Scientia Agricultura Sinica ›› 2012, Vol. 45 ›› Issue (19): 4075-4083.doi: 10.3864/j.issn.0578-1752.2012.19.020

• ANIMAL SCIENCE·RESOURCE INSECT • Previous Articles     Next Articles

Genome-Wide Association Study and Positional Candidate Gene Analysis on Age at Puberty of Gilts

 LI  Ping-Hua, LI  Jie, YANG  Zhu-Qing, ZHANG  Zhi-Yan, YANG  Bin, CHEN  Cong-Ying   

  1. 1.江西农业大学动物生物技术国家重点实验室培育基地，南昌 330045
  • Received:2012-02-20 Online:2012-10-01 Published:2012-06-13

PDF

1412

Cited

1

Abstract: 【Objective】Isolation and characterization of the causative gene or molecular marker for age at puberty will contribute to the selection and breeding of sows.【Method】The materials used in this study were F2 gilts from a white Duroc × Erhualian F2 resource population. F0, F1 and 316 well phenotyped F2 gilts were genotyped with Illumina porcine 60K SNP chip. Genome-wide association study (GWAS) and linkage and linkage-disequilibrium analysis (LDLA) were carried out to detect SNPs or haplotypes that were significantly associated with age at puberty of gilts. The associations of 3 SNPs within two candidate genes of Lin-28 Homolog B (LIN28B) and Trans-membrane Protein 38B (TMEM38B) with age at puberty of gilts were evaluated by standard association test, marker-assisted association test and F-drop test.【Result】The results from GWAS showed that the ASGA0032316 was the most significant SNP that was associated with age at puberty. It is located at 33.07 Mb of pig chromosome 7 (SSC7)  and exactly within the intron region of RAB23. At the same instant, several significant SNPs were also detected on chromosomes 1, 6, 12, 15 and 17. The results from LDLA analysis showed that all haplotypes that were associated with age at puberty at genome-wide significance level were located on SSC7. The most significant haplotype was located at 38.39-38.47 Mb and within the intergenic region of F1RVR7 and ZFAND3. In association analyses of positional candidate genes, although 3 SNPs from LIN28B and TMEM38B were significantly associated with age at puberty in standard association test (P＜0.05), it was not achieved significance level both in the marker-assisted association test and F-drop test (P＞0.05). 【Conclusion】The SNP and haplotype that were most significantly associated with age at puberty of gilts was detected on SSC7. Several other significantly associated SNPs were also detected on chromosomes 1, 6, 12, 15 and 17. The results from association tests suggested that LIN28B or TMEM38B gene on SSC1 is not the quantitative trait gene for age at puberty, or more SNPs from two genes need to be further analyzed.

Key words: age at puberty of gilts, genome-wide association study, linkage and linkage-disequilibrium analysis, positional candidate gene

[1]Rohrer G A, Ford J J, Wise T H. Identification of quantitative trait loci affecting female reproductive traits in a multigenetation Meishan-White composite swine population. Journal of Animal Science, 1999, 77(6): 1385-1391.

[2]Cassady J P, Johnson R K, Pomp D, Rohrer G A, van Vleck L D, Spiegel E K, Gilson K M. Identification of quantitative trait loci affecting reproductive in pigs. Journal of Animal Science, 2001, 79(3): 623-633.

[3]Holl J W, Cassady J P, Pomp D, Johnson R K. A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs. Journal of Animal Science, 2004, 82(12): 3421-3429.

[4]Yang G C, Ren J, Li S J, Mao H R, Guo Y M, Zou Z Z, Ren D R, Ma J W, Huang L S. Genome-wide identification of QTL for age at puberty in gilts using a large intercross F2 population between White Duroc×Erhualian. Genetics Selection Evolution, 2008, 40(5): 529-539.

[5]Seminara S B, Messager S, Chatzidaki E E, Thresher R R, Acierno J S, Shagoury J K, Bo-Abbas Y, Kuohung W, Schwinof K M, Hendrick A G, Zahn D, Dixon J, Kaiser U B, Slaugenhaupt S A, Gusella J F, ORahilly S, Carlton M B L, Crowley W F, Aparicio S A J R, Ch B, Colledge W H. The GPR54 as a regulator of puberty. The New England Journal of Medicine, 2003, 349(17): 1614-1627.

[6]Kaiser B U, Kuohung W. KiSS-1 and GPR54 as new players in gonadotropin regulation and puberty. Endocrine, 2005, 26(3): 277-284.

