鸡胸腺重和脾脏重性状的全基因组关联

doi:10.3864/j.issn.0578-1752.2012.15.019

Abstract

Abstract: 【Objective】 Genome-wide association study (GWAS) is a new strategy to identify genes and chromosome regions associated with complex traits.【Method】 A total of 728 Beijing-You chickens from 50 families were genotyped by 60K SNP Illumina iSelect chicken array. GWAS was performed to study the candidate loci affecting thymus weight and spleen weight at 100 days of age.【Result】 It was found that 24 SNPs were significantly associated with target traits at Bonferroni corrected 5% genome-wise threshold, including Janus kinase 1 (JAK1), zinc finger DHHC-type containing 8 (ZDHHC8)、vav 3 guanine nucleotide exchange factor (VAV3), SATB homeobox 1 (SATB1) and other genes near these SNPs，and 84 SNPs reached both the significance of ‘suggestive linkage’ and 5% chromosome-wise threshold.【Conclusion】 These indentified genes and SNPs offered essential information for understanding of the molecular mechanisms of immune organs development and facilitated the application of marker-assisted selection in diseases-resistance breeding program in chicken.

Key words: Beijing-You chicken, thymus mass, spleen mass, GWAS

ZHANG Lei, ZHENG Mai-Qing, LIU Ran-Ran, WEN Jie, WU Dan, HU Yao-Dong, SUN Yan-Fa, LI Peng, LIU Li, ZHAO Gui-苹. Genome-Wide Association of Thymus and Spleen Mass in Chicken[J].Scientia Agricultura Sinica, 2012, 45(15): 3165-3175.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2012.15.019

https://www.chinaagrisci.com/EN/Y2012/V45/I15/3165

References

[1]Hu Z L, Fritz E, Reecy J. AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 2007, 35: 604-609.

[2]王云. 鸡胸腺发育形态学研究[D]. 武汉：华中农业大学，2010.

Wang Y. Morphological study on the development of chicken thymus[D]. Wuhan: Huazhong Agricultural University, 2010.(in Chinese)

[3]Reina M, Georg K. Structure and function of the spleen. Nature Immunology, 2005, 5:606-616.

[4]Moller P, Erritzoe J. Predation against birds with low immunocompetence. Oecologia , 2000, 122:500-504.

[5]Grasman A. Assessing immunological function in toxicological studies of avian wildlife. Integrative and Comparative Biology, 2002, 42:34-42.

[6]Smith G, Hunt L. On the use of spleen mass as a measure of avian immune system. Oecologia, 2004, 138:28-31.

[7]Zhou H, Deeb N, Evock-Clover M. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. ii. body composition. Poultry Science, 2006, 85:1712-1721.

[8]Park H-B, Jacobsson L, Wahlberg P. QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth. Physiological Genomics, 2006, 25: 216-223.

[9]Gu X R, Feng C G, Ma L. Genome-wide association study of body weight in chicken f2 resource population. PLoS One, 2011, 6(7): 21872.

[10]Goddard M E, Hayes B J. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics, 2009, 10:381-391.

[11]Andersson L, Georges M. Domestic-animal genomics: deciphering the genetics of complex traits. Nature Reviews Genetics, 2004, 5: 202-212.

[12]卢昕. 对猪部分免疫性状的QTL定位及全基因组关联分析[D]. 北京: 中国农业大学, 2010.

Lu X. QTL mapping and genome-wide association study for some immune traits in swine[D]. Beijing: China Agriculture University, 2010. (in Chinese)

[13]Purcell S, Neale B, Todd-Brown K. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal Human Genetics, 2007, 81:559-575.

[14]Wang D, Sun Y, Stang P, Berlin J A. Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling. BMC Proceedings, 2009, 7: S109.

[15]Nicodemus K K, Liu W, Chase G A. Comparison of type I error for multiple test corrections in large single-nucleotide polymorphism studies using principal components versus haplotype blocking algorithms. BMC Genetics, 2005, 1: 78.

[16]Price A L, Zaitlen N A, Reich D. New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics, 2010, 11(7):459-463.

[17]Karlsson, K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nature Genetics, 2007, 39(11):1321-1328.

[18]Barendse W. A validated whole-genome association study of efficient food conversion in cattle. Genetics, 2007, 176(3):1893.

[19]Duijvesteijn N. A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6. BMC Genetics, 2010, 11(1):42.

[20]Fan B. Genome-wide association study identifies loci for body composition and structural soundness traits in pigs. PLoS One, 2011, 6(2): 14726.

