Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Scientific community, professional animal breeders, extension specialists, county extension agents, livestock producers, and general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This research has provided training opportunities for three MS students, one PhD student, and five undergraduate research assistants. How have the results been disseminated to communities of interest?This research has been published in scientific manuscripts andextension reports. Both myself and my graduate students have presented this research at local, regional, national, and international scientific meetings. Additionally, aspects of this work have been presented to local producers. What do you plan to do during the next reporting period to accomplish the goals?Under objective one, no further data collection is planned as this breeding project has been terminated. Collected phenotypes and DNA samples have been archived and will hopefully be used for future research. Under objective two, a manuscript should be submitted in late 2020 and an MS thesis and second manuscript should be completed in the first half of 2021. Under objective three, a PhD dissertation was submitted in July 2020. A manuscript is under preparation for late 2020 or early 2021.
Impacts
What was accomplished under these goals?
Establish a straight-bred uniform herd of Red Angus cattle at the Red Bluff Research Ranch and a long term breeding program that will result in data on the genetic basis of maternal trait, and the impacts of maternal selection on productive efficiency, longevity, and the genetic correlations between maternal traits and other economically important traits. Due to changes in management and breeding objectives with the MAES research herd. This project has been discontinued. The gathered phenotypic data and DNA samples have been archived for future use. Elucidate the molecular mechanisms that cause variation in carcass and meat quality and contribute to the development of biologically based predictors that can improve the accuracy and reliability of genetic selection and improvement beef cattle carcass and meat quality; Under this objective, two manuscripts are in preparation, animal feeding and sample collection has been completed in follow-up study looking at finishing steers and wethers in parallel to better prioritize the genes with similar patterns of expression between the two species. A MS thesis will also be completed in the next year. Quantify the negative impact of inbreeding depression on production and reproductive parameters in the Line 1 and Line 4 herds, examine pedigree and genomic inbreeding, identify molecular signatures of inbreeding depression associated with reduced productivity and potentially identify genomic signatures specific to inbreeding depression- a PhD dissertation has been completed and successfully defended and a manuscript is in preparation outlining the findings.
Publications
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
INBREEDING AND INBREEDING DEPRESSION IN LINEBRED BEEF CATTLE
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
POPULATION STRUCTURE, GENE FLOW, AND GENETIC DIVERSITY OF ROCKY MOUNTAIN BIGHORN SHEEP INFORMED BY GENOMIC ANALYSIS
- Type:
Journal Articles
Status:
Submitted
Year Published:
2020
Citation:
Flesch, E., T. A. Graves, J. M. Thomson, R.A. Garrot. 2020. Evaluating wildlife restoration using genomics: a bighorn sheep case study. Ecology and Evolution (Submitted)
- Type:
Journal Articles
Status:
Submitted
Year Published:
2020
Citation:
Engle, B., M. Hammond, J. A. Boles, J. M. Thomson. 2020. Gene expression and carcass traits are different between different quality grade groups in Hereford steers. Livestock Science. (Submitted)
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Heiber, J., J. M. Dafoe, C. T. Parsons, D. C. Anderson, D. L. Boss, J. A. Boles, J. M. Thomson. 2020. Inbreeding levels of the Line 1 and Line 4 Hereford cattle populations. American Society of Animal Science Annual Meeting July 2020
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
O'Shea, G., R. Lambert, B. Tripet, J. Berardinelli, J. Thomson, R. Garrott, V. Copie. 2020. 1H NMR Metabolic Profiling of Wild Ruminant Bighorn Sheep to Guide Wildlife Conservation Efforts. For presentation at Metabolomics Association of North America conference 2020.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Bouffiou, J., J. A. Boles, J. M. Thomson. 2020. Investigating the Relationship Between Temperament and Performance Traits in Feedlot Cattle. American Society of Animal Science Annual Meeting July 2020
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience: Scientific community, professional animal breeders, extension specialists, county extension agents, livestock producers and general public. Changes/Problems:Cattle management changes have altered the design of the experiment for Objective 1 in the proposed research. A change in the calving date for the Red Bluff cattle herd is not compatible with the current research.Alternatives are being explored to revise and expand the research and thesechanges will be proposed in late 2019 for implementation in early 2020. What opportunities for training and professional development has the project provided?This research has provided training opportunites for three MS students, one PhD student and five undergraduate research assistants. How have the results been disseminated to communities of interest?This research has been published in scientific manuscripts and extension reports. Both myself and my graduate students have presented this research at local, regional, national, and international scientific meetings. Additionally, aspects of this work have been presented to local beef producers. What do you plan to do during the next reporting period to accomplish the goals?Under objective one, recent management changes have resulted in roadblocks for this work. This work is being reevaluated and will hopefully continue after review and revision. Under objective 2, previous research has been submitted as one manuscript with another in preparation. A follow-up experiment has been started which will evaluate gene expression in finishing wethers and steers with different carcass fatness end-points. We wil be evaluating muscle and adipose gene expression as body composition changes/adiposity increases and will prioritize target genes with similar changes in the two species. Under objective 3, runs of homozygozity and genome-wide association analysis has been completed in the Line 4 cattle and will be completed by early 2020 in the Line 1 cattle. A mansucript is in preparation and a PhD thesis will be submitted in early 2020.
