利用全基因组高通量SNP标记定位二花脸×沙子岭家系中的断奶体重QTL

doi:10.3864/j.issn.0578-1752.2011.22.017

摘要/Abstract

摘要： 【目的】利用二花脸×沙子岭家系定位影响仔猪45日龄断奶体重的数量性状位点（quantitative trait loci，QTL）并搜寻QTL区间内与表型相关的位置候选基因，为最终鉴别因果基因奠定前期工作基础。【方法】构建二花脸×沙子岭猪F2资源家系，利用Illumina porcine 60k DNA芯片判定F2个体的基因型，对45日龄断奶体重表型进行全基因组连锁分析，定位影响二花脸×沙子岭家系F2家系仔猪45日龄断奶体重的QTL。在Ensemble（EMBL-EBI）和NCBI（National Center for Biotechnology Information）网站基因组数据库中搜寻相应的位置候选基因。【结果】在猪的2号染色体（sus scrofa chromosome 2，SSC2）上定位到了1个5%基因组水平显著的QTL，在猪的5号染色体（sus scrofa chromosome 5，SSC5）和猪的14号染色体（sus scrofa chromosome 14，SSC14）上分别定位到了1个1%基因组水平显著的QTL。在上述3个QTL区域内搜寻到了5个与仔猪45日龄断奶体重相关的候选基因，分别是SSC2上的CYP2R1、COPB1、PDE3B基因和SSC5上的NOP2、GDF3基因。【结论】本研究将影响二花脸×沙子岭家系仔猪45日龄断奶体重的QTL定位于SSC2、SSC5和SSC14，并揭示出5个与仔猪45日龄断奶体重相关的候选基因。

关键词: 猪, 断奶体重, QTL定位, 候选基因, 全基因组连锁分析

Abstract: 【Objective】An Erhualian×Shaziling F2 resource population was constructed to map quantitative trait loci (QTL) for liveweight of piglets at the weaning age of 45 days and identify positional candidate genes related to weaned liveweight, providing a start pointing to detect the causal genes in the future.【Method】The F2 resource population was constructed and genomic DNA of all weaned piglets was genotyped with Illumina porcine 60 k DNA chip. Whole-genome linkage analysis was conducted to detect QTL for liveweight of piglets weaned at day 45. Positional candidate genes were characterized from Ensemble (EMBL-EBI) and NCBI (National Center for Biotechnology Information) database.【Result】A total of 3 QTLs were detected for the measured phenotype including one 5% genome-wide QTL on sus scrofa chromosome 2 (SSC2) and one 1% genome-wide QTL on sus scrofa chromosome 5 (SSC5) and sus scrofa chromosome 14 (SSC14), respectively. Five candidate genes were identified, including CYP2R1, COPB1 and PDE3B on SSC2 and NOP2, GDF3 on SSC5. 【Conclusion】 The QTL for liveweight of piglets weaned at day 45 were mapped on SSC2, SSC5 and SSC14, and 5 positional candidate genes were identified.

Key words: swine, liveweight at weaning, QTL mapping, candidate gene, whole-genome linkage analysis

何余湧, 李完波, 张志燕, 杨明, 欧阳婧, 杨杰, 任军, 肖石军. 利用全基因组高通量SNP标记定位二花脸×沙子岭家系中的断奶体重QTL[J]. 中国农业科学, 2011, 44(22): 4694-4699.

HE Yu-Yong, LI Wan-Bo, ZHANG Zhi-Yan, YANG Ming, 欧Yang-Jing , YANG Jie, REN Jun, XIAO Shi-Jun. Detection of Quantitative Trait Loci for Live Weight at Weaning in an Erhualian×Shaziling Population Using Whole-Genome High-Density SNP Markers[J]. Scientia Agricultura Sinica, 2011, 44(22): 4694-4699.

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参考文献

[1]Wolter B F, Ellis M. The effects of weaning weight and rate of growth immediately after weaning on subsequent pig growth performance and carcass characteristics. Canadian Journal of Animal Science, 2001, 81: 363-369.

