Progress 03/01/21 to 02/28/25
Outputs
Target Audience:Throughou the project, there has been publications and presentations at various venues targeting academic and industry personnel in the field of animal genetics. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Several students and postdocs were trained in this project, who were authors on papers and presented work at conferences. How have the results been disseminated to communities of interest?- Peer reviewed publications - Conference presentations - Unviersity seminar talks What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Major goals were achieved 1) We developed and optimizeed the variant calling and genotype imputation pipelines to best suit the population structure and genome architecture of the domestic pigSus scrofaspecies and achieved high accuracy for existing genotyping platforms. 2)We developed and implemented a web server (swimgeno.org)with accessible user interface to allow users to efficiently utilize the resource. As of March 30, 2025.273 jobs, and 346,424 genomes have been imputed. 3) We evaluated and identifiedbest performing imputation strategies to guide future studies.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Quan J=, Yang M=, Cai G=, Ding R, Zhuang Z, Zhou S, Tan S, Ruan D, Wu J, Zheng E, Zhang Z, Liu L, Meng F, Wu J, Xu C, Qiu Y, Wang S, Lin M, Li S, Ye Y, Zhou F, Lin D, Li X, Deng S, Zhang Y, Yao Z, Gao X, Yang Y, Liu Y, Zhan Y, Liu Z, Zhang J, Ma F, Yang J, Chen Q, Yang J, Ye J, Dong L, Gu T, Huang S, Xu Z, Li Z, Yang J, Huang W, Wu Z (2024) Multi-omic characterization of allele-specific regulatory variation in hybrid pigs. Nat Commun 15(1):5587
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Progress 03/01/24 to 02/28/25
Outputs
Target Audience:The work is presented at a seminar at Iowa State University. Attendees include academicresearchers in the animal sciencefield. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project supports the training of a postdoctoral fellow (Dr. Mohammed Bedhane) and partially a graduate student (Leland Ackerson), who have attended conferences under this support. 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?
Nothing Reported
Impacts
What was accomplished under these goals?
We have made significant progress under the three major goals of the project. 1) The web server (swimgeno.org) is up and running since April 2022. As of March 30, 2025, the server has completed 273 imputation jobs for 346,424genomes. 2) New SNP chip platform support are added. 3) We have compared imputation using SNP-chip based and low-coverage sequencing based strategies. SNP-chip based imputation was found to achieve comparable accuracy with low coverage sequencing up to 3x in pigs using either a pure breed or multi-breed reference panel. The work is being written up for publication.
Publications
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Progress 03/01/23 to 02/29/24
Outputs
Target Audience: The work waspresented at National Swine Improvement Federation. Attendees include industry and academic researchers in the swine genetics field. In addtion, a publication has appeared in the journal Communications Biology. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The project supports the training of a postdoctoral fellow (Dr. Mohammed Bedhane) and partially a graduate student (Leland Ackerson), who have attended conferences. How have the results been disseminated to communities of interest?The main paper from this project has been published: Ding et al., The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs. Commun Biol 6:577, 2023 The work has also been presented at the National Swine Improvement Fedration annual meeting in St. Louis, MO in 2023. What do you plan to do during the next reporting period to accomplish the goals? We will focus on finishing the third aim of the project and develop a maintenance plan so the server can continue to be active after the project is complete.
Impacts
What was accomplished under these goals?
We have made significant progress under the three major goals of the project. 1) The variant calling pipeline has been optimized and fully implemented. 2) The web server (swimgeno.org) is up and running since April 2022. As of February 29, 2024, the server has completed 150 jobs for 227,633 genomes, up from 77 imputation jobs for 126,046 genomes a year ago. 3) We have compared imputation using SNP-chip based and low-coverage sequencing based strategies. A manuscript is being written to summarize the comparison results.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Ding R, Savegnago R, Liu J, Long N, Tan C, Cai G, Zhuang Z, Wu J, Yang M, Qiu Y, Ruan D, Quan J, Zheng E, Hong L, Li Z, Tan S, Bedhane M, Schnabel R, Steibel J, Gondro C, Yang J, Huang W, Wu Z (2023) The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs. Commun Biol 6(1):577
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Progress 03/01/22 to 02/28/23
Outputs
Target Audience:The work is presented at the Cattle/Swine Workshop at the Plant and Animal Genome Conference. Attendees include academic and industry researchers in the animal genetics field. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project supports the training of a postdoctoral fellow (initially Dr. Rodrigo Savegnago, and later Dr. Mohammed Bedhane) and partially a graduate student (Leland Ackerson), who have attended conferences. How have the results been disseminated to communities of interest?The results have been written up for publication (bioRxiv:https://www.biorxiv.org/content/10.1101/2022.05.18.492518v1) and is currently under review. The work has also been presented at the Plant and Animal Genome Conference 30 (January 2023) Cattle/Swine workshop as an invited talk.? What do you plan to do during the next reporting period to accomplish the goals?We will continue to work on the three goals. We plan to publish the papers and submit a new paper describing comparison of SNP-chip and low coverage sequencing based imputation. In addition, we will develop a maintenance plan for the web server even after the project concludes.
Impacts
What was accomplished under these goals?
We have made significant progress under the three major goals of the project. 1) The variant calling and imputation pipelines have been evaluated and optimized. We found the software combination Shapeit4/Impute5 to outperform others. This has been implemented on the web server. A manuscript describing the development of the resource and server is under review for publication. 2) The web server (swimgeno.org) is up and running since April 2022. As of February 27, 2023, the server has completed 77 imputation jobs for 126,046 genomes. 3) We have compared imputation using SNP-chip based and low-coverage sequencing based strategies. SNP-chip based imputation was found to achieve comparable accuracy with low coverage sequencing up to 3x in pigs using either a pure breed or multi-breed reference panel.
Publications
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Progress 03/01/21 to 02/28/22
Outputs
Target Audience:A preliminary report of the work is presented at the Swine Workshop for the USDA NRSP8 National Animal Genome Research Program. Attendees include academic and industry researchers in the swine genetics field. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project supports the training of a postdoctoral fellow (Dr. Rodrigo Savegnago), who have attended meetings. How have the results been disseminated to communities of interest?The results have been presented at the Swine Workshop of the NRSP8 National Animal Genome Research Program. The work shop was initially scheduled at the Plant and Animal Genome Confeference but was rescheduled and moved online. What do you plan to do during the next reporting period to accomplish the goals?We will continue to work on the three goals, which remain on track to be completed on schedule. A new postdoctoral fellow has been recruited (Dr. Mohammed Bedhane) to work on the project. No changes have been made to the goals or plans.
Impacts
What was accomplished under these goals?
We have made substantial progress under these goals. 1) We have developed and optimized the variant calling pipeline. The pipeline has been used to genotype DNA variants for more than 2,000 animals across multiple pig breeds. The genotype imputation pipeline has been developed and is being evaluated. 2) The web server has been developed and is waiting for the final pipeline to be served on the server. 3) We have evaluated mutliple strategies for imputation and found the combination of Shapeit4/Impute5 to be the best performing software combination, achieving accuracy > 98% as measured by concordance rate. We have also found that imputation using low density arrays achieve comparable accuracy with low coverage sequencing.
Publications
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