Impacts
What was accomplished under these goals?
Establish a straight-bred uniform herd of Red Angus cattle at the Red Bluff Research Ranch and a long term breeding program that will result in data on the genetic basis of maternal trait, and the impacts of maternal selection on productive efficiency, longevity, and the genetic correlations between maternal traits and other economically important traits. Under this objective, the cattle breeding has continued and DNA samples have been collected under all animals sired by Red Angus Sires. Phenotypic data is being recorded for maternal traits. 2. Elucidate the molecular mechanisms that cause variation in carcass and meat quality and contribute to the development of biologically based predictors that can improve the accuracy and reliability of genetic selection and improvement beef cattle carcass and meat quality; Under this objective, a proceedings was published, a manuscript has been submittedand a second manuscript is in preparation for submission. A follow-up study has begun looking at finishing steers and wethers in parallel to better priortize the genes with similar patterns of expression between the two species. 3. Quantify the negative impact of inbreeding depression on production and reproductive parameters in the Line 1 and Line 4 herds, examine pedigree and genomic inbreeding, identify molecular signatures of inbreeding depression associated with reduced productivity and potentially identify genomic signatures specific to inbreeding depression Under this objective a manuscript is in preparation for submission. This research will be a chapter in a graduate student thesis that is due to be defended in early 2020.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
A.F.Williams, J. A. Boles, M. Herrygers, J. Berardinelli, M.C. Meyers, J. M. Thomson. 2019. Blood lactate and rectal temperature can predict exit velocity of beef feedlot steers. Translational Animal Science XX:XX-XX doi: 10.1093/tas/txz135
- Type:
Journal Articles
Status:
Submitted
Year Published:
2019
Citation:
Engle, B., M. Hammond, J. A. Boles, J. M. Thomson. 2019. Gene expression and carcass traits are different between different quality grade groups in Hereford steers. Meat and Muscle Biology. (Submitted)
- Type:
Journal Articles
Status:
Submitted
Year Published:
2019
Citation:
Flesch, E., T. A. Graves, J. M. Thomson, R.A. Garrot. 2019. Evaluating wildlife restoration using genomics: a bighorn sheep case study. Molecular Ecology (Submitted)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Hieber, J. K., J. M. Dafoe, C. T. Parsons, D. C. Anderson, D. L. Boss, J. Thomson. 2019. PSVIII-24 Inbreeding levels of the Line 4 Hereford population. Journal of Animal Science. In Press.
- Type:
Other
Status:
Submitted
Year Published:
2019
Citation:
Bouffiou, J., J. K. Hieber, J. A. Boles, J, M Thomson. 2019. Investigating the Relationship Between Temperament and Performance Traits in Feedlot Cattle. (Vol 5) College of Agriculture Extension Research Report
- Type:
Other
Status:
Submitted
Year Published:
2019
Citation:
Hieber, J. K., J. M. Dafoe, C. T. Parsons, D. C. Anderson, D. L. Boss, J, M Thomson. 2019. Inbreeding levels of the Line 4 Hereford cattle population. (Vol 5) College of Agriculture Extension Research Report
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
S. A. Blatter, J. A. Boles, J. G. Berardinelli, J. M. Thomson. 2019 Gene Expression in muscle and adipose tissue of steers classed as Choice or Standard. In: M. L. Chizzotti (Ed.), Energy and Protein Metabolism and Nutrition; Belo Horizonte, Brazil. pp. 383-384. Wageningen Academic Publishers, The Netherlands. Doi: 10.3920/978-90-8686-891-9_115
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The scientific community, professional animal breeders, extension specialists, county extension agents, livestock producers, and the general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?An M.S student has successfully completed her degree. A PhD student will finish her comprehensive exam and will defend her thesis in 2019. A second M.S will be recruited to continue work related to objective 2. How have the results been disseminated to communities of interest?Two extension reports have been submitted for publication. A conference paper and presentation were presented at the Wester Section of the American Society of Animal Science meeting in June 2018. What do you plan to do during the next reporting period to accomplish the goals?The items related to objective 2 and 3 will be completed in the next year and should result in two publications being submitted as well as two conference presentations. Objective 1 is ongoing and sample collection will continue.