[21]Joanne H, Wendy D, Mensur D. Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the type-1 plasminogen activator inhibitor mRNA. The Journal of Biological Chemistry, 2001, 276(5): 3341- 3347.

[22]Lemos T, Passosa D,Nerya F. Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3. FEBS Letters, 2003, 533:14-20.

[23]Rodig S J, Meraz M A. Disruption of the Jak1 gene demonstrates obligatory and nonredundant roles of the Jaks in cytokine-induced biologic responses. Cell, 1998, 93:373-383.

[24]Carrio R, Torroella M, Iragavarapu V. Tumor-induced thymic atrophy: alteration in interferons and Jak/Stats signaling pathways. International Journal Oncology, 2011, 38(2): 547-553.

[25]Marg A. Neurotractin, a novel neurite outgrowth- promoting Ig-like protein that interacts with CEPU-1 and LAMP. The Journal of Cell Biology, 1999, 145:865-876.

[26]Schafer M, Brauer A U, Savaskan N E. Neurotractin/kilon promotes neurite outgrowth and is expressed on reactive astrocytes after entorhinal cortex lesion. Molecular and Cellular Neuroscience, 2005, 29: 580-590.

[27]Willer C J, Speliotes E K, Loos R J. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nature Genetics, 2009, 41: 25-34.

[28]Bockbrader K, Feng Y. Essential function, sophisticated regulation and pathological impact of the selective RNA-binding protein QKI in CNS myelin development. Future Neurology, 2008, 3:655-668.

[29]Feng Y, Bankston A. The star family member QKI and cell signaling. Advances in Experimental Medicine and Biology, 2010, 693:25-36.

[30]Yang G, Fu H, Zhang J, Lu X, Yu F, Jin L, Bai L, Huang B, Shen L, Feng Y, Yao L, Lu Z. RNA binding protein Quaking, a critical regulator of colon epithelial differentiation and a suppressor of colon cancer. Gastroenterology, 2010, 138(1): 231-240.

[31]Mezquita J, Pau M, Mezquita C. Four isoforms of the signal- transduction and RNA-Binding protein QKI expressed during chicken spermatogenesis. Molecular Reproduction and Development, 1998, 50:70-78.

[32]傅海燕. RNA结合蛋白QKI在造血系统髓系分化中的表达调控及其功能研究[D]. 西安：第四军医大学，2009.

Fu H Y. Functional elucidation of RNA binding protein QKI in the process of myeloid haematopoiesis[D]. Xi’an: the Fourth Military Medical University, 2009. (in Chinese)

[33]Eggenschwiler J T, Espinoza E, Anderson K V. Rab23 is an essential negative regulator of the mouse sonic hedgehog ignaling pathway Nature, 2001, 412(6843): 194-198.

[34]吕艳杰. 鸡胚胸腺和法氏囊发育过程中Shh和Bmp2表达的研究[D]. 济南: 山东大学, 2005.

Lü Y J. Expression patterns of Shh and Bmp2 in the developing chicken thymus and bursa of fabricius[D]. Ji’nan: Shandong University, 2005. (in Chinese)

[35]Divya S, Ariadne L H, Susan V O. Reduced thymocyte development in sonic hedgehog knockout embyros. Immunology, 2004, 172: 2296-2306.

[36]Mukai J, Liu H, Burt R. Evidence that the gene encoding ZDHHC8 contributes to the risk of schizophrenia. Nature Genetics, 2004, 36:725-731.

[37]Chen W Y, Shi Y Y, Zheng Y L. Case-control study and transmission disequilibrium test provide consistent evidence for association between schizophrenia and genetic variation in the 22q11 gene ZDHHC8. Human Molecular Genetics, 2004, 13:2991-2995.

[38]Faul T, Gawlik M, Bauer M. ZDHHC8 as a candidate gene for schizophrenia: Analysis of a putative functional intronic marker in case-control and family-based association studies. BMC Psychiatry, 2005, 5: 35.

[39]Glaser B, Schumacher J, Williams H J. No association between the putative functional ZDHHC8 single nucleotide polymorphism rs175174 and schizophrenia in large European samples. Biological Psychiatry, 2005, 58(1): 78-80.

[40]Owens D M, Keyse S M. Differential regulation of MAP kinase signaling by dual-specificity protein phosphatases. Oncogene, 2007, 26: 3203-3213.

[41]Lang R, Hammer M, Mages J. DUSP meet immunology: dual specificity MAPK phosphatases in control of the inflammatory response. The Journal of Immunology, 2006, 177: 7497-7504.

