|
Special Issue:
动物科学合辑Animal Science
|
|
|
|
| Genetic parameter estimation and genome-wide association study (GWAS) of red blood cell count at three stages in a Duroc×Erhualian pig population |
NAN Jiu-hong1*, YIN Li-lin1*, TANG Zhen-shuang1, CHEN Jian-hai1, ZHANG Jie1, WANG Hai-yan1, 2, DU Xiao-yong1, 2, LIU Xiang-dong1, 3 |
1 Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P.R.China
2 Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R.China
3 Key Lab of Swine Healthy Breeding of Ministry of Agriculture and Rural Affairs, Guangxi Yangxiang Co., Ltd., Guigang 537100, P.R.China |
|
|
|
|
Abstract Red blood cells play an essential role in the immune system. Moreover, red blood cell count (RBC) is an important clinical indicator of various diseases, including anemia, type 2 diabetes and the metabolic syndrome. Thus, it is necessary to reveal the genetic mechanism of RBC for animal disease resistance breeding. However, quite a few studies had focused on porcine RBC, especially at different stages. Thus, studies on porcine RBC at different stages are needed for disease resistant breeding. In this study, the porcine RBC of 20-, 33-, and 80-day old were measured, and genetic parameter estimation and genome-wide association study (GWAS) were both performed. As a result, the heritability was about 0.6 at the early stages, much higher than that at 80 days. Nine novel genome wide significant single nucleotide polymorphisms (SNPs), located at Sus scrofa chromosome (SSC)3, 4, 8, 9, 10 and 15, respectively, were identified. Further, TGFβ2, TMCC2 and PPP1R15B genes were identified as important candidate genes of porcine red blood cell count. So different SNPs and candidate genes were found significantly associated with porcine RBC at different stages, suggesting that different genes might play key roles on porcine RBC at different stages. Overall, new evidences were offered in this study for the genetic bases of animal RBC, and that the SNPs and candidate genes would be useful for disease resistant breeding of pig.
|
|
Received: 19 October 2018
Accepted:
|
| Fund: This work was supported by the National Natural Science Foundation of China (31572375, NSFC-CGIAR31361140365), the Fundamental Research Funds for the Central Universities of China (2662016PY006), the National High Technology Research and Development Program of China (2013AA102502), the earmarked fund for China Agriculture Research System (CARS-35), and the Dabeinong Group Promoted Project for Young Scholar of Huazhong Agricultural University, China (2017DBN019). |
|
Corresponding Authors:
Correspondence LIU Xiang-dong, E-mail: liuxiangdong@mail.hzau.edu.cn; DU Xiao-yong, E-mail: duxiaoyong@mail.hzau.edu.cn
|
| About author: * These authors contributed equally to this study. |
Cite this article:
NAN Jiu-hong, YIN Li-lin, TANG Zhen-shuang, CHEN Jian-hai, ZHANG Jie, WANG Hai-yan, DU Xiao-yong, LIU Xiang-dong .
2020.
Genetic parameter estimation and genome-wide association study (GWAS) of red blood cell count at three stages in a Duroc×Erhualian pig population. Journal of Integrative Agriculture, 19(3): 793-799.
|
Abbott D, Wang K, Shapiro A, Trudy B, Di P, Di Jorge P. 2007. genome wide scan of complete blood count (CBC) measures suggests strong linkage of red blood cell (RBC) count to chromosome 4q25. Blood, 110, 11.
Arnold S J, Stappert J, Bauer A, Kispert A, Herrmann B G, Kemler R. 2000. Brachyury is a target gene of the Wnt/beta-catenin signaling pathway. Mechanisms of Development, 91, 249–258.
Dal Colletto G M, Fulker D W, Barretto O C, Kolya M. 1993. Genetic and environmental effects on blood cells. Acta Geneticae Medicae et Gemellologiae, 42, 245.
Flori L, Gao Y, Laloë D, Lemonnier G, Leplat J J, Teillaud A, Cossalter A M, Laffitte J, Pinton P, De V C. 2011. Immunity traits in pigs: Substantial genetic variation and limited covariation. PLoS ONE, 6, e22717.
Garner C, Tatu T, Reittie J E, Littlewood T, Darley J, Cervino S, Farrall M, Kelly P, Spector T D, Thein S L. 2000. Genetic influences on F cells and other hematologic variables: A twin heritability study. Blood, 95, 342–346.
Harding H P, Novoa I, Zhang Y, Zeng H, Wek R, Schapira M, Ron D. 2000. Regulated translation initiation controls stress-induced gene expression in mammalian cells. Molecular Cell, 6, 1099–1108.
Harding H P, Zhang Y, Scheuner D, Chen J J, Kaufman R J, Ron D. 2009. Ppp1r15 gene knockout reveals an essential role for translation initiation factor 2 alpha (eIF2α) dephosphorylation in mammalian development. Proceedings of the National Academy of Sciences of the United States of America, 106, 1832–1837.
Hinckley J D, Abbott D, Burns T L, Heiman M, Shapiro A D, Wang K, Di P J. 2013. Quantitative trait locus linkage analysis in a large Amish pedigree identifies novel candidate loci for erythrocyte traits. Molecular Genetics & Genomic Medicine, 1, 131–141.