Impacts
What was accomplished under these goals?
Establish a straight-bred uniform herd of Red Angus cattle at the Red Bluff Research Ranch and a long-term breeding program that will result in data on the genetic basis of maternal traits, and the impacts of maternal selection on productive efficiency, longevity, and the genetic correlations between maternal traits and other economically important traits. Under this objective, we have continued to breed the MAES cattle herd using Red Angus sires selected on the basis of their EPDs for maternal traits. All of the retained animals from 2016, 2017 and all 2018 female offspring have had blood collected for DNA extraction and DNA has been archived for future analysis. Elucidate the molecular mechanisms that cause variation in carcass and meat quality and contribute to the development of biologically based predictors that can improve the accuracy and reliability of genetic selection and improvement beef cattle carcass and meat quality. This objective has been completed as outlined in the original proposal. Fifteen steers, born at the Red Bluff Research Ranch, Norris, MT, were selected at weaning based on weight and date of birth, the selection parameters were: ± 22.7 kg and birthdates within a 14-day window. Steers were relocated to the Montana State University Bozeman Area Research and Teaching Farm and placed in a single pen in the feedlot. At the start of the study, steers weighed an average of 315 kg. Each steer received a Synovex One Feedlot implant per standard feedlot protocol. Steers were fed an ad libitum standard feedlot diet and had free access to water. Steers were randomly allocated to one of three endpoints based on body weight, with average endpoint weights of 431 kg, 522 kg, and 612 kg for Standard, Select, and Choice quality grades, respectively. These weight-based endpoints achieved the desired marbling endpoints reported in Table 1. Upon harvest, RNA was collected from muscle and adipose tissue and analyzed using RNA-seq. RESULTS AND DISCUSSION Carcass weight from animals classified in the Choice quality grade were greater (P = 0.002) than carcass weights from animals classified as Select or Standard (Table 1). Furthermore, fat thickness was greater (P = 0.007)for carcasses from animals classified as Choice and Select than from animals classified as Standard.The use of the weights as endpoints did place most of the carcasses in the correct grade categories as indicated by the significant differences in marbling for each category.In contrast, there was no difference in ribeye area between the different categories, indicating that muscle growth had slowed even at the lower fat categories. Table 1. Carcass characteristics of steaks from carcasses classified as Choice, Select and Standard Choice Select Standard Carcass Wt (kg) 339.3a 275.7b 243.1b Fat Thickness (cm) 1.4a 1.0a 0.5b Ribeye area (cm2) 70.9 64.0 66.9 Marbling scorey 510a 382b 285c a,b,c Means within a row with differing superscripts are significantly different (P≤ 0.05) yMarbling scores: 200 = traces, 300 = slight, 400 = small, 500 = modest, 600= moderate. ZN= 9.81 kg KEGG pathway enrichment KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of manually curated databases dealing with genomes, biological pathways, diseases, drugs and chemical substances. Pathway enrichment analysis identifies significantly enriched metabolic pathways of signal transduction pathways associated with DEGs compared with the whole genome background. The greatest differences in pathway enrichment was seen in adipose and muscle tissues between the carcasses classified as Choice and Standard. Thus, these differences are the focus in this report. In the comparison between muscle from Standard and Choice carcasses, 15 genes were down regulated and 20 were up regulated. The insulin receptor substrate 1 (IRS 1) gene was the only known functionally important gene to be differentially expressed. Interestingly, there was an increased expression of Major Histocompatability Complex genes in muscle, generally indicating a sign of inflammation or increased macrophage migration to the tissue in fattening animals. Alternatively, this could mean an altered stress response. There were 49 down-regulated genes and 113 up-regulated genes in the comparison between adipose tissue from Standard and Choice carcasses.Upregulated genes included:, CAB39L, FGF-1, GRIN1, LEP, HK2, YWHAG, ACC1, SCD1 and ELOVL3. These genes are mostly related to the metabolism of fat and energy.For example, up-regulation of ACC1, HK2, and the down-regulation of EIF43BP1 would inhibit protein synthesis and promote lipogenesis and glycolysis.This suggests a change from actively growing muscle to depositing fat in Steers that graded Choice.Furthermore, up regulation of leptin which can cause the inhibition of insulin resistance, and the down regulation of gluconeogenesis, which can contribute to altered fat metabolism. In conclusion, many changes were observed in gene expression in adipose and muscle tissues between steers that were classified as Choice or Standard. KEGG pathway enrichment indicated some overlap and interaction between the different genes that