猪13号染色体上拷贝数变异区内基因信息发掘及遗传规律分析

doi:10.3724/SP.J.1005.2014.0354

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HEREDITAS ›› 2014, Vol. 36 ›› Issue (4): 354-359.doi: 10.3724/SP.J.1005.2014.0354

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Investigation of genes within copy number variation regions in pig chromosome 13 and analysis of the genetic law

Jing Liu, Yanan Wang, Yaqi Sun, Hongyang Wang, Chao Wang, Zhongzhen Peng, Bang Liu

Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China

Received:2013-10-14 Revised:2014-12-30 Online:2014-04-20 Published:2014-03-20

Abstract

Abstract:

Copy number variation (CNV), referring to a genome structure variation, has attracted researchers’ great interests. Thirty-two CNV regions (CNV region, CNVR) have been detected on chromosome 13 in our previous work. In order to detect the genes located in these CNVRs, we first obtained the annotated information from Ensembl database, and searched gene functional enrichments using DAVID online tools. In the 32 CNVRs, a total of 236 genes were identified, in which 169 genes were annotated. Gene Ontology (GO) analysis revealed that these genes mainly participate in proteolysis, cell adhesion, and macromolecular catabolic process. To study the genetic law of these CNVs, we chose the RCAN1 (regulators of calcineurin 1) gene as the candidate. We quantified the copy number of RCAN1 gene in 38 Laiwu pigs by using QPCR method, and analyzed the genetic laws in three Laiwu families including 15 pigs. QPCR results showed that both duplication and deletion occurred in RCAN1 gene among Laiwu pigs and the heredity mode corresponds with Mendelian genetic law.

Key words: copy number variation, chromosome 13, RCAN1 gene, genetic law, Laiwu pigs

Jing Liu, Yanan Wang, Yaqi Sun, Hongyang Wang, Chao Wang, Zhongzhen Peng, Bang Liu. Investigation of genes within copy number variation regions in pig chromosome 13 and analysis of the genetic law[J]. HEREDITAS, 2014, 36(4): 354-359.

References

[1] Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Månér S, Massa H, Walker M, Chi MY, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. Large-scale copy number polymorphism in the human genome. Sci-ence, 2004, 305(5683): 525–528 <\p>

[2] Lupski JR, Stankiewicz P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet, 2005, 1(6): e49. <\p>

[3] McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM. Common deletion polymorphisms in the human genome. Nat Genet, 2006, 38(1): 86−92. <\p>

[4] Kleinjan DA, van Heyningen V. Long–range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet, 2005, 76(1): 8−32. <\p>

[5] 余少波. 猪全基因组CNV发掘与CNV图谱构建<\p>

[学位论文]. 华中农业大学, 2011. <\p>

[6] Ballester M, Castelló A, Ibáñez E, Sánchez A, Folch JM. Real–time quantitative PCR–based system for determining transgene copy number in transgenic animals. Biotechniques, 2004, 37(4): 610–613. <\p>

[7] Li Y, Mei SQ, Zhang XY, Peng XW, Liu G, Tao H, Wu HY, Jiang SW, Xiong YZ, Li FG. Identification of ge-nome–wide copy number variations among diverse pig breeds by array CGH. BMC Genomics, 2012, 13(1): 725. <\p>

[8] Liu JS, Zhang L, Xu LY, Ren HX, Lu J, Zhang XN, Zhang SF, Zhou XL, Wei CH, Zhao FP, Du LX. Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. BMC Genomics, 2013, 14(1): 229. <\p>

[9] Liu GE, Hou YL, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, de A Regitano LC, Smith TPL, Song JZ, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW. Analysis of copy number varia-tions among diverse cattle breeds. Genome Res, 2010, 20(5): 693–703. <\p>

[10] Wang JY, Jiang JC, Fu WX, Jiang L, Ding XD, Liu JF, Zhang Q. A genome–wide detection of copy number variations using SNP genotyping arrays in swine. BMC Genomics, 2012, 13(1): 273. <\p>

[11] Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high–resolution survey of deletion polymorphism in the human genome. Nat Genet, 2006, 38(1): 75–81. <\p>

[12] Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler–Smith C, Hurles ME, Carter NP, Scherer SW, Lee C. Copy number variation: New insights in genome diversity. Genome Res, 2006, 16(8): 949–961. <\p>

[13] 曾勇庆, 王根林, 魏述东, 王林云, 杨海玲, 曹洪防, 徐云华. 含不同比例莱芜猪血缘杂交猪胴体品质及肉质特性的研究. 遗传, 2005, 27(1): 65–69. <\p>

[14] Park JK, Oh YH, Chung KC. Two key genes closely impli-cated with the neuropathological characteristics in Down syndrome: DYRK1A and RCAN1. BMB Rep, 2009, 42(1): 6–15. <\p>

[15] Ermak G, Sojitra S, Yin F, Cadenas E, Cuervo AM, Davies KJ. Chronic expression of RCAN1–1L protein induces mitochondrial autophagy and metabolic shift from oxida-tive phosphorylation to glycolysis in neuronal cells. J Biol Chem, 2012, 287(17): 14088–14098.<\p>

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Investigation of genes within copy number variation regions in pig chromosome 13 and analysis of the genetic law

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