GENETIC VARIANCE OF NOVEL TRAITS IN THE BEEF INDUSTRY

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1019988
• Project Start Date: Oct 1, 2019
• Project End Date: Sep 30, 2024
• Program Code: [(N/A)]- (N/A)

Recipient Organization
SOUTH DAKOTA STATE UNIVERSITY
PO BOX 2275A
BROOKINGS,SD 57007

Performing Department
Animal Science

Non Technical Summary
Genetic selection tools such as expected progeny differences and DNA testing are widely available in the US beef industry. However, genetic selection tools for economically relevant traits and lowly heritable traits are less widely available and frequently are less accurate. For example, genetic selection tools are not available for water intake in beef cattle.Climate change models predict that water will become scarcer in some geographical regions of the US. Therefore, genetic selection for cattle that require less water may be beneficial to some beef producers. Our overarching hypothesis is that water requirements vary among animals based on their body weight, age, climatic factors, and genetics. Specifically, we aim to (1) correlate water requirements of beef calves and yearlings at different ages, body weights, feed intakes, and climatic factors, (2) determine whether the sire of the animal contributes to water intake variation, (3) identify genes associated with thirst in beef calves, and (4) develop student reflection strategies that can be used in the classroom to improve attainment of learning outcomes. This latter objective is important because university students will be trained to manage beef herds and need to learn best practices of genetic improvement for novel traits such as water intake.We expect to estimate updated water requirements in beef calves that can be used by beef producers to predict water needs of their herd. We also expect to determine if genetics affects water intake variation and identify genes important for the thirst response in cattle. Identification of these genes will be an important first step towards understanding genetic variation of water requirements of our beef herd. Finally, we expect to develop a student reflection strategy that will improve attainment of learning outcomes in undergraduate animal science students. This project will impact the beef industry by helping producers understand genetic and environmental effects that affect water intake of cattle.

Animal Health Component

20%

Research Effort Categories

Basic

80%

Applied

20%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3310	1081	100%

Knowledge Area
303 - Genetic Improvement of Animals;

Subject Of Investigation
3310 - Beef cattle, live animal;

Field Of Science
1081 - Breeding;

Keywords

genetic improvement

water intake

climate change

environmental effect

beef cattle

student reflection

transcriptomics

thirst

Goals / Objectives
Genetic selection tools such as expected progeny differences and genomic testing are available to beef producers. These tools allow producers to select for many cattle traits, including weight gain, feed intake, calving ease, and carcass yield and quality. Fewer selection tools are available for traits that are difficult or expensive to phenotype, are lowly heritable, or both. Examples include fertility, disease resistance, and water intake. Current selection tools for these traits typically have lower accuracy. Still, these traits are among the more economically relevant for beef producers. Our long-term goal is to improve our understanding of genetic variation in these traits, which will lead to more accurate selection tools for beef cattle.Specifically, our main focus in this grant is water intake. Climate change is predicted to result in less water availability, and therefore understanding the factors affecting water intake in beef cattle will be important for best management practices of US beef herds. Genetic selection tools for water intake are currently not available to beef producers. To develop these tools, knowledge of the genetic and environmental factors affecting water intake is critical. Equally critical is our ability to disseminate animal breeding concepts to undergraduate students, who will be making future genetic selection decisions in beef herds. Their comprehension of animal breeding concepts and advanced genetic selection tools will lead to faster genetic improvement in economically relevant traits, including fertility, disease resistance, and water intake. Towards this end, our specific objectives are as follows:Objective 1. Correlate climatic conditions and cattle husbandry information with water intake in beef cattle.Objective 2. Assess the effect of sire on water intake of beef calves.Objective 3. Discover genes expressed in the renal cortex and hypothalamus associated with water restriction in beef calves.Objective 4. Translate project findings into classroom activities that improve student learning outcomes.