[2]Bidanel J P, Milan D, Iannuccelli N, Amigues Y, Boscher M Y, Bourgeois, Caritez J C, Gruand J, LeRoy P, Lagant H, Quintanilla, Renard C, Gellin J, Ollivier L, Chevalet C. Detection of quantitative trait loci for growth and fatness in pigs. Genetics Selection Evolution, 2001, 33: 289-309.

[3]Thomsen H, Lee H K, Rothschild M F, Malek M, Dekkers J C M. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine. Journal of Animal Science, 2004, 82(8): 2213-2228.

[4]Beeckmann P, Jr Schröffel J, Moser G, Bartenschlager H, Reiner G, Geldermann H. Linkage and QTL mapping for Sus scrofa Chromosome 3. Journal of Animal Breeding and Genetics, 2003, 120(1): 20-27.

[5]Cepica S, Stratil A, Kopecny M, Blazkova P, Jr Schröffel J, Davoli R, Fontanesi L, Reiner G, Bartenschlager H, Moser G, Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 4. Journal of Animal Breed Genetics, 2003, 120(1): 28-37.

[6]Ramos A M, Pita R H, Malek M, Lopes P S, Guimaraes S E F, Rothschild M F. Analysis of the mouse high-growth region in pigs. Journal of Animal Breeding and Genetics, 2009, 126(5): 404-412.

[7]Li X P, Do K T, Kim J J, Huang J, Zhao S H, Lee Y, Rothschild M F, Lee C K, Kim K S. Molecular characteristics of the porcine DLK1 and MEG3 genes. Animal Genetics, 2008, 39(2): 189-192.

[8]QTL for bodyweight (16 days and 21 days) in the pig genome. http://www.animalgenome.org/cgi-bin/QTLdb/SS/qtraitology?class_ID=4

[9]Liu G S, Kim J J, Jonas E, Wimmers K, Ponsuksili S, Murani E, Phatsara C, Tholen E, Juengst H, Tesfaye D, Chen J L, Schellander K. Combined line-cross and half-sib QTL analysis in Duroc–Pietrain population. Mammalian Genome, 2008, 19: 429-438.

[10]Sanchez M P, Riquet J, Iannuccelli N, Gogué J, Billon Y, Demeure O, Caritez J C, Burgaud G, Fève K, Bonnet M, Péry C, Lagant H, Le Roy P, Bidanel J P, Milan D. Effects of quantitative trait loci on chromosomes 1, 2, 4, and 7 on growth, carcass, and meat quality traits in backcross Meishan×Large White pigs. Journal of Animal Science, 2006, 84: 526-537.

[11]Wang L, Yu T P, Tuggle C K, Liu H C, Rothschild M F. A directed search for quantitative trait loci on chromosomes 4 and 7 in pigs. Journal of Animal Science, 1998, 76: 2560-2567.

[12]Liu G, Jennen D G J, Tholen E, Juengst H, Kleinwachter T, Holker M, Tesfaye D, Un G, Schreinemachers H J, Murani E, Ponsuksili S, Kim J J, Schellander K, Wimmers K. A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics, 2007, 38: 241-252.

[13]Guo Y M, Lee G J, Archibald A L, Haley C S. Quantitative trait loci for production traits in pigs: a combined analysis of two Meishan×Large White populations. Animal Genetics, 2008, 5: 486-495.

[14]Alfonso L, Haley C S. Power of different F2 schemes for QTL detection in livestock. Animal Science, 1998, 66: 1-8.

[15]Rothschild M F, Messer L, Day A, Wales R, Short T, Southwood O, Plastow G. Investigation of the retinol-binding protein 4(RBP4) gene as a candidate gene for increased litter size in pigs. Mammalian Genome, 2000, 11(1): 75-77.

[16]邵玉娟. 猪繁殖性状相关候选基因MAN2B2，MSR和RGS12的遗传效应分析[D]. 武汉: 华中农业大学, 2005.

