indicated that most of the S ewes were cycling at the time of ram introduction and were not induced to cycle by the introduction of breeding males (i.e., the so-called “ram effect”). Animals in the S line had modest increases in body weight and scrotal circumference. A modest negative trend in the additive maternal effect on birth weight was observed but was reversed by additional selection on EBV for maternal birth weight. The heritability of litter size in autumn lambing was low (0.04) and could potentially limit the response to selection for this trait. Conclusions Selection improved realized ewe fertility in out-of-season mating, with absolute increases of approximately 1% per year in the percentage of joined ewes that lambed in the autumn. Genetic antagonisms with other performance traits were generally small. A modest antagonism with maternal breeding values for birth weight was observed but it could be accommodated by selection on EBV for maternal birth weight. Our results support results of previous studies that indicate that these selected ewes had one of the shortest seasonal anestrous periods reported for temperate sheep breeds and that spring-lambing lactating ewes from the selection line were capable of relatively rapid rebreeding in the spring.
Effects of birth-rearing type on weaning weights in meat sheep are systematically associated with differences in mean performance among flocks
Notter, David R.; Brown, Daniel J. (2015-07-03)
Background Adjustment of body weights for systematic environmental effects such as dam age and litter size is essential for accurate prediction of breeding values in meat sheep and often accomplished by pre-adjusting records using simple multiplicative adjustment factors, which are derived as ratios of least-squares means of weights of lambs in target and reference classes. However, increasing use of multibreed genetic evaluations that incorporate data from both purebred and commercial flocks has generated concerns regarding the ability of simple additive or multiplicative adjustment factors to properly correct for environmental effects in flocks that differ widely in mean performance. Thus, consistency of adjustment factors across flocks and systematic effects of the level of flock performance on these factors were evaluated using data from the US National Sheep Improvement Program. Methods We used birth and weaning weights of lambs from 29 flocks that had at least 500 records per flock and represented several terminal-sire sheep breeds. Effects of lamb sex, dam age class and litter size on birth weights, and of dam age class and combined effects of type of birth and rearing on weaning weights were evaluated. Interactions between these effects and flock were assessed. Bias associated with different adjustment protocols was evaluated for high- and low-performance flocks. Results Effects of litter size and differences between yearling and adult dams varied (P < 0.001) among flocks. For weaning weights, additive adjustment factors were not associated with the level of flock performance, but multiplicative adjustment factors were strongly and inversely related to flock means for weaning weights (W). Flock-specific adjustment factors (F = αWβ) reduced bias in adjusted weaning weights associated with differences in flock performance. By contrast, simple multiplicative adjustment factors were appropriate to adjust birth weights. Conclusions Differences in weaning weights among single, twin, and triplet lambs were inversely related to the level of flock performance. Use of simple multiplicative adjustment factors led to adjustment bias when applied across flocks with large differences in mean performance. This bias was reduced by using additive adjustment factors or multiplicative factors that were derived as simple exponential functions of flock means for weaning weight.
The effects of dietary macronutrient composition on lipid metabolismassociated factor gene expression in the adipose tissue of chickens are influenced by fasting and refeeding
Wang, Guoqing; McConn, Betty R.; Liu, Dongmin; Cline, Mark A.; Gilbert, Elizabeth R. (BMC, 2017-05-10)
Background: Broiler chickens are compulsive feeders that become obese as juveniles and are thus a unique model for metabolic disorders in humans. However, little is known about the relationship between dietary composition, fasting and refeeding and adipose tissue physiology in chicks. Our objective was to determine how dietary macronutrient composition and fasting and refeeding affect chick adipose physiology during the early post-hatch period. Methods: Chicks were fed one of three isocaloric diets after hatch: high-carbohydrate (HC; control), high-fat (HF; 30% of ME from soybean oil) or high-protein (HP; 25% vs. 22% crude protein). At 4 days post-hatch, chicks were fed (continuous ad libitum access to food), fasted (3 h food withdrawal), or refed (fasted for 3 h and refed for 1 h). Subcutaneous, clavicular, and abdominal adipose tissue was collected for histological analysis and to measure gene expression, and plasma to measure non-esterified fatty acid (NEFA) concentrations (n = 6–10 per group). Results: Adipose tissue weights were reduced in chicks that were fed the HP diet and adipocyte diameter was greater in the adipose tissue of chicks that ate the HF diet. Consumption of diets differing in protein and fat content also affected gene expression; mRNAs encoding fatty acid binding protein 4 and a lipolytic enzyme, monoglyceride lipase, were greater in chicks fed the HC and HF than HP diet in all three adipose tissue depots. Fasting influenced gene expression in a depot-dependent manner, where most fasting and refeeding-induced changes were observed in the clavicular fat of chicks that consumed the HC diet. Fasting increased plasma NEFA concentrations in chicks fed the HC and HP diets. Conclusions: The decreased adipose tissue deposition in chicks fed the HP diet is likely explained by decreased rates of adipogenesis. Consumption of the HF diet was associated with greater adipose tissue deposition and larger adipocytes, likely as a result of greater rates of adipocyte hypertrophy. The depot-dependent effects of diet and fasting on gene expression may help explain mechanisms underlying metabolic distinctions among subcutaneous and visceral fat depots in humans.