Project Methods
Objective 1. Correlate climatic conditions and cattle husbandry information with water intake in beef cattle.Weaned and yearling calves (n=48) will be housed at the South Dakota State University Cow-Calf Education and Research Facility (CCERF) from 9/2019 until 9/2020. Individual water and feed intake of calves will be measured with an automated Insentec system. Feed and water will not be restricted. Temperature, humidity, wind speed, precipitation, solar radiation, and air pressure will be recorded at a Mesonet automated weather station 2.4 miles from the CCERF. Body weights will be measured at regular intervals (at least once each 28 days). The effects of climate, body weight, and feed intake on water intake will be correlated with a linear model for weaned and yearling calves. Weaned calves will be studied in Fall 2019 and yearling calves in Summer 2020. Data will be analyzed with freely available R software.Objective 2. Assess the effect of sire on water intake of beef calves. Multiple sires (n~8 per year) are bred to cows by artificial insemination at the CCERF, resulting in multiple calves with the same sire. This breeding management strategy allows estimation of a sire effect. Sire will be included in our linear model (described in objective one). A sire effect that is statistically different from zero suggests that water intake variation is heritable. If feasible, a heritability estimate for water intake variation will be calculated, but precision of the estimate may be low depending on sample size. Eight Insentec waterers (n=3 calves per waterer) are available, which limits the number of calves that can participate in the study at any single point in time. Objective 3. Discover genes expressed in the renal cortex and hypothalamus associated with water restriction in beef calves. Beef calves (n=6) will be randomly allocated into a control or treatment group (n=3 calves per group). Twelve hours before slaughter, water will be withheld from calves in the treatment group while the control calves will continue to access water ad libitum. At slaughter at the SDSU Meat Lab, the renal cortex of the kidney and hypothalamus containing the supraoptic and paraventricular nuclei will be collected. Tissue samples will be frozen at -80 degrees C until RNA can be isolated. The RNA will be isolated from tissues by guanidinium-thiocyanate-phenol chloroform extraction, sequencing libraries will be prepared with a TruSeq Stranded RNA Library PrepKit, and the libraries will be sequenced with a NexGen 500 Sequencer at the SDSU Genomic Sequencing Facility. Fifty million reads per sample will be sequenced (single-end reads; 50 cycles).Single-end reads will be uploaded to CLC Genomics Workbench Software, which is freely available on an SDSU server. This software package includes a suite of programs that include the ability to map reads to a genome and RNA-seq analysis. After quality control (e.g., trimming adapter sequences, eliminating sequencing artifacts), sequencing reads will be mapped to the most recent version of the annotated bovine genome with an expectation-maximization algorithm and using default mapping parameters. Total number of reads per transcript will be normalized for library size (i.e., total number of reads per library). Differentially abundant transcripts between treatment and control groups will be tested with a generalized linear model assuming a negative binomial distribution of read counts.Objective 4. Translate project findings into classroom activities that improve student learning outcomes. Six laboratory sections of an Introductory Animal Science class will be randomly allocated to treatment (n=3) and control (n=3) groups. Treatment laboratory sections will be required to submit a reflection assignment each lab period and control laboratory sections will not be required to submit a reflection assignment. The written assignment will include questions asking students to summarize the central learning outcomes of the class period, reflect on how well they achieved these learning outcomes, and ask questions about the material. This assignment will be distributed during the last five minutes of each class period (treatment group only). Grades will be compared between treatment and control groups. This objective is related to research objectives 1-3 because we need to effectively transfer information learned from animal science research to individuals who will utilize this information in their chosen career path (e.g., Animal Science majors).

