Progress 05/01/19 to 10/31/23
Outputs
Target Audience: The target audience for our work is primary poultry breeders, poultry integrators who are experiencing wooden breast in broiler production. On the academic side, the audience is poultry geneticists, physiologists, and food quality scientists who are interested in solving the wooden breast disorder that is found across commercial broiler production. Changes/Problems:We faced some delays in the middle of the project due to COVID. But after the no-cost extension, we were able to complete our project as planned. However, due to the longer time we have to support students in this project, we had to reduce the scope of Aim 3 in this project (RNAseq work). What opportunities for training and professional development has the project provided? The projectfunded the Ph.D. project of Mr. Travis Williams. Following his graduation, Dr. Williams has accepted a position at a major poultry primary breeder company. Ms. Mridula Gupta is also a graduate student who was partly funded by this project and generated data for aim 3 of the project. In addition to these two graduate students, two undergraduate technicians were supportedon this project. Both plan to obtain positions in the poultry industry and gain valuable experience raising and caring for broiler breeders, incubating eggs, and caring for production broilers. How have the results been disseminated to communities of interest?A total of three peer-reviewed publications have been published using funds from this project. Two PhD dissertations incorporated data from this project. Besides these academic avenues, we also presented this data at the Annual Poultry Science Association meetings and at the Plant and Animal Genomes Conference. Three publications are being prepared for submission to different peer-reviewed journals. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Our research accomplished its major goal of characterizing genome structural variants in commercial broiler breeds using a family-trio-based study design. Our data shed light on the complex genetic landscape governing commercial broiler chickens, focusing on the wooden breast condition, a significant concern in poultry production. These studies are instrumental in understanding the genetic origins and the widespread incidence of this condition, offering vital insights into the breeding practices of commercial broiler lines. Unlike the more diverse genetic makeup observed in random breed heritage lines, commercial broilers exhibit a stark contrast in their genetic relationships, which has profound implications on their health and growth characteristics. One of the foundational analyses delved deep into the genetic relationships among parent stocks of commercial broiler lines. It unveiled an unexpected degree of close genetic relatedness, specifically highlighting a prevalence of 2nd-degree and 3rd-degree relationships. This finding is particularly striking when contrasted with the genetic diversity found in random breed heritage lines, which exhibited greater heterogeneity and more distant genetic relatedness estimates. The study's approach involved validating genetic pedigrees through the innovative use of low coverage sequencing information. This technique confirmed the expected genetic connections and provided a clearer picture of the breeding practices that have led to such a high level of relatedness in commercial lines. The relatedness measures in these populations have great significance for understanding the penetrance and frequency of disorders like WB in commercial flocks. The higher degree of genetic relatedness among breeders would indicate that any genetically based disorder would have a much higher probability of expressing in the broiler populations. Next, webuilt upon the foundations laid by the tri-based experiment, incorporating the validated pedigrees to undertake a more in-depth genetic analysis of family trios to identify inherited structural variants. We meticulously selected 54 unique, offspring sex-specific family trios, encompassing a total of 90 individuals across two commercial lines and a single heritage breed. These selected trios underwent deep whole genome sequencing, with average coverage exceeding 50X, a significant depth that allows for a comprehensive analysis of the genomic structural variants with high confidence. The primary aim of this extensive sequencing was to investigate and understand the genomic structural variations in offspring exhibiting the wooden breast condition. The study's approach, focusing on high-depth genome sequencing, provided unprecedented detail in understanding the genetic factors contributing to this condition. The outcomes of these comprehensive studies are both revealing and significant. We identified a staggering number of high-impact structural variants in the high-yield and high-efficiency commercial broiler lines: 2,458 and 1,951, respectively. These variants showed major genomic alterations that are likely contributing to the wooden breast condition. The findings underscore the substantial functional effects of genomic selection for traits like rapid growth and enhanced metabolic rates on broilers. While beneficial for certain production traits, this genetic selection appears to have also selected for genetic variants that have detrimental effects on muscle structure and function. Primary among the genes affected by structural variants (deletions) were genes affect actin and myosin structure and function, and also a major structural protein that has implications for how we view wooden breast disorder. Our subsequent study aims to demonstrate the impacts of these deletions in detail at the tissue level. These studies highlight a crucial aspect of poultry genetics - the balance between desirable production traits and the overall health and well-being of the animals. The high number of structural variants suggests that current breeding practices, heavily focused on efficiency and yield, might need to be re-evaluated to consider broiler chickens' long-term health and genetic diversity. Furthermore, these findings open avenues for future research, particularly in developing breeding strategies that maintain high production standards while ensuring the genetic health of broilers.