[42]Rubin B, Tucker R, Martin D. Teneurins: A novel family of neuronal cell surface proteins in vertebrates, homologous to the drosophila pair-rule gene product ten-m. Developmental Biology, 1999, 216: 195-209.

[43]Vinatzer U, Gollinger M, Müllauer L. Mucosa-associated lymphoid tissue lymphoma: novel translocations including rearrangements of ODZ2, JMJD2C, and CNN3. Clinical Cancer Research, 2008, 14(20):6426-6431.

[44]Krcmery J, Camarata T, Kulisz A. Nucleocytoplasmic functions of the PDZ-LIM protein family:new insights in organ development. Bioessays, 2010, 32(2):100-108.

[45]Krause A, Zacharias W, Camarata T. Tbx5 and Tbx4 transcription factors interact with a new chicken PDZ-LIM protein in limb and heart development. Developmental Biology, 2004, 273:106-120.

[46]王勇. CK1α激酶通过磷酸化蛋白RIP影响TNF/NF-κB信号通路的转导[D]. 北京：中国协和医科大学，2005.

Wang Y. Regulation of TNF/NF-κB signaling pathway by CK1α via phosporyrlating RIP protein[D]. Beijing: Peking Union Medical College, 2005. (in Chinese)

[47]Baba M, Hong S, Sharma N. Folliculin encoded by the BHD gene interacts with a binding protein, FNIP1, and AMPK, and is involved in AMPK and mTOR signaling. PNAS, 2006, 103(42): 15552-15557.

[48]Hong S, Oh H B, Valera V. Tumor suppressor FLCN inhibits tumorigenesis of a FLCN-null renal cancer cell line and regulates expression of key molecules in TGF-β signaling. Molecular Cancer , 2010, 9:160.

[49]Hobert O, Westphal H. Functions of LIM-homeobox genes. Trends in Genetics, 2000, 16(2):75-83.

[50]Sun X N, Saitsu H, Shiota K. Expression dynamics of the LIM-homeobox genes, Lhx1 and Lhx9, in the diencephalon during chick development. International Journal Developmental Biology, 2008, 52: 33-41.

[51]Baltimore D, Boldin M P, O'connell R M. MicroRNAs: new regulators of immune cell development and function. Nature Immunology, 2008, 9(8):839-845.

[52]Woznik M, Rodner C, LEMON K. Mumps virus small hydrophobic protein targets ataxin-1 ubiquitin-like interacting protein (ubiquilin4). Journal of General Virology, 2010, 91:2773-2781.

[53]Wenzel D, Stoll K, Klevit R. E2s: structurally economical and functionally replete. Biochemical Journal, 2010, 433(1): 31-42.

[54]Tybulewicz V L. Vav-family proteins in T-cell signalling. Current Opinion in Immunology, 2005, 17(3):267-274.

[55]Turner M. B-cell development and antigen receptor signalling. Biochemical Society Transaction, 2002, 30(4):812-815.

[56]Inabe K, Ishiai M, Scharenberg A. Vav3 modulates B cell receptor responses by regulating phosphoinositide 3-kinase activation. The Journal of Experimental Medicine, 2002, 195(2):189-200.

[57]Akhtar W, Veenstra J C. TBP-related factors: a paradigm of diversity in transcription initiation. Cell & Bioscience, 2011, 1:23.

[58]Morita M, Shimozawa N, Kashiwayama Y. ABC subfamily D proteins and very long chain fatty acid metabolism as novel targets in adrenoleukodystrophy. Current Drug Targets, 2011, 12(5): 694-706.

[59]Blanco S, Kurowski A, Nichols J. The RNA-methyltransferase Misu (Nsun2) poises epidermal stem cells to differentiate. PLoS Genetics, 2011, 7(12): 1002403.

[60]Hussain S, Benavente S, Nascimento E. The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability. The Journal of Cell Biology, 2009, 186(1):27-40.

[61]Krangel M. T cell development: better living through chromatin. Nature Immunology, 2007, 8(7): 687-694.

[62]Sedwick C. SATB1 makes a splash in t cell wnt signaling. PLoS Biology, 2010, 8(1): 1000295.

