Hostname: page-component-848d4c4894-x5gtn Total loading time: 0 Render date: 2024-06-01T18:47:20.683Z Has data issue: false hasContentIssue false
  • English
  • Français

Association analysis of SSTR2 copy number variation with cattle stature and its expression analysis in Chinese beef cattle

Published online by Cambridge University Press:  26 September 2019

J. Cheng ,
R. Jiang ,
X. K. Cao ,
M. Liu ,
Y. Z. Huang ,
X. Y. Lan ,
H. Cao ,
C. Z. Lei  and
H. Chen Open the ORCID record for H. Chen [Opens in a new window]
J. Cheng
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
R. Jiang
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
X. K. Cao
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
M. Liu
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
Y. Z. Huang
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
X. Y. Lan
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
H. Cao
Affiliation:
Shaanxi Kingbull Animal Husbandry Co., Ltd., Yangling, Shaanxi 712100, China
C. Z. Lei
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
H. Chen*
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
*
Author for correspondence: H. Chen, E-mail: chenhongnwsuaf@163.com
Get access Rights & Permissions [Opens in a new window]

Abstract

Copy number variations (CNVs), as an important source of genetic variation, can affect a wide range of phenotypes by diverse mechanisms. The somatostatin receptor 2 (SSTR2) gene plays important roles in cell proliferation and apoptosis. Recently, this gene was mapped to a CNV region, which encompasses quantitative trait loci of cattle economic traits including body weight, marbling score, etc. Therefore, SSTR2 CNV may exhibit phenotypic effects on cattle growth traits. In the current study, distribution of SSTR2 gene CNVs was investigated in six Chinese cattle breeds (XN, QC, NY, JA, LX and PN), and the results showed higher CNV polymorphisms in XN, QC and NY cattle. Next, association analysis between growth traits and SSTR2 CNV was performed for XN, QC and NY cattle. In NY, individuals with fewer copies showed better performance than those with more copies. Further, the effects of SSTR2 CNV on the SSTR2 mRNA level were also investigated, but revealed no significant correlation in either muscle or adipose tissue of adult NY cattle. The results suggested the potential for use of SSTR2 CNV as a marker for the molecular breeding of NY cattle.

Keywords

Association analysiscattle staturecopy number variationsmRNA expressionSSTR2
Type
Animal Research Paper
Information
The Journal of Agricultural Science , Volume 157 , Issue 4 , May 2019 , pp. 365 - 374
Copyright
Copyright © Cambridge University Press 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Altshuler, DM, Gibbs, RA, Peltonen, L, Dermitzakis, E, Schaffner, SF, Yu, F, Bonnen, PE, de Bakker, PIW, Deloukas, P, Gabriel, SB, Gwilliam, R, Hunt, S, Inouye, M, Jia, X, Palotie, A, Parkin, M, Whittaker, P, Chang, K, Hawes, A, Lewis, LR, Ren, Y, Wheeler, D, Muzny, DM, Barnes, C, Darvishi, K, Hurles, M, Korn, JM, Kristiansson, K, Lee, C, McCarroll, SA, Nemesh, J, Keinan, A, Montgomery, SB, Pollack, S, Price, AL, Soranzo, N, Gonzaga-Jauregui, C, Anttila, V, Brodeur, W, Daly, MJ, Leslie, S, McVean, G, Moutsianas, L, Nguyen, H, Zhang, Q, Ghori, MJR, McGinnis, R, McLaren, W, Takeuchi, F, Grossman, SR, Shlyakhter, I, Hostetter, EB, Sabeti, PC, Adebamowo, CA, Foster, MW, Gordon, DR, Licinio, J, Manca, MC, Marshall, PA, Matsuda, I, Ngare, D, Wang, VO, Reddy, D, Rotimi, CN, Royal, CD, Sharp, RR, Zeng, C, Brooks, LD, McEwen, JE and Int HapMap, C (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58.Google Scholar
