1
|
Liu Z, Fu S, He X, Liu X, Shi C, Dai L, Wang B, Chai Y, Liu Y, Zhang W. Estimates of Genomic Heritability and the Marker-Derived Gene for Re(Production) Traits in Xinggao Sheep. Genes (Basel) 2023; 14:genes14030579. [PMID: 36980850 PMCID: PMC10048694 DOI: 10.3390/genes14030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Xinggao sheep are a breed of Chinese domestic sheep that are adapted to the extremely cold climatic features of the Hinggan League in China. The economically vital reproductive trait of ewes (litter size, LS) and productive traits of lambs (birth weight, BWT; weaning weight, WWT; and average daily gain, ADG) are expressed in females and later in life after most of the selection decisions have been made. This study estimated the genetic parameters for four traits to explore the genetic mechanisms underlying the variation, and we performed genome-wide association study (GWAS) tests on a small sample size to identify novel marker trait associations (MTAs) associated with prolificacy and growth. We detected two suggestive significant single-nucleotide polymorphisms (SNPs) associated with LS and eight significant SNPs for BWT, WWT, and ADG. These candidate loci and genes also provide valuable information for further fine-mapping of QTLs and improvement of reproductive and productive traits in sheep.
Collapse
Affiliation(s)
- Zaixia Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Shaoyin Fu
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiaolong He
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xuewen Liu
- College of Agronomy, Animal Husbandry and Bioengineering, Xing’an Vocational and Technical College, Ulanhot 137400, China
| | - Caixia Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lingli Dai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Biao Wang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Yuan Chai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yongbin Liu
- School of Life Science, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (Y.L.); (W.Z.)
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Correspondence: (Y.L.); (W.Z.)
| |
Collapse
|
2
|
Wang Y, Li Y, Hao M, Liu X, Zhang M, Wang J, Xiong M, Shugart YY, Jin L. Robust Reference Powered Association Test of Genome-Wide Association Studies. Front Genet 2019; 10:319. [PMID: 31024629 PMCID: PMC6465778 DOI: 10.3389/fgene.2019.00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/21/2019] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified abundant genetic susceptibility loci, GWAS of small sample size are far less from meeting the previous expectations due to low statistical power and false positive results. Effective statistical methods are required to further improve the analyses of massive GWAS data. Here we presented a new statistic (Robust Reference Powered Association Test) to use large public database (gnomad) as reference to reduce concern of potential population stratification. To evaluate the performance of this statistic for various situations, we simulated multiple sets of sample size and frequencies to compute statistical power. Furthermore, we applied our method to several real datasets (psoriasis genome-wide association datasets and schizophrenia genome-wide association dataset) to evaluate the performance. Careful analyses indicated that our newly developed statistic outperformed several previously developed GWAS applications. Importantly, this statistic is more robust than naive merging method in the presence of small control-reference differentiation, therefore likely to detect more association signals.
Collapse
Affiliation(s)
- Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yi Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China.,Institute of Sixth-Sector Industrialization Research, Fudan University, Shanghai, China
| | - Meng Hao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoyu Liu
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Menghan Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China
| | - Jiucun Wang
- Human Phenome Institute, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Momiao Xiong
- Human Genetics Center, School of Public Health, University of Texas Houston Health Sciences Center, Houston, TX, United States
| | - Yin Yao Shugart
- Human Phenome Institute, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- Human Phenome Institute, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| |
Collapse
|