Effects of sex on response of the bovine preimplantation embryo to insulin-like growth factor 1, activin A, and WNT7A
Tríbulo, Paula; Jumatayeva, Gulnur; Lehloenya, Khoboso; Moss, James I.; Negrón-Pérez, Verónica M.; Hansen, Peter J. (2018-07-28)
Background Alterations in maternal environment can sometimes affect embryonic development in a sexually-dimorphic manner. The objective was to determine whether preimplantation bovine embryos respond to three maternally-derived cell signaling molecules in a sex-dependent manner. Results Actions of three embryokines known to increase competence of bovine embryos to develop to the blastocyst stage, insulin-like growth factor 1 (IGF1), activin A, and WNT member 7A (WNT7A), were evaluated for actions on embryos produced in vitro with X- or Y- sorted semen from the same bull. Each embryokine was tested in embryos produced by in vitro fertilization of groups of oocytes with either pooled sperm from two bulls or with sperm from individual bulls. Embryos were treated with IGF1, activin A, or WNT7A on day 5 of culture. All three embryokines increased the proportion of cleaved zygotes that developed to the blastocyst stage and the effect was similar for female and male embryos. As an additional test of sexual dimorphism, effects of IGF1 on blastocyst expression of a total of 127 genes were determined by RT-qPCR using the Fluidigm Delta Gene assay. Expression of 18 genes was affected by sex, expression of 4 genes was affected by IGF1 and expression of 3 genes was affected by the IGF1 by sex interaction. Conclusion Sex did not alter how IGF1, activin A or WNT7A altered developmental competence to the blastocyst stage. Thus, sex-dependent differences in regulation of developmental competence of embryos by maternal regulatory signals is not a general phenomenon. The fact that sex altered how IGF1 regulates gene expression is indicative that there could be sexual dimorphism in embryokine regulation of some aspects of embryonic function other than developmental potential to become a blastocyst.
Exposure to maternal obesity alters gene expression in the preimplantation ovine conceptus
McCoski, Sarah R.; Vailes, McCauley T.; Owens, Connor E.; Cockrum, Rebecca R.; Ealy, Alan D. (2018-10-11)
Background Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even after a short exposure to maternal obesity around the time of conception. The hypothesis of this work is that maternal obesity influences the ovine preimplantation conceptus early in pregnancy, and this exposure will affect gene expression in embryonic and extraembryonic tissues. Results Obese and lean ewe groups were established by overfeeding or normal feeding, respectively. Ewes were then bred to genetically similar rams. Conceptuses were collected at day 14 of gestation. Morphological assessments were made, conceptuses were sexed by genomic PCR analysis, and samples underwent RNA-sequencing analysis. While no obvious morphological differences existed between conceptuses, differentially expressed genes (≥ 2-fold; ≥ 0.2 RPKM; ≤ 0.05 FDR) were detected based on maternal obesity exposure (n = 21). Also, differential effects of maternal obesity were noted on each conceptus sex (n = 347). A large portion of differentially expressed genes were associated with embryogenesis and placental development. Conclusions Findings reveal that the preimplantation ovine conceptus genome responds to maternal obesity in a sex-dependent manner. The sexual dimorphism in response to the maternal environment coupled with changes in placental gene expression may explain aberrations in phenotype observed in offspring derived from obese females.