Publications
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Progress 05/01/22 to 04/30/23
Outputs
Target Audience:Poultry primary breeder companies, poultry producers, poultry scientists, and consumers. Changes/Problems:We need a no-cost extension due to COVID and also the student taking some time to do an internship. We are back on track now and expect to complete this project in the remaining time. The project scope for AIm 3 is slighly modified as noted in previous reports. Other than that the project will be completed as originally proposed. What opportunities for training and professional development has the project provided?
Nothing Reported
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?Completion of the project.
Impacts
What was accomplished under these goals?
The final report will contain all these details.
Publications
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Progress 05/01/21 to 04/30/22
Outputs
Target Audience: The target audience for our work is primary poultry breeders, poultry integrators who are experiencing wooden breast in broiler production. On the academic side, the audience is poultry geneticists, physiologists, and food quality scientists who are interested in solving the wooden breast disorder that is found across commercial broiler production. Changes/Problems:We experienced problems early in the project securing the appropriate breeders for our study. After those delays and once our live animal part was completed, we experienced several delays due to COVID. This also set us back in troubleshooting some issues with template quality prior to sequencing. We are now on track, thanks to the project period extension. What opportunities for training and professional development has the project provided? The project is helping fund the Ph.D. project of Mr. Travis Williams, whose primary goals are to generate data for Aims 1 and 2 of the project. Mr. Williams would like to eventually work in the industry as a breeder with thorough knowledge of the latest genomics approaches, and this project is helping provide the necessary training for that career. Ms. Mridula Gupta is also a graduate student who is partly funded by this project and will generate data towards Aim 3. In addition to these two graduate students two, undergraduate technicians are working on this project. Both plan to obtain positions in the poultry industry and are gaining valuable experience raising and caring for broiler breeders, incubation of eggs, and care of production broilers. How have the results been disseminated to communities of interest?One peer reviewed publication which was partly based on this project has been funded (see list of publications). Besides, we have also been presenting the preliminary and completed parts of the projects at student symposia and other venues while we wrap up the complete analyses. What do you plan to do during the next reporting period to accomplish the goals?Once the trios are selected, we will be receiving deep sequencing data for our samples in the next two months. The analyses are expected to take 3-4 months. Due to the delays early in the project (and due to COVID) we obtained an extension. Currently we are in a good position to complete the project within the next year.
Impacts
What was accomplished under these goals?