[7]李世军. 猪初情期候选基因IGFALS和KISS1R 的定位、全长基因分离、表达和遗传多态鉴别研究[D]. 南昌: 江西农业大学, 2006.

Li S J. Mapping, isolation and molecular characterization of IGFALS and KISS1R gene as two candidate genes for age at puberty in gilts[D]. Nanchang: Jiangxi Agricultural University, 2006.

[8]Stavrou I, Zois C, Ioannidis J P A, Tsatsoulis A. Association of polymorphisms of the oestrogen receptor alpha gene with the age of menarche. Human Reproduction, 2002, 17(4): 1101-1105.

[9]Long J R, Xu H, Zhao L J, Liu P Y, Shen H, Liu Y J, Xiong D H, Xiao P, Liu Y Z, Dvornyk V, Li J L, Recker R R, Deng H W. The oestrogen receptor alpha gene is linked and/or associated with age of menarche in different ethnic groups. Journal of Medical Genetics, 2005, 42(10): 796-800.

[10]Xita N, Tsatsoulis A, Stavrou I, Georgiou I. Association of SHBG gene polymorphism with menarche. Molecular Human Reproduction, 2005, 11(6): 459-462.

[11]Domene H M, Bengolea S V, Martinez A S, Ropelato M G, Pennisi P, Scaglia P, Heinrich J J, Jasper H G. Deficiency of the circulating insulin-like growth factor system associated with inactivation of the acid-labile subunit gene. The New England Journal of Medicine, 2004, 350(6): 570-577.

[12]Li S, Ren J, Huang L S. Characterization of the porcine insulin-like growth factor binding protein, acid-labile subunit gene: full-length cDNA and DNA sequence, polymorphisms and expression profile. Journal of Animal Breeding Genetics, 2007, 124(3): 133-138.

[13]Sedlmeyer I L, Pearce C L, Trueman J A, Butler J L, Bersaglieri T, Read A P, Clayton P E, Kolonel L N, Henderson B E, Hirschhorn J N, Palmert M R. Determination of sequence variation and haplotype structure for the gonadotropin-releasing hormone (GnRH) and GnRH receptor genes: investigation of role in pubertal timing. The Journal of Clinical Endocrinology and Metabolism, 2005, 90(2): 1091-1099.

[14]Jorm A F, Christensen H, Rodgers B, Jacomb P A, Easteal S. Association of adverse childhood experiences, age of menarche, and adult reproductive behavior: does the androgen receptor gene play a role? American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 2004, 125B(1): 105-111.

[15]Sharp L, Cardy A H, Cotton S C, Little J. CYP17 gene polymorphisms: prevalence and associations with hormone levels and related factors. a HuGE review. American Journal of Epidemiology, 2004, 160(8): 729-740.

[16]Gorai I, Tanaka K, Inada M, Morinaga H, Uchiyama Y, Kikuchi R, Chaki O, Hirahara F. Estrogen-metabolizing gene polymorphisms, but not estrogen receptor-alpha gene polymorphisms, are associated with the onset of menarche in healthy postmenopausal Japanese women. The Journal of Clinical Endocrinology and Metabolism, 2003, 88(2): 799-803.

[17]Lai J, Vesprini D, Chu W, Jernstrom H, Narod S A. CYP gene polymorphisms and early menarche. Molecular Genetics and Metabolism, 2001, 74(4): 449-457.

[18]Nonneman D J, Wise T H, Ford J J, Kuehn L A, Rohrer G A. Characterization of the aldo-keto reductase 1C gene cluster on pig chromosome 10: possible associations with reproductive traits. BMC Veterinary Research, 2006, 2: 28.

[19]Viswanathan S R, Daley G Q, Gregory R I. Selective blockade of microRNA processing by Lin28. Science, 2008, 320(5872): 97-100.

[20]Ong K K, Elks C E, Li S X, Zhao J H, Luan J A, Andersen L B, Bingham S A, Brage S, Smith G D, Ekelund U, Gillson C J, Glaser B, Golding J, Hardy R, Khaw K T, Kuh D, Luben R, Marcus M, McGeehin M A, Ness A R, Northstone K, Ring S M, Rubin C, Sims M A, Song K, Strachan D P, Vollenweider P, Waeber G, Waterworth D M, Wong A, Deloukas P, Barroso I, Mooser V, Loos R J, Wareham N J. Genetic variation in LIN28B is associated with the timing of puberty. Nature Genetics, 2009, 41(6): 729-733.