Kloft N, Neukirch C, Von H G, Bobkiewicz W, Weis S, Boller K, Husmann M. 2012. A subunit of eukaryotic translation initiation factor 2α-phosphatase (CreP/PPP1R15B) regulates membrane traffic. Journal of Biological Chemistry, 287, 35299.
Lasley J F. 1978. Genetics of Livestock Improvement. Prentice-Hall, Inc., Upper Saddle River, New Jersey.
Liu X, Huang J, Yang S, Zhao Y, Xiang A, Cao J, Fan B, Wu Z, Zhao J, Zhao S. 2014. Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a. Developmental & Comparative Immunology, 44, 35.
Liu X, Huang M, Fan B, Buckler E S, Zhang Z. 2016. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genetics, 12, e1005767.
Luo W, Chen S, Cheng D, Wang L, Li Y, Ma X, Song X, Liu X, Li W, Liang J. 2012. Genome-wide association study of porcine hematological parameters in a Large white×Minzhu F2 resource population. International Journal of Biological Sciences, 8, 870–881.
Madsen P, Jensen J. 2013. A user’s guide to DMU. Version 6, release 5.2. Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
Majka M, Janowska-Wieczorek A, Ratajczak J, Ehrenman K, Pietrzkowski Z, Kowalska M A, Gewirtz A M, Emerson S G, Ratajczak M Z. 2001. Numerous growth factors, cytokines, and chemokines are secreted by human CD34(+) cells, myeloblasts, erythroblasts, and megakaryoblasts and regulate normal hematopoiesis in an autocrine/paracrine manner. Blood, 97, 3075–3085.
Miao Y, Soudy F, Zhong X, Liao M, Zhao S, Li X. 2017. Candidate gene identification of feed efficiency and coat color traits in a C57BL/6J×Kunming F2 mice population using genome-wide association study. Biomed Research International, 2017, 1–7.
Mpetile Z, Young J M, Gabler N K, Dekkers J C M, Tuggle C K. 2015. Assessing peripheral blood cell profile of Yorkshire pigs divergently selected for residual feed intake. Journal of Animal Science, 93, 892–899.
Purcell S, Neale B M, Toddbrown K, Thomas L, Ferreira M A R, Bender D, Maller J B, Sklar P, De Bakker P I W, Daly M J. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81, 559–575.
Reiner G, Clemens N, Fischer R, Kohler F, Berge T, Hepp S, Willems H. 2009. Mapping of quantitative trait loci for clinicalchemical traits in swine. Animal Genetics, 40, 57–64.
Shau H, Gupta R K, Golub S H. 1993. Identification of a natural killer enhancing factor (NKEF) from human erythroid cells. Cellular Immunology, 147, 1–11.
Siegel I, Liu T L, Gleicher N. 1981a. Red cell immune adherence. Lancet, 318, 878–879.
Siegel I, Liu T L, Gleicher N. 1981b. The red-cell immune system. Lancet, 318, 556–559.
Simmons D. 2010. Increased red cell count in diabetes and pre-diabetes. Diabetes Research & Clinical Practice, 90, e50.
Thompson P D, Hannah T, Andy B, Harry N, Steve K, Jan N, May T. 2010. Claudin 13, a member of the claudin family regulated in mouse stress induced erythropoiesis. PLoS ONE, 5, e12667.
Vanraden P M. 2008. Efficient methods to compute genomic predictions. Journal of Dairy Science, 91, 4414–4423.
Wang J Y, Luo Y R, Fu W X, Lu X, Zhou J P, Ding X D, Liu J F, Zhang Q. 2013. Genome-wide association studies for hematological traits in swine. Animal Genetics, 44, 34–43.
Wang Z S, Song Z C, Bai J H, Fei L, Tao W, Ji Q, Jian H. 2013. Red blood cell count as an indicator of microvascular complications in Chinese patients with type 2 diabetes mellitus. Vascular Health & Risk Management, 2013, 237.
Yang Q, Kathiresan S, Lin J, Tofler G H, Odonnell C J. 2007. Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. BMC Medical Genetics, 8, 1–11.
Yang S, Liu X, Li X, Sun S, Sun F, Fan B, Zhao S. 2013. MicroRNA-124 reduces caveolar density by targeting caveolin-1 in porcine kidney epithelial PK15 cells. Molecular & Cellular Biochemistry, 384, 213–219.
Zhang J, Chen J H, Liu X D, Wang H Y, Liu X L, Li X Y, Wu Z F, Zhu M J, Zhao S H. 2016. Genomewide association studies for hematological traits and T lymphocyte subpopulations in a Duroc×Erhualian F-2 resource population. Journal of Animal Science, 94, 5028–5041.
Zhang Z, Hong Y, Gao J, Xiao S, Ma J, Zhang W, Ren J, Huang L. 2013. Genome-wide association study reveals constant and specific loci for hematological traits at three time stages in a White Duroc×Erhualian F2 resource population. PLoS ONE, 8, e63665. |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
