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Lara MK, Chitre AS, Chen D, Johnson BB, Nguyen K, Cohen KA, Muckadam SA, Lin B, Ziegler S, Beeson A, Sanches TM, Solberg Woods LC, Polesskaya O, Palmer AA, Mitchell SH. Genome-wide association study of delay discounting in Heterogeneous Stock rats. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12909. [PMID: 39119916 PMCID: PMC11310854 DOI: 10.1111/gbb.12909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/27/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
Delay discounting refers to the behavioral tendency to devalue rewards as a function of their delay in receipt. Heightened delay discounting has been associated with substance use disorders and multiple co-occurring psychopathologies. Human and animal genetic studies have established that delay discounting is heritable, but only a few associated genes have been identified. We aimed to identify novel genetic loci associated with delay discounting through a genome-wide association study (GWAS) using Heterogeneous Stock (HS) rats, a genetically diverse outbred population derived from eight inbred founder strains. We assessed delay discounting in 650 male and female HS rats using an adjusting amount procedure in which rats chose between smaller immediate sucrose rewards or a larger reward at various delays. Preference switch points were calculated and both exponential and hyperbolic functions were fitted to these indifference points. Area under the curve (AUC) and the discounting parameter k of both functions were used as delay discounting measures. GWAS for AUC, exponential k, and one indifference point identified significant loci on chromosomes 20 and 14. The gene Slc35f1, which encodes a member of the solute carrier family, was the sole gene within the chromosome 20 locus. That locus also contained an eQTL for Slc35f1, suggesting that heritable differences in the expression might be responsible for the association with behavior. Adgrl3, which encodes a latrophilin subfamily G-protein coupled receptor, was the sole gene within the chromosome 14 locus. These findings implicate novel genes in delay discounting and highlight the need for further exploration.
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Affiliation(s)
- Montana Kay Lara
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Apurva S. Chitre
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Denghui Chen
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Benjamin B. Johnson
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Khai‐Minh Nguyen
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Katarina A. Cohen
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Sakina A. Muckadam
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Bonnie Lin
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Shae Ziegler
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Angela Beeson
- Department of Internal Medicine, Wake Forest School of MedicineWake Forest UniversityWinston‐SalemNorth CarolinaUSA
| | - Thiago M. Sanches
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Wake Forest School of MedicineWake Forest UniversityWinston‐SalemNorth CarolinaUSA
| | - Oksana Polesskaya
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Abraham A. Palmer
- Department of PsychiatryUniversity of California San DiegoLa JollaCaliforniaUSA
- Institute for Genomic MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Suzanne H. Mitchell
- Department of Behavioral Neuroscience, Psychiatry, the Oregon Institute of Occupational Health SciencesOregon Health & Science UniversityPortlandOregonUSA
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Chen D, Chitre AS, Nguyen KMH, Cohen K, Peng B, Ziegler KS, Okamoto F, Lin B, Johnson BB, Sanches TM, Cheng R, Polesskaya O, Palmer AA. A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603984. [PMID: 39071405 PMCID: PMC11275765 DOI: 10.1101/2024.07.17.603984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping-by-sequencing and more recently generated by low-coverage whole-genome-sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21x coverage) and low-coverage whole-genome-sequencing data from 8,760 heterogeneous stock rats (mean 0.27x coverage), we can impute 7.32 million bi-allelic single-nucleotide polymorphisms with a concordance rate >99.76% compared to high-coverage (mean 33.26x coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping-by-sequencing or low-coverage whole-genome-sequencing for accurate genotyping, and demonstrate techniques that may also be useful for other genetic studies in non-human subjects.