[63]Beyer M, Thabet Y, Müller R U. Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation. Nature Immunology, 2011, 12(9):898-907.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

Genome-Wide Association of Thymus and Spleen Mass in Chicken

PDF

Cited

Abstract

Cite this article

share this article

References

Related Articles 13

Metrics

Comments

Recommended 0

[1]	PANG HongBo, CHENG Lu, YU MingLan, CHEN Qiang, LI YueYing, WU LongKun, WANG Ze, PAN XiaoWu, ZHENG XiaoMing. Genome-Wide Association Study of Cold Tolerance at the Germination Stage of Rice [J]. Scientia Agricultura Sinica, 2022, 55(21): 4091-4103.
[2]	XIE XiaoYu, WANG KaiHong, QIN XiaoXiao, WANG CaiXiang, SHI ChunHui, NING XinZhu, YANG YongLin, QIN JiangHong, LI ChaoZhou, MA Qi, SU JunJi. Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis and Candidate Gene Prediction of Boll Opening Rate in Upland Cotton [J]. Scientia Agricultura Sinica, 2022, 55(2): 248-264.
[3]	ZHANG PengXia,ZHOU XiuWen,LIANG Xue,GUO Ying,ZHAO Yan,LI SiShen,KONG FanMei. Genome-Wide Association Analysis for Yield and Nitrogen Efficiency Related Traits of Wheat at Seedling Stage [J]. Scientia Agricultura Sinica, 2021, 54(21): 4487-4499.
[4]	ZHANG Fang,REN Yi,CAO JunMei,LI FaJi,XIA XianChun,GENG HongWei. Genome-wide Association Analysis of Wheat Grain Size Related Traits Based on SNP Markers [J]. Scientia Agricultura Sinica, 2021, 54(10): 2053-2063.
[5]	JunYi GAI,JianBo HE. Major Characteristics, Often-Raised Queries and Potential Usefulness of the Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis [J]. Scientia Agricultura Sinica, 2020, 53(9): 1699-1703.
[6]	XiaoShuai HAO,MengMeng FU,ZaiDong LIU,JianBo HE,YanPing WANG,HaiXiang REN,DeLiang WANG,XingYong YANG,YanXi CHENG,WeiGuang DU,JunYi GAI. Genome-Wide QTL-Allele Dissection of 100-Seed Weight in the Northeast China Soybean Germplasm Population [J]. Scientia Agricultura Sinica, 2020, 53(9): 1717-1729.
[7]	ZHOU QingYuan, WANG Qian, YE Sang, CUI MinSheng, LEI Wei, GAO HuanHuan, ZHAO YuFeng, XU XinFu, TANG ZhangLin, LI JiaNa, CUI Cui. Genome-Wide Association Analysis of Tribenuron-Methyl Tolerance Related Traits in Brassica napus L. Under Germination [J]. Scientia Agricultura Sinica, 2019, 52(3): 399-413.
[8]	HE YaJun, WU DaoMing, YOU JingCan, QIAN Wei. Genome-Wide Association Analysis of Salt Tolerance Related Traits in Brassica napus and Candidate Gene Prediction [J]. Scientia Agricultura Sinica, 2017, 50(7): 1189-1201.
[9]	WEI DaYong, TAN ChuanDong, CUI YiXin, WU DaoMing, LI JiaNa, MEI JiaQin, QIANWei. Genome-Wide Association Study of the Fertility Restorer Loci for pol CMS in Rapeseed (Brassica napus L.) [J]. Scientia Agricultura Sinica, 2017, 50(5): 802-810.
[10]	WANG Xiao, ZHANG Qin, YU Ying. Genome-Wide Association Study on Mastitis Resistance Based on Somatic Cell Scores in Chinese Holstein Cows [J]. Scientia Agricultura Sinica, 2017, 50(4): 755-763.
[11]	LIU Nian, SUN Yan-yan, BAI Hao, HUA Deng-ke, XUE Fu-guang, LIU Ran-ran, LI Dong-li, WEN Jie, CHEN Ji-lan . iTRAQ-Based Proteomic Analysis for Identification of Candidate Proteins Underlying Beak Deformity in Chickens [J]. Scientia Agricultura Sinica, 2015, 48(21): 4390-4396.
[12]	ZHOU Li-Sheng, YANG Jie, LIU Xian-Xian, ZHANG Zhi-Yan, YANG Bin, MA Jun-Wu. Genome-Wide Association Analyses for Musle pH 72 h Value and Meat Color Traits in Sutai Pigs [J]. Scientia Agricultura Sinica, 2014, 47(3): 564-573.
[13]	WANG Ji-Ying, WANG Hai-Xia, CHI Rui-Bin, GUO Jian-Feng, WU Ying. Progresses in Research of Genome-Wide Association Studies in Livestock and Poultry [J]. Scientia Agricultura Sinica, 2013, 46(4): 819-829.