Beckmann, JS, Estivill, X and Antonarakis, SE (2007) Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nature Reviews Genetics 8, 639–646.Google Scholar
Bennewitz, J, Reinsch, N, Guiard, V, Fritz, S, Thomsen, H, Looft, C, Kuhn, C, Schwerin, M, Weimann, C, Erhardt, G, Reinhardt, F, Reents, R, Boichard, D and Kalm, E (2004) Multiple quantitative trait loci mapping with cofactors and application of alternative variants of the false discovery rate in an enlarged granddaughter design. Genetics 168, 1019–1027.Google Scholar
Boichard, D, Grohs, C, Bourgeois, F, Cerqueira, F, Faugeras, R, Neau, A, Rupp, R, Amigues, Y, Boscher, MY and Leveziel, H (2003) Detection of genes influencing economic traits in three French dairy cattle breeds. Genetics Selection Evolution 35, 77–101.Google Scholar
Buscail, L, Esteve, JP, Saint-Laurent, N, Bertrand, V, Reisine, T, O'Carroll, AM, Bell, GI, Schally, AV, Vaysse, N and Susini, C (1995) Inhibition of cell proliferation by the somatostatin analogue RC-160 is mediated by somatostatin receptor subtypes SSTR2 and SSTR5 through different mechanisms. Proceedings of the National Academy of Sciences USA 92, 1580–1584.Google Scholar
Cao, XK, Huang, YZ, Ma, YL, Cheng, J, Qu, ZX, Ma, Y, Bai, YY, Tian, F, Lin, FP and Ma, YL (2018) Integrating CNVs into meta-QTL identified GBP4 as positional candidate for adult cattle stature. Functional & Integrative Genomics 18, 559–567.Google Scholar
Chen, JS, Liang, QM, Li, HS, Yang, J, Wang, S and Long, JW (2009) Octreotide inhibits growth of colonic cancer SW480 cells by modulating the Wnt/β-catenin pathway. Pharmazie: An International Journal of Pharmaceutical Sciences 64, 126–131.Google Scholar
Corbi-Botto, CM, Morales-Durand, H, Zappa, ME, Sadaba, SA, Peral-Garcia, P, Giovambattista, G and Diaz, S (2019) Genomic structural diversity in Criollo Argentino horses: analysis of copy number variations. Gene 695, 26–31.Google Scholar
Di Gerlando, R, Sardina, MT, Tolone, M, Sutera, AM, Mastrangelo, S and Portolano, B (2019) Genome-wide detection of copy-number variations in local cattle breeds. Animal Production Science 59, 815–822.Google Scholar
Doan, R, Cohen, N, Harrington, J, Veazey, K, Juras, R, Cothran, G, McCue, ME, Skow, L and Dindot, SV (2013) Identification of copy number variants in horses. Genome Research 22, 899–907.Google Scholar
Fontanesi, L, Martelli, PL, Beretti, F, Riggio, V, Dall'Olio, S, Colombo, M, Casadio, R, Russo, V and Portolano, B (2010) An initial comparative map of copy number variations in the goat (Capra hircus) genome. Bmc Genomics 11, 639.Google Scholar
Gilbert, R, Bailey, D and Shannon, N (1993) Linear body measurements of cattle before and after 20 years of selection for postweaning gain when fed two different diets. Journal of Animal Science 71, 1712–1720.Google Scholar
Guryev, V, Saar, K, Adamovic, T, Verheul, M, Van Heesch, SAAC, Cook, S, Pravenec, M, Aitman, T, Jacob, H, Shull, JD, Hubner, N and Cuppen, E (2008) Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538–545.Google Scholar
