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Wu P, Chen D, Wang K, Wang S, Liu Y, Jiang A, Xiao W, Jiang Y, Zhu L, Xu X, Qiu X, Li X, Tang G. Whole-genome sequence association study identifies cyclin dependent kinase 8 as a key gene for the number of mummified piglets. Anim Biosci 2023; 36:29-42. [PMID: 36108685 PMCID: PMC9834657 DOI: 10.5713/ab.22.0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE Pigs, an ideal biomedical model for human diseases, suffer from about 50% early embryonic and fetal death, a major cause of fertility loss worldwide. However, identifying the causal variant remains a huge challenge. This study aimed to detect single nucleotide polymorphisms (SNPs) and candidate genes for the number of mummified (NM) piglets using the imputed whole-genome sequence (WGS) and validate the potential candidate genes. METHODS The imputed WGS was introduced from genotyping-by-sequencing (GBS) using a multi-breed reference population. We performed genome-wide association studies (GWAS) for NM piglets at birth from a Landrace pig populatiGWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase on. A total of 300 Landrace pigs were genotyped by GBS. The whole-genome variants were imputed, and 4,252,858 SNPs were obtained. Various molecular experiments were conducted to determine how the genes affected NM in pigs. RESULTS A strong GWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase 8 (CDK8) gene, which plays a crucial role in embryonic retardation and lethality. Based on the molecular experiments, we found that Y-box binding protein 1 (YBX1) was a crucial transcription factor for CDK8, which mediated the effect of CDK8 in the proliferation of porcine ovarian granulosa cells via transforming growth factor beta/small mother against decapentaplegic signaling pathway, and, as a consequence, affected embryo quality, indicating that this pathway may be contributing to mummified fetal in pigs. CONCLUSION A powerful imputation-based association study was performed to identify genes associated with NM in pigs. CDK8 was suggested as a functional gene for the proliferation of porcine ovarian granulosa cells, but further studies are required to determine causative mutations and the effect of loci on NM in pigs.
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Affiliation(s)
- Pingxian Wu
- Chongqing Academy of Animal Sciences, Rongchang 402460, Chongqing,
China
| | - Dejuan Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China,Aks Vocational and Technical College, Aksu, 843000, Xinjiang,
China
| | - Kai Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China
| | - Shujie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China
| | - Yihui Liu
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan,
China
| | - Anan Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China
| | - Weihang Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Yaan 625014, Sichuan,
China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China
| | - Xu Xu
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan,
China
| | - Xiaotian Qiu
- National Animal Husbandry Service, Beijing, 100125, Beijing,
China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan,
China,Corresponding Author: Guoqing Tang, E-mail:
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Jordan KW, Bradbury PJ, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E, Katz A, Pearce S, Carter AH, Prather S, Pumphrey M, Chen J, Cook J, Liu S, Rudd JC, Wang Z, Chu C, Ibrahim AMH, Turkus J, Olson E, Nagarajan R, Carver B, Yan L, Taagen E, Sorrells M, Ward B, Ren J, Akhunova A, Bai G, Bowden R, Fiedler J, Faris J, Dubcovsky J, Guttieri M, Brown-Guedira G, Buckler E, Jannink JL, Akhunov ED. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. G3 (Bethesda) 2021; 12:6423995. [PMID: 34751373 PMCID: PMC9210282 DOI: 10.1093/g3journal/jkab390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/21/2021] [Indexed: 12/04/2022]
Abstract
To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10−14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.
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Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Peter J Bradbury
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Zachary R Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jim Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Esten Mason
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Arron H Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Samuel Prather
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, 83210, USA
| | - Jason Cook
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Shuyu Liu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jackie C Rudd
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Zhen Wang
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Chenggen Chu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jonathan Turkus
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Eric Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Ragupathi Nagarajan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Brett Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Ellie Taagen
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Mark Sorrells
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Brian Ward
- USDA-ARS, Plant Science Research Unit, Raleigh, NC, 27695, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Robert Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Jason Fiedler
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Justin Faris
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Mary Guttieri
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | | | - Ed Buckler
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Jean-Luc Jannink
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
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Pégard M, Rogier O, Bérard A, Faivre-Rampant P, Paslier MCL, Bastien C, Jorge V, Sánchez L. Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding population. BMC Genomics 2019; 20:302. [PMID: 30999856 PMCID: PMC6471894 DOI: 10.1186/s12864-019-5660-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/29/2019] [Indexed: 12/30/2022] Open
Abstract
Background Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation by breeders. Low density panels imputed to higher densities offer a cheaper alternative during the first stages of genomic resources development. Our study is the first to explore the imputation in a tree species: black poplar. About 1000 pure-breed Populus nigra trees from a breeding population were selected and genotyped with a 12K custom Infinium Bead-Chip. Forty-three of those individuals corresponding to nodal trees in the pedigree were fully sequenced (reference), while the remaining majority (target) was imputed from 8K to 1.4 million SNPs using FImpute. Each SNP and individual was evaluated for imputation errors by leave-one-out cross validation in the training sample of 43 sequenced trees. Some summary statistics such as Hardy-Weinberg Equilibrium exact test p-value, quality of sequencing, depth of sequencing per site and per individual, minor allele frequency, marker density ratio or SNP information redundancy were calculated. Principal component and Boruta analyses were used on all these parameters to rank the factors affecting the quality of imputation. Additionally, we characterize the impact of the relatedness between reference population and target population. Results During the imputation process, we used 7540 SNPs from the chip to impute 1,438,827 SNPs from sequences. At the individual level, imputation accuracy was high with a proportion of SNPs correctly imputed between 0.84 and 0.99. The variation in accuracies was mostly due to differences in relatedness between individuals. At a SNP level, the imputation quality depended on genotyped SNP density and on the original minor allele frequency. The imputation did not appear to result in an increase of linkage disequilibrium. The genotype densification not only brought a better distribution of markers all along the genome, but also we did not detect any substantial bias in annotation categories. Conclusions This study shows that it is possible to impute low-density marker panels to whole genome sequence with good accuracy under certain conditions that could be common to many breeding populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5660-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie Pégard
- BioForA, INRA, ONF, 45075, Orléans, France, 2163 Avenue de la Pomme de Pin CS 40001 ARDON, Orléans Cedex 2, 45075, France
| | - Odile Rogier
- BioForA, INRA, ONF, 45075, Orléans, France, 2163 Avenue de la Pomme de Pin CS 40001 ARDON, Orléans Cedex 2, 45075, France
| | - Aurélie Bérard
- Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, 91000, 2 rue Gaston Crémieux, Evry, 9100, France
| | - Patricia Faivre-Rampant
- Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, 91000, 2 rue Gaston Crémieux, Evry, 9100, France
| | - Marie-Christine Le Paslier
- Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, 91000, 2 rue Gaston Crémieux, Evry, 9100, France
| | - Catherine Bastien
- BioForA, INRA, ONF, 45075, Orléans, France, 2163 Avenue de la Pomme de Pin CS 40001 ARDON, Orléans Cedex 2, 45075, France
| | - Véronique Jorge
- BioForA, INRA, ONF, 45075, Orléans, France, 2163 Avenue de la Pomme de Pin CS 40001 ARDON, Orléans Cedex 2, 45075, France
| | - Leopoldo Sánchez
- BioForA, INRA, ONF, 45075, Orléans, France, 2163 Avenue de la Pomme de Pin CS 40001 ARDON, Orléans Cedex 2, 45075, France.
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