would tend to have contradictory responses in the tissue.However, organisms are complex systems, with metabolic processes under multiple levels of regulation, so considerably more research is necessary to clarify what these changes mean to determining and predicting quality grade in cattle. Further a BAIR ranch foundation proposal was funded to repeat the above experiment and to include a parrallel experiment in sheep in order to further our understanding of the above results and to continue to increase our understanding on the complex regulation of muscle and adipose co-regulation in finishing meat animals. Quantify the negative impact of inbreeding depression on production and reproductive parameters in the Line 1 and Line 4 herds, examine pedigree and genomic inbreeding, identify molecular signatures of inbreeding depression associated with reduced productivity and potentially identify genomic signatures specific to inbreeding depression. Under this objective, the Line 1 pedigree and genotypes have been acquired. The Line 4 pedigree has been reconstructed and pedigree analysis used to identify approximately 245 samples that have been genotyped for further analysis.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Golder, H. M., J. Thomson, S. E. Denham, C. S. McSweeney, I. J. Lean. 2018. Genetic Markers are Associated with Ruminal Metabolome and Microbiome in Dairy Heifers.
Front. Genet.s : 9
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Hieber, J. K., R. L. Endecott, J.M. Thomson. 2018. Identification of genetic markers and QTL for carcass quality traits within the American Simmental Association Carcass Merit Program. Transl. Anim. Sci. 2018.2.S39-S43. Doi:10.1093/tas/txy-32
- Type:
Other
Status:
Awaiting Publication
Year Published:
2018
Citation:
Hieber, J. K., R. L. Endecott, J.M. Thomson. 2018. Identification of genetic markers and QTL for carcass quality traits within the American Simmental Association Carcass Merit Program. (Vol 4) College of Agriculture Extension Research Report
- Type:
Other
Status:
Awaiting Publication
Year Published:
2018
Citation:
Blatter, S. A., J. A. Boles, J.M. Thomson, J. G. Berardinelli. 2018. Molecular Pathways for muscle and adipose tissue are altered between animals classed as Choice or Standard. (Vol 4) College of Agriculture Extension Research Report
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
E. Flesch, J.J. Rotella, , J. Thomson, T. A. Graves, R. A. Garrott. 2018. Evaluating sample size to estimate genetic management metrics in the genomics era. Mol Ecol Res 18:1077-1091
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Progress 07/01/17 to 09/30/17
Outputs
Target Audience:Scientific community, professional animal breeders, extension specialists, county extension agents, livestock producers and general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One MS student and one PhD student have been recruited to work on aspects of these objectives. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?The items related to objective 2 should be completed in the next reporting period and a publication will be submitted for publication along with a conference presentation.
Impacts
What was accomplished under these goals?
1. Establish a straight-bred uniform herd of Red Angus cattle at the Red Bluff Research Ranch and a long term breeding program that will result in data on the genetic basis of maternal trait, and the impacts of maternal selection on productive efficiency, longevity, and the genetic correlations between maternal traits and other economically important traits. This plan was implemented in 2016 with the purchase of 46 purebred Red Angus cattle by MAES to act as a nuclei for the new herd and to jumpstart the direction of the proposed research. The current population of cows and heifers were bred to Red Angus sires in spring 2016 and 2017. Additionally, individuals were identified to be culled to increase uniformity of the breeding females and to make room for the purchased animals. The herd has been added to the American Red Angus Association Registry and all offspring retained from 2016 and 2017 have been registered. 2. Elucidate the molecular mechanisms that cause variation in carcass and meat quality and contribute to the development of biologically based predictors that can improve the accuracy and reliability of genetic selection and improvement beef cattle carcass and meat quality Fifteen steers were finished to the designated endpoints of standard, select, and choice quality grades. They were harvested at Pioneer Meats in Big Timber MT and samples of muscle and adipose tissue were collected and flash frozen for RNAseq analysis. This analysis is ongoing and an MS thesis is in progress. 3. Quantify the negative impact of inbreeding depression on production and reproductive parameters in the Line 1 and Line 4 herds, examine pedigree and genomic inbreeding, identify molecular signatures of inbreeding depression associated with reduced productivity and potentially identify genomic signatures specific to inbreeding depression There is nothing to report on this objective.
Publications
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