Henrichsen, CN, Chaignat, E and Reymond, A (2009) Copy number variants, diseases and gene expression. Human Molecular Genetics 18, R1–R8.Google Scholar
Heron, I, Thomas, F, Dero, M, Gancel, A, Ruiz, J, Schatz, B and Kuhn, J (1993) Pharmacokinetics and efficacy of a long-acting formulation of the new somatostatin analog BIM 23014 in patients with acromegaly. The Journal of Clinical Endocrinology & Metabolism 76, 721–727.Google Scholar
Hindson, BJ, Ness, KD, Masquelier, DA, Belgrader, P, Heredia, NJ, Makarewicz, AJ, Bright, IJ, Lucero, MY, Hiddessen, AL, Legler, TC, Kitano, TK, Hodel, MR, Petersen, JF, Wyatt, PW, Steenblock, ER, Shah, PH, Bousse, LJ, Troup, CB, Mellen, JC, Wittmann, DK, Erndt, NG, Cauley, TH, Koehler, RT, So, AP, Dube, S, Rose, KA, Montesclaros, L, Wang, S, Stumbo, DP, Hodges, SP, Romine, S, Milanovich, FP, White, HE, Regan, JF, Karlin-Neumann, GA, Hindson, CM, Saxonov, S and Colston, BW (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Analytical Chemistry 83, 8604–8610.Google Scholar
Hollox, EJ and Hoh, BP (2014) Human gene copy number variation and infectious disease. Human Genetics 133, 1217–1233.Google Scholar
Huang, H, Cao, J, Guo, G, Li, X, Wang, Y, Yu, Y, Zhang, S, Zhang, Q and Zhang, Y (2019) Genome-wide association study identifies QTLs for displacement of abomasum in Chinese Holstein cattle. Journal of Animal Science 97, 1133–1142.Google Scholar
Jiang, L, Jiang, J, Yang, J, Liu, X, Wang, J, Wang, H, Ding, X, Liu, J and Zhang, Q (2013) Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics 14, article no. 131. doi: https://doi.org/10.1186/1471-2164-14-131Google Scholar
Kader, A, Liu, X, Dong, K, Song, S, Pan, J, Yang, M, Chen, X, He, X, Jiang, L and Ma, Y (2016) Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array. Animal Genetics 47, 560–569.Google Scholar
Karczewski, KJ and Snyder, MP (2018) Integrative omics for health and disease. Nature Reviews Genetics 19, 299–310.Google Scholar
Karim, L, Takeda, H, Lin, L, Druet, T, Arias, JA, Baurain, D, Cambisano, N, Davis, SR, Farnir, F, Grisart, B, Harris, BL, Keehan, MD, Littlejohn, MD, Spelman, RJ, Georges, M and Coppieters, W (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics 43, 405–413.Google Scholar
Karimi, K, Esmailizadeh, A, Wu, DD and Gondro, C (2018) Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set. Animal Production Science 58, 1192–1200.Google Scholar
Liu, M, Li, B, Huang, Y, Yang, M, Lan, X, Lei, C, Qu, W, Bai, Y and Chen, H (2016) Copy number variation of bovine MAPK10 modulates the transcriptional activity and affects growth traits. Livestock Science 194, 44–50.Google Scholar
Liu, M, Zhou, Y, Rosen, BD, Van Tassell, CP, Stella, A, Tosser-Klopp, G, Rupp, R, Palhière, I, Colli, L, Sayre, B, Crepaldi, P, Fang, L, Mészáros, G, Chen, H and Liu, GE and the ADAPTmap Consortium (2018) Diversity of copy number variation in the worldwide goat population. Heredity 122, 636–646.Google Scholar
MacDonald, JR, Ziman, R, Yuen, RKC, Feuk, L and Scherer, SW (2014) The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Research 42, D986–D992.Google Scholar
McCarroll, SA and Altshuler, DM (2007) Copy-number variation and association studies of human disease. Nature Genetics 39(suppl), S37-S42.Google Scholar