Fine mapping and replication of QTL in outbred chicken advanced intercross lines
Besnier, Francois; Wahlberg, Per; Rönnegård, Lars; Ek, Weronica; Andersson, Leif; Siegel, Paul B.; Carlborg, Örjan (2011-01-17)
Background Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.
Frequency of off-targeting in genome edited pigs produced via direct injection of the CRISPR/Cas9 system into developing embryos
Carey, Kayla; Ryu, Junghyun; Uh, Kyungjun; Lengi, Andrea J.; Clark-Deener, Sherrie; Corl, Benjamin A.; Lee, Kiho (2019-05-06)
Background The CRISPR/Cas9 system can effectively introduce site-specific modifications to the genome. The efficiency is high enough to induce targeted genome modifications during embryogenesis, thus increasing the efficiency of producing genetically modified animal models and having potential clinical applications as an assisted reproductive technology. Because most of the CRISPR/Cas9 systems introduce site-specific double-stranded breaks (DSBs) to induce site-specific modifications, a major concern is its potential off-targeting activity, which may hinder the application of the technology in clinics. In this study, we investigated off-targeting events in genome edited pigs/fetuses that were generated through direct injection of the CRISPR/Cas9 system into developing embryos; off-targeting activity of four different sgRNAs targeting RAG2, IL2RG, SCD5, and Ig Heavy chain were examined. Results First, bioinformatics analysis was applied to identify 27 potential off-targeting genes from the sgRNAs. Then, PCR amplification followed by sequencing analysis was used to verify the presence of off-targeting events. Off-targeting events were only identified from the sgRNA used to disrupt Ig Heavy chain in pigs; frequency of off-targeting was 80 and 70% on AR and RBFOX1 locus respectively. A potential PAM sequence was present in both of the off-targeting genes adjacent to probable sgRNA binding sites. Mismatches against sgRNA were present only on the 5′ side of AR, suggesting that off-targeting activities are systematic events. However, the mismatches on RBFOX1 were not limited to the 5′ side, indicating unpredictability of the events. Conclusions The prevalence of off-targeting is low via direct injection of CRISPR/Cas9 system into developing embryos, but the events cannot be accurately predicted. Off-targeting frequency of each CRISPR/Cas9 system should be deliberately assessed prior to its application in clinics.
GCA: an R package for genetic connectedness analysis using pedigree and genomic data
Yu, Haipeng; Morota, Gota (2021-02-15)
Background Genetic connectedness is a critical component of genetic evaluation as it assesses the comparability of predicted genetic values across units. Genetic connectedness also plays an essential role in quantifying the linkage between reference and validation sets in whole-genome prediction. Despite its importance, there is no user-friendly software tool available to calculate connectedness statistics. Results We developed the GCA R package to perform genetic connectedness analysis for pedigree and genomic data. The software implements a large collection of various connectedness statistics as a function of prediction error variance or variance of unit effect estimates. The GCA R package is available at GitHub and the source code is provided as open source. Conclusions The GCA R package allows users to easily assess the connectedness of their data. It is also useful to determine the potential risk of comparing predicted genetic values of individuals across units or measure the connectedness level between training and testing sets in genomic prediction.
Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight
Wahlberg, Per; Carlborg, Örjan; Foglio, Mario; Tordoir, Xavier; Syvänen, Ann-Christine; Lathrop, Mark; Gut, Ivo G.; Siegel, Paul B.; Andersson, Leif (2009-05-27)
Background We have performed Quantitative Trait Loci (QTL) analysis of an F2 intercross between two chicken lines divergently selected for juvenile body-weight. In a previous study 13 identified loci with effects on body-weight, only explained a small proportion of the large variation in the F2 population. Epistatic interaction analysis however, indicated that a network of interacting loci with large effect contributed to the difference in body-weight of the parental lines. This previous analysis was, however, based on a sparse microsatellite linkage map and the limited coverage could have affected the main conclusions. Here we present a revised QTL analysis based on a high-density linkage map that provided a more complete coverage of the chicken genome. Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines. Results We constructed a linkage map comprising 434 genetic markers, covering 31 chromosomes but leaving seven microchromosomes uncovered. The analysis showed that seven regions harbor QTL that influence growth. The pair-wise interaction analysis identified 15 unique QTL pairs and notable is that nine of those involved interactions with a locus on chromosome 7, forming a network of interacting loci. The analysis of ~13,000 SNPs showed that a substantial proportion of the genetic variation present in the founder population has been lost in either of the two selected lines since ~60% of the SNPs polymorphic among lines showed fixation in one of the lines. With the current marker coverage and QTL map resolution we did not observe clear signs of selective sweeps within QTL intervals. Conclusion The results from the QTL analysis using the new improved linkage map are to a large extent in concordance with our previous analysis of this pedigree. The difference in body-weight between the parental chicken lines is caused by many QTL each with a small individual effect. Although the increased chromosomal marker coverage did not lead to the identification of additional QTL, we were able to refine the localization of QTL. The importance of epistatic interaction as a mechanism contributing significantly to the remarkable selection response was further strengthened because additional pairs of interacting loci were detected with the improved map.
Genetic analysis of production, physiological, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data
Rowland, Kaylee; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J. (2019-06-25)
Background Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In this study, we recorded several production traits, feed intake, body weight, digestibility, and egg quality of 400 commercial white egg-laying hens before and during a 4-week heat treatment. For the phenotypes that had estimated heritabilities (using 600k SNP chip data) higher than 0, SNP associations were tested using the same 600k genotype data. Results Seventeen phenotypes had heritability estimates higher than 0, including measurements at various time points for feed intake, feed efficiency, body weight, albumen weight, egg quality expressed in Haugh units, egg mass, and also for change in egg mass from prior to heat exposure to various time points during the 4-week heat treatment. Quantitative trait loci (QTL) were identified for 10 of these 17 phenotypes. Some of the phenotypes shared QTL including Haugh units before heat exposure and after 4 weeks of heat treatment. Conclusions Estimated heritabilities differed from 0 for 17 traits, which indicates that they are under genetic control and that there is potential for improving these traits through selective breeding. The association of different QTL with the same phenotypes before heat exposure and during heat treatment indicates that genomic control of traits under heat stress is distinct from that under thermoneutral conditions. This study contributes to the knowledge on the genomic control of response to heat stress in laying hens.
Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens
Lillie, Mette; Sheng, Zheya; Honaker, Christa F.; Dorshorst, Benjamin J.; Ashwell, Christopher M.; Siegel, Paul B.; Carlborg, Örjan (2017-01-18)
Background Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. Results We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented. Conclusions The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection.
Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach
Zan, Yanjun; Payen, Thibaut; Lillie, Mette; Honaker, Christa F.; Siegel, Paul B.; Carlborg, Örjan (2019-08-14)
Background Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens. Results We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb. Conclusions A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes.
Hypothalamus-adipose tissue crosstalk: neuropeptide Y and the regulation of energy metabolism
Zhang, W.; Cline, Mark A.; Gilbert, Elizabeth R. (Biomed Central, 2014-06-10)
Neuropeptide Y (NPY) is an orexigenic neuropeptide that plays a role in regulating adiposity by promoting energy storage in white adipose tissue and inhibiting brown adipose tissue activation in mammals. This review describes mechanisms underlying NPY’s effects on adipose tissue energy metabolism, with an emphasis on cellular proliferation, adipogenesis, lipid deposition, and lipolysis in white adipose tissue, and brown fat activation and thermogenesis. In general, NPY promotes adipocyte differentiation and lipid accumulation, leading to energy storage in adipose tissue, with effects mediated mainly through NPY receptor sub-types 1 and 2. This review highlights hypothalamus-sympathetic nervous system-adipose tissue innervation and adipose tissue-hypothalamus feedback loops as pathways underlying these effects. Potential sources of NPY that mediate adipose effects include the bloodstream, sympathetic nerve terminals that innervate the adipose tissue, as well as adipose tissue-derived cells. Understanding the role of central vs. peripherally-derived NPY in whole-body energy balance could shed light on mechanisms underlying the pathogenesis of obesity. This information may provide some insight into searching for alternative therapeutic strategies for the treatment of obesity and associated diseases.

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