[21]Sulem P, Gudbjartsson D F, Rafnar T, Holm H, Olafsdottir E J, Olafsdottir G H, Jonsson T, Alexandersen P, Feenstra B, Boyd H A, Aben K K, Verbeek A L M, Roeleveld N, Jonasdottir A, Styrkarsdottir U, Steinthorsdottir V, Karason A, Stacey S N, Gudmundsson J, Jakobsdottir M, Thorleifsson G, Hardarson G, Gulcher J, Kong A, Kiemeney L A, Melbye M, Christiansen C, Tryggvadottir L, Thorsteinsdottir U, Stefansson K. Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche. Nature Genetics, 2009, 41(6): 734-738.

[22]Perry J R B, Stolk L, Franceschini N, Lunetta K L, Zhai G J, McArdle P F, Smith A V, Aspelund T, Bandinelli S, Boerwinkle E, Cherkas L, Eiriksdottir G, Estrada K, Ferrucci L, Folsom A R, Garcia M, Gudnason V, Hofman A, Karasik D, Kiel D P, Launer L J, Meurs J V, Nalls M A, Rivadeneira F, Shuldiner A R. Meta-analysis of genome-wide association data identifies two loci influencing age at menarche. Nature Genetics, 2009, 41(6): 648-650.

[23]Ren J, Guo Y M, Ma J W, Huang L S. Growth and Meat Quality QLT in Pigs with Special Reference to a Very Large White Duroc×Erhualian Resource Population. Proceedings of the 8th World Congress on Genetics Applied in Livestock Production, 2006: 13-11.

[24]陈从英, 朱万成, 李平华, 魏  娜, 郭源梅, 高  军. 催乳素(PRL)和催乳素受体(PRLR)基因在白色杜洛克×二花脸F2资源群体中的遗传变异及其与母猪杀婴行为和产仔数的关联性. 中国农业科学, 2010, 43(11): 2347-2354.

Chen C Y, Zhu W C, Li P H, Wei N, Guo Y M, Gao J. Associations of porcine prolactin (PRL) and prolactin receptor (PRLR) with sow maternal infanticide behavior and litter size in a White Duroc × Erhualian F2 resource population. Scientia Agricultura Sinica, 2010, 43(11): 2347-2354. (in Chinese)

[25]Elisson L. Relationships between puberty and production traits in the gilt. 2. Oestroous symptoms at puberty. Animal Reproduction Science, 1991, 25(3): 255-264.

[26]Noguera J L, Rodríguez C, Varona L, Tomãs A, Muñoz G, Ramirez O, Barragán C, Arquá M, Bidanel J P, Amills M, Ovilo C, Sánchez A. A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL. BMC Genomics, 2009, 10: 636-647.

[27]Zhao H H, Rothschild M F, Fernando R L, Dekkers J C M. Tests of candidate genes in breed cross populations for QTL mapping in livestock. Mammalian Genome, 2003, 14(7): 472-482.