McClure, MC, Morsci, NS, Schnabel, RD, Kim, JW, Yao, P, Rolf, MM, McKay, SD, Gregg, SJ, Chapple, RH, Northcutt, SL and Taylor, JF (2010) A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Animal Genetics 41, 597–607.Google Scholar
Mills, RE, Walter, K, Stewart, C, Handsaker, RE, Chen, K, Alkan, C, Abyzov, A, Yoon, SC, Ye, K, Cheetham, RK, Chinwalla, A, Conrad, DF, Fu, Y, Grubert, F, Hajirasouliha, I, Hormozdiari, F, Iakoucheva, LM, Iqbal, Z, Kang, S, Kidd, JM, Konkel, MK, Korn, J, Khurana, E, Kural, D, Lam, HYK, Leng, J, Li, R, Li, Y, Lin, CY, Luo, R, Mu, XJ, Nemesh, J, Peckham, HE, Rausch, T, Scally, A, Shi, X, Stromberg, MP, Stuetz, AM, Urban, AE, Walker, JA, Wu, J, Zhang, Y, Zhang, ZD, Batzer, MA, Ding, L, Marth, GT, McVean, G, Sebat, J, Snyder, M, Wang, J, Ye, K, Eichler, EE, Gerstein, MB, Hurles, ME, Lee, C, McCarroll, SA and Korbel, JO and 1000 Genomes Project (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470, 59–65.Google Scholar
Moemke, S, Scholz, H, Doll, K, Rehage, J and Distl, O (2008) Mapping quantitative trait loci for left-sided displacement of the abomasum in German Holstein dairy cows. Journal of Dairy Science 91, 4383–4392.Google Scholar
Olias, P, Adam, I, Meyer, A, Scharff, C and Gruber, AD (2014) Reference genes for quantitative gene expression studies in multiple avian species. PLoS ONE 9, article no. e99678. doi: 10.1371/journal.pone.0099678Google Scholar
Pang, AW, MacDonald, JR, Pinto, D, Wei, J, Rafiq, MA, Conrad, DF, Park, H, Hurles, ME, Lee, C, Venter, JC, Kirkness, EF, Levy, S, Feuk, L and Scherer, SW (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biology 11, article no. R52. doi: https://doi.org/10.1186/gb-2010-11-5-r52Google Scholar
Rauch, F, Lalic, L, Roughley, P and Glorieux, FH (2010) Relationship between genotype and skeletal phenotype in children and adolescents with osteogenesis imperfecta. Journal of Bone and Mineral Research 25, 1367–1374.Google Scholar
Ritchie, MD, Holzinger, ER, Li, R, Pendergrass, SA and Kim, D (2015) Methods of integrating data to uncover genotype–phenotype interactions. Nature Reviews Genetics 16, 85–97.Google Scholar
Sambrook, J, Russell, D and Russell, D (2001) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.Google Scholar
Sebat, J, Lakshmi, B, Troge, J, Alexander, J, Young, J, Lundin, P, Maner, 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 and Wigler, M (2004) Large-scale copy number polymorphism in the human genome. Science 305, 525–528.Google Scholar
Shi, T, Xu, Y, Yang, M, Huang, Y, Lan, X, Lei, C, Qi, X, Yang, X and Chen, H (2016) Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle. Animal Science Journal 87, 336–343.Google Scholar
Wang, X, Nahashon, S, Feaster, TK, Bohannon-Stewart, A and Adefope, N (2010) An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 11, article no. 351. doi: https://doi.org/10.1186/1471-2164-11-351Google Scholar
Wang, J, Wang, H, Jiang, J, Kang, H, Feng, X, Zhang, Q and Liu, JF (2013 a) Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays. PLoS ONE 8, article no. e68683. doi: 10.1371/journal.pone.0068683Google Scholar
Wang, S, Bao, Z, Liang, QM, Long, JW, Xiao, ZS, Jiang, ZJ, Liu, B, Yang, J and Long, ZX (2013 b) Octreotide stimulates somatostatin receptor-induced apoptosis of SW480 colon cancer cells by activation of glycogen synthase kinase-3β, A Wnt/β-catenin pathway modulator. Hepato-gastroenterology 60, 1639–1646.Google Scholar