Shao Y J. The genetic effect analysis of porcine MAN2B2, MSR, RGS12 gene affecting reproduction traits[D]. Wuhan: Huazhong Agricultural University, 2005. (in Chinese)

[17]李永辉. NCOA1基因与猪产仔性状的相关及序列分析[D]. 长沙: 湖南农业大学, 2005 .

Li Y H. The correlation of NCOA1 gene with litter size in swine and sequence analysis[D]. Changsha: Hunan Agricultural University, 2005. (in Chinese)

[18]武艳萍. 猪转化生长因子β1基因多态性与猪产仔数关系的研究[D]. 北京: 中国农业大学, 2005.

Wu Y P. Association of transforming growth factor-β1 gene polymorphisms with litter size in pigs[D]. Beijing: China Agricultural University, 2005. (in Chinese)

[19]张淑君, 熊远著, 邓昌彦, 郑嵘, 蒋思文, 肖森木, 夏瑜, 徐建祥, 刘晓华, 王春芳, 阮征, 宫时玉. 卵泡刺激素受体基因作为产仔数候选基因的研究. 华中农业大学学报, 2002(6): 506-508.

Zhang S J, Xiong Y Z, Deng C Y, Zheng R, Jiang S W, Xiao S M, Xia Y, Xu J X, Liu X H, Wang C F, Ruan Z, Gong S Y. Study on follicle stimulating hormone receptor as candidate gene for litter size in pigs. Journal of Hua Zhong Agricultural University, 2002(6): 506-508. (in Chinese)

[20]Ding N S, Ren D R, Guo Y M, Ren J, Yan Y, Ma J W, Chen K F, Huang L S. Genetic variation of porcine prostaglandin-endoperoxide synthase 2(PTGS2) gene and its association with reproductive traits in an Erhua lian×Duroc F2 population. Acta Genetica Sinica, 2006, 33(3): 213-219.

[21]Santana B A A, Biase F H, Antunes R C, Borges M, Franco M M, Goulart L R. Association of the estrogen receptor gene PvuII restriction polymorphism with expected progeny differences for reproductive and performance traits in swine herds in Brazil. Genetics and Molecular Biology, 2006, 2: 273-277.

[22]Linville R C, Pomp D, Johnson R K, Rothschild M F. Candidate gene analysis for loci affecting litter size and ovulation rate in swine. Journal of Animal Science, 2001, 79(1): 60-67.

[23]Cheng J B, Levine M A, Bell N H, Mangelsdorf D J, Russell D W. Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase. Proceedings of the National Academy of Sciences, 2004, 101(20): 7711-7715.

[24]Qiu H F, Xu X W, Fan B, Rothschild M F, MartinY, Liu B. Investigationof LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2. Molecular Biology Reports, 2010, 37(1): 629-636.

[25]Ahmad F, Lindh R, Tang Y, Weston M, Degerman E, Manganiello V C. Insulin-induced formation of macromolecular complexes involved in activation of cyclic nucleotide phosphodiesterase 3B(PDE3B) and its interaction with PKB. Biochemical Journal, 2007, 404(2): 257-268.

[26]Choi Y H, Park S, Hockman S, Zmuda-Trzebiatowska E, Svennelid F, Haluzik M, Gavrilova O, Ahmad F, Pepin L, Napolitano M, Taira M, Sundler F, Holst L S, Degerman E, Manganiello V C. Alterations in regulation of energy homeostasis in cyclic nucleotide phosphodiesterase 3B-null mice. Journal of Clinical Investigation, 2006,116: 3240-3251.

[27]Hong B, Wu K, Brockenbrough J S, Wu P, Aris J P. Temperature sensitive nop2 alleles defective in synthesis of 25S rRNA and large ribosomal subunits in Saccharomyces cerevisiae. Nucleic Acids Research, 2001, 29(14): 2927-2937.

[28]Andersson O, Korach-Andre M, Reissmann E, Ibáñez C F, Bertolino P. Growth/differentiation factor 3 signals through ALK7 and regulates accumulation of adipose tissue and diet-induced obesity. Proceedings of the National Academy of Sciences, 2008, 105(20): 7252-7256.