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Our target audiences are beef producers, employees working in the beef industry, animal scientists, university faculty, and graduate and undergraduate students. Our main effort to target beef producers and employees working in the beef industry was through extension and outreach presentations at the SDSU Beef Day on January 16, 2020 in Brookings, SD. Our research plans (objectives 1 and 3) were presented to this audience by two of the graduate students working on this project. These students presented their work at a poster session. Our main effort to target animal scientists and university faculty was through publication of peer-reviewed research. In particular, a research article on the effect of instructional changes caused by Covid-19 was published in the Journal of the European Honors Council (Celik Wiltse et al., 2020). Our main effort to target graduate and undergraduate students was to involve these students in our research. Four M.S. and seven B.S. students are being trained through this project. Changes/Problems:The anterior pituitary gland will be harvested for Goal 3 instead of the adrenal cortex. The adrenal cortex will not be available to us until about an hour after slaughter and thus we are concerned about RNA quality in this tissue. The anterior pituitary gland can be collected at the same time as the hypothalamus shortly after slaughter. The anterior pituitary gland is part of the endocrine system and changes in gene expression are expected in response to thirst. What opportunities for training and professional development has the project provided?Four M.S. students and seven B.S. students have been trained or are being trained. 1) Bradie Schmidt, M.S., graduated in May 2020 and has published one journal article, one scientific conference abstract, a thesis, and one abstract for the general public. She is currently working as an instructor for Dawson Community College. 2) Zachary McDaniel, M.S., is expected to graduate in summer 2021. Zachary is working on goal 1 and has published one abstract for the general public. He also participated in a USDA Higher Education Challenge project to improve communication skills in M.S. students. 3) Himali Wickremasinghe, M.S., is expected to graduate in summer 2021. Himali is working on goal 3 and has published one abstract for the general public. She also participated in a USDA Higher Education Challenge project to improve communication skills in M.S. students. 4) Alex Kelly, M.S., is expected to graduate in summer 2022. Alex will work on an aspect of goal 1 which is to be determined. The B.S. students (Danielle Capp, Hannah Clark, Willow Dean, Josephine Greden, Anna Rauber-Ramos, Laura Szabo, and Samantha Thyen) are working to support the objectives of this project by primarily assisting graduate students with their work or generating preliminary data for future funding opportunities. All but one of these students are Animal Science majors (J. Greden is majoring in agricultural economics). How have the results been disseminated to communities of interest?Our main effort to target beef producers and employees working in the beef industry was through extension and outreach presentations at the SDSU Beef Day on January 16, 2020 in Brookings, SD. Our research plans (goals 1 and 3) were presented to this audience by two of the graduate students working on this project. These students presented their work at a poster session. Our main effort to target animal scientists and university faculty was through publication of peer-reviewed research. The effect of instructional changes caused by Covid-19 was published in the Journal of the European Honors Council (Celik Wiltse et al., 2020) and partitioning of variance components of beef carcass traits as measured by ultrasound was published in Translational Animal Science (Schmidt et al., 2020). Our main effort to target graduate and undergraduate students was to involve these students in our research. Four M.S. and seven B.S. students are being trained through this project. What do you plan to do during the next reporting period to accomplish the goals?Goal 1: Correlate climatic conditions and cattle husbandry information with water intake in beef cattle. We plan to continue collecting liquid water intake, feed intake, body weights, and weather data on the steers purchased in August and fed through the middle of November. The effect of body weight, feed intake, and weather on fluid water intake will be evaluated with a linear model and a prediction equation will be developed for water intake in beef steers. We anticipate submission of a journal article describing this research at the end of Year 2 or early in Year 3. Goal 2: Assess the effect of sire on water intake of beef calves This goal will be started in Year 3. Goal 3: Discover genes expressed in the renal cortex and hypothalamus associated with water restriction in beef calves. Three steers will be restricted from drinking water at 8 PM on October 22nd. On the morning of October 23rd, these steers and three controls (non-restricted water intake) will be slaughtered. The hypothalamus and anterior pituitary gland will be collected from these steers. The RNA will be isolated from these tissues, sequencing libraries created, and RNA sequenced to identify differences in transcript abundance between water restricted and control steers. We anticipate submission of a journal article describing this research at the end of Year 2 or beginning of Year 3. Goal 4: Translate project findings into classroom activities that improve student learning outcomes We continue to collect data to further understand the scholarship of teaching and learning. We have collected survey data on the effect of self-reflections on attainment of learning outcomes. Self-reflection after each class period improved self-reported attainment of learning outcomes but did not affect final exam scores. We plan on publishing results of this research by the end of Year 2 or beginning of Year 3.