Wang, J, Jiang, J, Wang, H, Kang, H, Zhang, Q and Liu, JF (2014) Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds. PLoS ONE 9, article no. e87571. doi: 10.1371/journal.pone.0087571Google Scholar
Xu, Y, Zhang, L, Shi, T, Zhou, Y, Cai, H, Lan, X, Zhang, C, Lei, C and Chen, H (2013) Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle. Mammalian Genome 24, 508–516.Google Scholar
Xu, Y, Jiang, Y, Shi, T, Cai, H, Lan, X, Zhao, X, Plath, M and Chen, H (2017) Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds. PLoS ONE 12, article no. e0183921. doi: 10.1371/journal.pone.0183921Google Scholar
Yalcin, B, Wong, K, Agam, A, Goodson, M, Keane, TM, Gan, X, Nellaker, C, Goodstadt, L, Nicod, J, Bhomra, A, Hernandez-Pliego, P, Whitley, H, Cleak, J, Dutton, R, Janowitz, D, Mott, R, Adams, DJ and Flint, J (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477, 326–329.Google Scholar
Yamada, Y, Post, SR, Wang, K, Tager, HS, Bell, GI and Seino, S (1992 a) Cloning and functional characterization of a family of human and mouse somatostatin receptors expressed in brain, gastrointestinal tract, and kidney. Proceedings of the National Academy of Sciences USA 89, 251–255.Google Scholar
Yamada, Y, Reisine, T, Law, SF, Ihara, Y, Kubota, A, Kagimoto, S, Seino, M, Seino, Y, Bell, GI and Seino, S (1992 b) Somatostatin receptors, an expanding gene family: cloning and functional characterization of human SSTR3, a protein coupled to adenylyl cyclase. Molecular Endocrinology 6, 2136–2142.Google Scholar
Yamada, Y, Kagimoto, S, Kubota, A, Yasuda, K, Masuda, K, Someya, Y, Ihara, Y, Li, Q, Imura, H, Seino, S and Y, S (1993) Cloning, functional expression and pharmacological characterization of a fourth (hSSTR4) and a fifth (hSSTR5) human somatostatin receptor subtype. Biochemical and Biophysical Research Communications 195, 844–852.Google Scholar
Yang, L, Xu, L, Zhu, B, Niu, H, Zhang, W, Miao, J, Shi, X, Zhang, M, Chen, Y, Zhang, L, Gao, X, Gao, H, Li, L, Liu, GE and Li, J (2017 a) Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese cattle. Scientific Reports 7, article no. 14299. doi: https://doi.org/10.1038/s41598-017-14768-0Google Scholar
Yang, M, Lv, J, Zhang, L, Li, M, Zhou, Y, Lan, X, Lei, C and Chen, H (2017 b) Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle. Scientific Reports 7, article no. 46599. doi: 10.1038/srep46599Google Scholar
Zhang, F, Gu, W, Hurles, ME and Lupski, JR (2009) Copy number variation in human health, disease, and evolution. Annual Review of Genomics and Human Genetics 10, 451–481.Google Scholar
Zhang, L, Jia, S, Yang, M, Xu, Y, Li, C, Sun, J, Huang, Y, Lan, X, Lei, C, Zhou, Y, Zhang, C, Zhao, X and Chen, H (2014) Detection of copy number variations and their effects in Chinese bulls. BMC Genomics 15, article no. 480. doi: https://doi.org/10.1186/1471-2164-15-480Google Scholar
Zhang, RQ, Wang, JJ, Zhang, T, Zhai, HL and Shen, W (2019) Copy-number variation in goat genome sequence: a comparative analysis of the different litter size trait groups. Gene 696, 40–46.Google Scholar
Zheng, X, Kuang, Y, Lv, W, Cao, D, Sun, Z, Jin, W and Sun, X (2017) Quantitative trait loci for morphometric traits in multiple families of common carp (Cyprinus carpio). Science China Life Sciences 60, 287–297.Google Scholar