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Affiliation(s)
- Denghui Chen
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Apurva S. Chitre
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Khai-Minh H. Nguyen
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Katarina Cohen
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Beverly Peng
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Kendra S. Ziegler
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Faith Okamoto
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Bonnie Lin
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Benjamin B. Johnson
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Thiago M. Sanches
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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Guo Y, Cui Y, Sun M, Zhu X, Zhang Y, Lu J, Li C, Lv J, Guo M, Liu X, Chen Z, Du X, Huo X. Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils. Genes (Basel) 2024; 15:817. [PMID: 38927752 PMCID: PMC11202554 DOI: 10.3390/genes15060817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
The Mongolian gerbil is a distinctive experimental animal in China, as its genetic qualities possess significant value in the field of medical biology research. Here, we aimed to establish an economical and efficient panel for genetic quality detection in Mongolian gerbils using single-nucleotide polymorphism (SNP) markers. To search for SNPs, we conducted whole-genome sequencing (WGS) in 40 Mongolian gerbils from outbred populations. Reliable screening criteria were established to preliminarily select SNPs with a wide genome distribution and high levels of polymorphism. Subsequently, a multiple-target regional capture detection system based on second-generation sequencing was developed for SNP genotyping. Based on the results of WGS, 219 SNPs were preliminarily selected, and they were established and optimized in a multiple-amplification system that included 206 SNP loci by genotyping three outbred populations. PopGen.32 analysis revealed that the average effective allele number, Shannon index, observed heterozygosity, expected heterozygosity, average heterozygosity, polymorphism information content, and other population genetic parameters of the Capital Medical University (CMU) gerbils were the highest, followed by those of Zhejiang gerbils and Dalian gerbils. Through scientific screening and optimization, we successfully established a novel, robust, and cost-effective genetic detection system for Mongolian gerbils by utilizing SNP markers for the first time.
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Affiliation(s)
- Yafang Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Yutong Cui
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Minghe Sun
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Xiao Zhu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Yilang Zhang
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Jing Lu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Changlong Li
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Jianyi Lv
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Meng Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Xin Liu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Zhenwen Chen
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Xiaoyan Du
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Xueyun Huo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
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Lara MK, Chitre AS, Chen D, Johnson BB, Nguyen KM, Cohen KA, Muckadam SA, Lin B, Ziegler S, Beeson A, Sanches T, Solberg Woods LC, Polesskaya O, Palmer AA, Mitchell SH. Genome-wide association study of delay discounting in Heterogenous Stock rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.570851. [PMID: 38168347 PMCID: PMC10760013 DOI: 10.1101/2023.12.12.570851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Delay discounting refers to the behavioral tendency to devalue rewards as a function of their delay in receipt. Heightened delay discounting has been associated with substance use disorders, as well as multiple co-occurring psychopathologies. Genetic studies in humans and animal models have established that delay discounting is a heritable trait, but only a few specific genes have been associated with delay discounting. Here, we aimed to identify novel genetic loci associated with delay discounting through a genome-wide association study (GWAS) using Heterogenous Stock rats, a genetically diverse outbred population derived from eight inbred founder strains. We assessed delay discounting in 650 male and female rats using an adjusting amount procedure in which rats chose between smaller immediate sucrose rewards or a larger reward at variable delays. Preference switch points were calculated for each rat and both exponential and hyperbolic functions were fitted to these indifference points. Area under the curve (AUC) and the discounting parameter k of both functions were used as delay discounting measures. GWAS for AUC, exponential k, and indifference points for a short delay identified significant loci on chromosomes 20 and 14. The gene Slc35f1, which encodes a member of the solute carrier family of nucleoside sugar transporters, was the only gene within the chromosome 20 locus. That locus also contained an eQTL for Slc35f1, suggesting that heritable differences in the expression of that gene might be responsible for the association with behavior. The gene Adgrl3, which encodes a member of the latrophilin family of G-protein coupled receptors, was the only gene within the chromosome 14 locus. These findings implicate novel genes in delay discounting and highlight the need for further exploration.
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Affiliation(s)
- Montana Kay Lara
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Apurva S. Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Benjamin B. Johnson
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Katarina A. Cohen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sakina A. Muckadam
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bonnie Lin
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shae Ziegler
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Angela Beeson
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Thiago Sanches
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Suzanne H. Mitchell
- Departments of Behavioral Neuroscience, Psychiatry, the Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239 USA
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