Impacts
What was accomplished under these goals? Goal 1: Correlate climatic conditions and cattle husbandry information with water intake in beef cattle. (67% Accomplished) Daily water and feed intake were collected on 27 steers from December 11, 2019 until June 8, 2020. Intake data was measured with Insentec feeders and waterers at the SDSU Cow-Calf Education and Research Facility (CCERF). Steers were weighed approximately every 28 days and daily body weights were predicted. Daily body weight was predicted by calculating average daily gain (ADG) between weigh dates and interpolating weight from ADG. Daily weather data was collected from a Mesonet weather station located 2.4 miles from the CCERF. Preliminary analyses show that: 1) liquid water intake increased as body weight and age increased (0.074 kg water intake per 1 kg body weight, P<0.05), and 2) liquid water intake increased as wind chill increased (0.364 kg water intake per 1 kg body weight; P<0.05). The increased fluid water intake with increased body weight was expected from previous reports in the literature, but little to no data has been published describing the relationship between water intake and wind chill values. Beef producers can expect decreased fluid water intake as wind chill decreases. Data on the relationships between water intake, body weight, and age can be used to update predicted water requirements of beef cattle. An additional 25 steers were purchased in August 2020 to measure the effects of temperature, humidity, wind speed, and body weight on liquid water and feed intake in the summer and fall months. This work was planned to begin at the start of summer, but as described in Goal 3, the Covid pandemic caused the start to be delayed until August. These steers are also housed at the CCERF and have been weighed approximately every 28 days. The same data is being collected on these steers including daily feed and liquid water intake and weather, except humidity is also being recorded. Average daily gain and predicted body weight will also be calculated. These steers were on the trial at the end of the reporting period. We have not analyzed data on these steers. Goal 2: Assess the effect of sire on water intake of beef calves. (­0% Accomplished) This objective will be started later during this project. Goal 3: Discover genes expressed in the renal cortex and hypothalamus associated with water restriction in beef calves. (0% Accomplished) This research will identify genes and pathways associated with the thirst response in cattle. Our plan was to begin objective 2 in late spring or summer 2020. South Dakota State University ordered its non-essential research activities to cease in March 2020 in response to the Covid-19 pandemic. Many research activities resumed in June 2020, but goal 2 required use of the SDSU Meat Laboratory for animal slaughter and tissue collection. Because of work backlogs, the SDSU Meat Laboratory was not available for completion of this objective until fall 2020. Therefore, our plan is to begin goal 2 at that time. An improved understanding of genes and pathways affecting the thirst response could lead to improvements in DNA testing and management in range environments where water is limited. Goal Four: Translate project findings into classroom activities that improve student learning outcomes. (50% Accomplished) Classes at SDSU switched abruptly to online delivery in March 2020 due to the Covid-19 pandemic. The pandemic provided an opportunity to explore factors affecting academic success after the abrupt switch to online learning. Our objectives were: 1) to identify factors affecting student learning and connectivity following this transition, and 2) to evaluate differences between honors and non-honors students. Students (n=230) were surveyed with Likert-type, descriptive, and open-ended questions about their experiences following the transition. Clear, frequent communication between students and SDSU was identified as the most appreciated aspect of SDSU's response. Students who reported struggling academically following the transition were more likely to be facing difficulties with finances and access to or use of online learning technology. Honors students reported fewer technology barriers and financial stressors than non-honors students. Degree completion and social connections drove the desire to return to face-to-face classes, but this enthusiasm was dampened by COVID-19-related health concerns. Communication, structure, and flexibility were identified as factors affecting student success.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: McDaniel, Z.S., M.G. Gonda, and C.L. Wright. 2020. Estimating the effects weather, dry matter intake, and body weight on daily water intake in weaned calves. SDSU Beef Day 2020, Brookings, SD. Proceedings, p. 98. Presented January 16.
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Chathurika, W.V.A.H., M.G. Gonda, Z. McDaniel, C.L. Wright, J.L. Gonzalez-Hernandez, and J. Clapper. 2020. Identification of genes associated with water restriction expressed in the renal cortex and hypothalamus in cattle. SDSU Beef Day 2020, Brookings, SD. Proceedings, p. 99. Presented January 16.
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Schmidt, B., M.D. MacNeil, and M.G. Gonda. 2020. Evaluation of variation attributable to lab and technician for measurement of beef carcass traits made by ultrasound. SDSU Beef Day 2020, Brookings, SD. Proceedings, p.16. Presented January 16.
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Schmidt, B., M.D. MacNeil, and M.G. Gonda. 2020. Evaluation of variation attributable to lab and technician for measurements of beef carcass traits made using ultrasound. Midwest American Society of Animal Science. Omaha, NE. Presented March 3.
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Schmidt, B., M.D. MacNeil, and M.G. Gonda. 2020. Partitioning variation in measurements of beef carcass traits collected using ultrasound. Beef Improvement Federation Annual Meeting. Gainesville, FL. Virtually presented on June 11, 2020.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Schmidt, B.M., M.D. MacNeil, and M.G. Gonda. 2020. Partitioning variation in measurements of beef carcass traits using ultrasound. Translational Animal Science 4(3): 1-10.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Celik Wiltse, E., M.G. Gonda, C. Massmann, K. Williams, and R. Bott-Knutson. 2020. Assessment of the impact of COVID-19 on honors student learning, institutional connections, and intent to return to campus. Journal of the European Honors Council 4 (Special Issue 1): 1-22.
• Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Schmidt, B.M. 2020. Partitioning variation in measurements of beef carcass traits made using ultrasound. M.S. Thesis, South Dakota State University, Brookings, SD. Defended April 30, 2020.