The goals were to a) identify genome structural variants in commercial broiler strains that exhibit WBD We now have generated sequence data from our experiment. We also completed sexing of the birds from the DNA samples, and are now working on selecting the trios for analyses. The sequencing libraries have been successfully prepared and once the trios are identified, we will go ahead with high-depth sequencing for structural variant calling. b)incidence of somatic mutations arising due to the fast growth rate in the short life span of a broiler, and We have successfully generated the DNA isolates from a non-muscular cell lineage (spleen) and we are submitting these samples for sequencing to proceed with somatic mutation calling. c) determine the parental source of regulatory variants driving wooden breast in commercial broilers. We are currently working on the analyses of these datasets which were generated in the last few months.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Hubert S, Athrey G. 2022. Transcriptomic signals of mitochondrial dysfunction and OXPHOS dynamics in fast-growth chicken. PeerJ 10:e13364 https://doi.org/10.7717/peerj.13364
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Progress 05/01/20 to 04/30/21
Outputs
Target Audience: The target audience for our work is primary poultry breeders, poultry integrators who are experiencing wooden breast in broiler production. On the academic side, the audience is poultry geneticists, physiologists, and food quality scientists who are interested in solving the wooden breast disorder that is found across commercial broiler production. Changes/Problems:Our project is reaching its planned scientific goals, but we are behind schedule due to our initial delays in securing the birds to begin our study. This was later compounded by delays in securing lab supplies which were back-ordered for much of 2020 and early 2021. We plan to apply for an extension of the project performance period. What opportunities for training and professional development has the project provided? The project is helping fund the Ph.D. project of Mr. Travis Williams, whose primary goals are to generate data for Aims 1 and 2 of the project. Mr. Williams would like to eventually work in the industry as a breeder with thorough knowledge of the latest genomics approaches, and this project is helping provide the necessary training for that career. Ms. Mridula Gupta is also a graduate student who is partly funded by this project and will generate data towards Aim 3. In addition to these two graduate students two, undergraduate technicians are working on this project. Both plan to obtain positions in the poultry industry and are gaining valuable experience raising and caring for broiler breeders, incubation of eggs, and care of production broilers. 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?In the next few months we will complete the sequencing work and also begin the analysis of data. We are currently on track to send off the samples for sequencing in late September/ early October 2021. Following that, we have a plan in place to complete the planned analyses. We also plan to ask for an extension of the project performance period, which is slightly behind schedule due to our initial difficulties obtaining the broiler breeders, and other supplies bottlenecks we faced due to COVID.
Impacts
What was accomplished under these goals?
We have successfully completed our live animal work (including breeding) to generate broilers of different growth rates. The samples have been collected and nucleic acid isolations have been completed. We are currently sexing and assigning parentage to the broilers samples in preparation for sequencing (for Objectives 1 and 2) For objective 3, we have completed the RNA isolations and are preparing the samples for sequencing.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Hubert SM and Athrey G. Energy metabolism and sources of oxidative stress in wooden breast - a review F1000Research 2020, 9:319
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Ibrahim MMA, Nelson JR, Archer GS and Athrey G (2021) Effects of Monochromatic Lighting During Incubation and Vaccination on the Splenic Transcriptome Profiles of Chicken. Front. Genet. 12:628041. doi: 10.3389/fgene.2021.628041
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Progress 05/01/19 to 04/30/20
Outputs
Target Audience:The target audience for our work is primary poultry breeders, poultry integrators who are experiencing wooden breast in broiler production. On the academic side, the audience is poultry geneticists, physiologists, and food quality scientists who are interested in solving the wooden breast disorder that is found across commercial broiler production. Changes/Problems:We had some difficulty obtaining breeders for commercial strains. This initially caused minor delays, but we are on track to complete our objectives. Starting in March 2020, we have had to shut down our lab due to COVID-19. We have been keeping our live animal work going, but the completion of the grow-out stage, the sampling, and then processing of these samples will all depend on external factors dictated to us by the state and the university administration. We are expecting some delays in data generation. What opportunities for training and professional development has the project provided?The project is helping fund the Ph.D. project of Mr. Travis Williams, whose primary goals are to generate data for Aims 1 and 2 of the project. Mr. Williams would like to eventually work in the industry as a breeder with thorough knowledge of the latest genomics approaches, and this project is helping provide the necessary training for that career. Ms. Mridula Gupta is also a graduate student who is partly funded by this project and will generate data towards Aim 3. In addition to these two graduate students two, undergraduate technicians are working on this project. Both plan to obtain positions in the poultry industry and are gaining valuable experience raising and caring for broiler breeders, incubation of eggs, and care of production broilers. 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?In the next project year, our live animal works will be completed, and we are expecting to generate the planned genomics data for the three aims of the project. Depending on the timeline for the generation of sequence data we are hoping to make great progress on the analysis in the second half of the project year. However, much of this will depend on what kind of delays we might encounter due to the COVID-19 disruptions.
Impacts
What was accomplished under these goals?
We have successfully implemented our live animal work (including breeding) to generate broilers of different growth rates. At the time of this report, we have begun raising the broilers from our controlled crossing experiments. At slaughter age, we will sample these individuals and collect tissues for genomics analyses.
Publications
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