[28]Ng E L, Tang B L. Rab GTPases and their roles in brain neurons and glia. Brain Research Reviews, 2008, 58(1): 236-246.
[1] ZHOU GuangFei, MA Liang, MA Lu, ZHANG ShuYu, ZHANG HuiMin, SONG XuDong, ZHANG ZhenLiang, LU HuHua, HAO DeRong, MAO YuXiang, XUE Lin, CHEN GuoQing. Genome-Wide Association Study of Husk Traits in Maize [J]. Scientia Agricultura Sinica, 2025, 58(3): 431-442.
[2] LI Ming, CHENG YuKun, BAI Bin, LEI Bin, GENG HongWei. Genome-Wide Association Study on Spike Architecture Traits and Elite Haplotype Mining in Winter Wheat [J]. Scientia Agricultura Sinica, 2025, 58(18): 3583-3597.
[3] XIANG AiHui, BAI RongJi, HAO YuQiong, ZHAO JiaJia, WU BangBang, LI XiaoHua, ZHENG XingWei, GUAN PanFeng, ZHENG Jun. Identification of Dwarf Genes and Mining of Plant Height Genetic Loci in Shanxi Wheat [J]. Scientia Agricultura Sinica, 2025, 58(17): 3372-3388.
[4] ZHENG MinHua, CHEN Luo, XING JiaLe, XIE YueLan, JIANG XianYa, NIE Shuai, CAI FuGe, WU HaoXiang, LU ZhanHua, SUN Wei, HUO Xing, BAI Song, ZHAO JunLiang, YANG Wu. Genome-Wide Association Study and Genetic Improvement Study of Rice Blast Resistance [J]. Scientia Agricultura Sinica, 2025, 58(14): 2707-2719.
[5] LI Ning, GAO LiFeng, HUANG Xin, SHI HuaWei, YANG JinWen, SHI YuGang, CHEN Ming, JIA JiZeng, SUN DaiZhen. Screening of Wheat Varieties with Low Nitrogen Tolerance and Genome-Wide Association Studies of Low Nitrogen Stress Tolerance Index [J]. Scientia Agricultura Sinica, 2025, 58(13): 2487-2503.
[6] ZHAO ZhenJian, WANG Kai, CHEN Dong, SHEN Qi, YU Yang, CUI ShengDi, WANG JunGe, CHEN ZiYang, YU ShiXin, CHEN JiaMiao, WANG XiangFeng, TANG GuoQing. Integrated Aanalysis of Genome and DNA Methylation for Screening Key Genes Related to Pork Quality Traits [J]. Scientia Agricultura Sinica, 2024, 57(7): 1394-1406.
[7] SHOU XinYue, LIU Zhi, CHEN YueHan, LI ChenHui, SUN BinCheng, SUN RuJian, HAN DeZhi, LU WenCheng, SHEN YongHui, WANG XiaoBo, YAN Long. Genome-Wide Association Analysis of Soybean Nodulation-Related Traits in the Northern Hebei [J]. Scientia Agricultura Sinica, 2024, 57(11): 2102-2113.
[8] TAN LiZhi, ZHAO YiQiang. Principle, Optimization and Application of Mixed Models in Genome- Wide Association Study [J]. Scientia Agricultura Sinica, 2023, 56(9): 1617-1632.
[9] YANG MingLu, ZHANG HaiLiang, LUO HanPeng, HUANG XiXia, ZHANG HanLin, ZHANG ShiShi, WANG Yan, LIU Lin, GUO Gang, WANG YaChun. Estimation of Genetic Parameters and Genome-Wide Association Study of Heat Indicators in Holstein Cattle Based on Collar-Mounted Device [J]. Scientia Agricultura Sinica, 2023, 56(5): 995-1006.
[10] WANG Mai, DONG QingFeng, GAO ShenAo, LIU DeZheng, LU Shan, QIAO PengFang, CHEN Liang, HU YinGang. Genome-Wide Association Studies and Mining for Favorable Loci of Root Traits at Seedling Stage in Wheat [J]. Scientia Agricultura Sinica, 2023, 56(5): 801-820.
[11] YANG ShengNan, CHENG Li, TAN YueXia, ZHU YanSong, JIANG Dong. Genome Wide Association Study for Resistance to Citrus Brown Spot Disease [J]. Scientia Agricultura Sinica, 2023, 56(18): 3642-3654.
[12] BaoHua CHU,FuGuo CAO,NingNing BIAN,Qian QIAN,ZhongXing LI,XueWei LI,ZeYuan LIU,FengWang MA,QingMei GUAN. Resistant Evaluation of 84 Apple Cultivars to Alternaria alternata f. sp. mali and Genome-Wide Association Analysis [J]. Scientia Agricultura Sinica, 2022, 55(18): 3613-3628.
[13] CHANG LiGuo,HE KunHui,LIU JianChao. Mining of Genetic Locus of Maize Stay-Green Related Traits Under Multi-Environments [J]. Scientia Agricultura Sinica, 2022, 55(16): 3071-3081.
[14] ZHANG LinLin,ZHI Hui,TANG Sha,ZHANG RenLiang,ZHANG Wei,JIA GuanQing,DIAO XianMin. Characterizations of Transcriptional and Haplotypic Variations of SiTOC1 in Foxtail Millet [J]. Scientia Agricultura Sinica, 2021, 54(11): 2273-2286.
[15] WANG JiQing,REN Yi,SHI XiaoLei,WANG LiLi,ZHANG XinZhong,SULITAN· GuZhaLiAYi,XIE Lei,GENG HongWei. Genome-Wide Association Analysis of Superoxide Dismutase (SOD) Activity in Wheat Grain [J]. Scientia Agricultura Sinica, 2021, 54(11): 2249-2260.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd