Abstract
The biological functions of long noncoding RNAs (lncRNAs), which play an important role in regulating development and gene expression, may be affected by variations in lncRNA gene loci or associated genomic sequences. However, the functions of many lncRNAs remain unknown. To analyse correlations between mutations in pouMU1 with chicken growth and carcass traits, 860 chickens from a Gushi \(\times \) Anka F2 resource population and 96 Lushi, Xichuan, Changshun and recessive white chickens were used to evaluate the genetic effect of the pouMU1 gene. We performed quantitative real-time polymerase chain reaction (qRT-PCR) to analyse the relative expression levels of pouMU1 in nine different tissues and stages of development. pouMU1 expression was highest in pectoralis and leg muscles, whereas no expression was observed in the heart, liver and abdominal fat. Using direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods, two novel sequence mutations (g.1198A>G and g.1238-1239del/insGA) were detected in the pouMU1 gene. SPSS software was used for statistical analysis in association studies. Based on the association data, the presence of both variants was significantly associated with leg muscle fibre width and leg muscle fibre roundness (\(P < 0.05\)) and highly associated with leg muscle fibre girth and body weight at 0 week of age (\(P < 0.01\)). These data suggest that pouMU1 might participate in regulating chicken muscle development and growth, and the findings offer new insight into the functions of sequence mutations in lncRNAs.
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Ardlie K. G., Kruglyak L. and Seielstad M. 2002 Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3, 299–309.
Baldassarre A. and Masotti A. 2012 Long non-coding RNAs and p53 regulation. Int. J. Mol. Sci. 13, 16708–16717.
Barrett J. C., Fry B., Maller J. and Daly M. J. 2005 Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265.
Batista P. J. and Chang, H. Y. 2013 Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298–1307.
Cabili M. N., Trapnell C., Goff L., Koziol M., Tazon-Vega B., Regev A. and Rinn J. L. 2011 Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915–1927.
Cesana M., Cacchiarelli D., Legnini I., Santini T., Sthandier O., Chinappi M. et al. 2011 A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358–369.
Chen J., Cui X., Shi C., Chen L., Yang L., Pang L. et al. 2015 Differential lncRNA expression profiles in brown and white adipose tissues. Mol. Genet. Genomics 290, 699–707.
Chen L. L. 2016 Linking long noncoding RNA localization and function. Trends Biochem. Sci. 41, 761–772.
Chen X., Hao Y., Cui Y., Fan Z., He S., Luo J. et al. 2016 LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics 33, 112–118.
Edwards C. A. and Ferguson-Smith A. C. 2007 Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol. 19, 281–289.
Esteller M. 2011 Non-coding RNAs in human disease. Nat. Rev. Genet. 12, 861–874.
Flynn R. A. and Chang H. Y. 2014 Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell 14, 752–761.
Goff L. A. and Rinn J. L. 2015 Linking RNA biology to lncRNAs. Genome Res. 25, 1456–1465.
Guttman M., Amit I., Garber M., French C., Lin M. F., Feldser D. et al. 2009 Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227.
Han R. L., Li Z. J., Li M. J., Li J. Q., Lan X. Y., Sun G. R. et al. 2011 Novel 9-bp indel in visfatin gene and its associations with chicken growth. Br. Poult. Sci. 52, 52–57.
Han R. L., Wei Y., Kang X. T., Chen H., Sun G. R., Li G. X. et al. 2012 Novel SNPs in the PRDM16 gene and their associations with performance traits in chickens. Mol. Biol. Rep. 39, 3153–3160.
Hrdlickova B., de Almeida R. C., Borek Z. and Withoff S. 2014 Genetic variation in the non-coding genome: involvement of micro-RNAs and long non-coding RNAs in disease. Biochim. Biophys. Acta 1842, 1910–1922.
Kashi K., Henderson L., Bonetti A. and Carninci P. 2016 Discovery and functional analysis of lncRNAs: methodologies to investigate an uncharacterized transcriptome. Biochim. Biophys. Acta 1859, 3–15.
Klattenhoff C. A., Scheuermann J. C., Surface L. E., Bradley R. K., Fields P. A., Steinhauser M. L. et al. 2013 Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152, 570–583.
Kretz M., Webster D. E., Flockhart R. J., Lee C. S., Zehnder A., Lopez-Pajares V. et al. 2012 Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev. 26, 338–343.
Kung J. T. Y., Colognori D. and Lee J. T. 2013 Long noncoding RNAs: past, present, and future. Genetics 193, 651–669.
Li H., Sun G. R., Lv S. J., Wei Y., Han R. L., Tian Y. D. 2012a Association study of polymorphisms inside the miR-1657 seed region with chicken growth and meat traits. Br. Poult. Sci. 53, 770–776.
Li H., Sun G. R., Tian Y. D., Han R. L., Li G. X. and Kang X., 2013 MicroRNAs-1614-3p gene seed region polymorphisms and association analysis with chicken production traits. J. Appl. Genet. 54, 209–213.
Li M., Sun X., Cai H., Sun Y., Plath M., Li C. et al. 2016 Long non-coding RNA ADNCR suppresses adipogenic differentiation by targeting miR-204. Biochim. Biophys. Acta Gene Regul. Mec. 1859, 871–882.
Li Z. J., Lan X. Y., Sun J. J., Wang J., Huang Y. Z., Guo W. J. et al. 2012b Molecular characterization and haplotype combination of PrRP gene polymorphism and its association with production traits in Chinese native goats. Small Rumin. Res. 105, 69–78.
Liu B. H. 1998 Statistical genomics: linkage, mapping, and QTL analysis. CRC Press, Boca Raton.
Lv S. J., Su L., Li H., Han R. L., Sun G. R. and Kang X. T. 2012 Polymorphisms of the interleukin-15 gene and their associations with fatness and muscle fibre traits in chickens. J. Appl. Genet. 53, 443–448.
Marty A., Amigues Y., Servin B., Renand G., Levéziel H. and Rocha D. 2010 Genetic variability and linkage disequilibrium patterns in the bovine DNAJA1 gene. Mol. Biotechnol. 44, 190–197.
Mei X., Kang X., Liu X., Jia L., Li H., Li Z. et al. 2016 Identification and SNP association analysis of a novel gene in chicken. Anim. Genet. 47, 125–127.
Mercer T. R., Dinger M. E. and Mattick J. S. 2009 Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 10, 155–159.
Nei M. and Roychoudhury A. K. 1974 Sampling variances of heterozygosity and genetic distance. Genetics 76, 379–390.
Papait R., Kunderfranco P., Stirparo G. G., Latronico M. V. and Condorelli G. 2013 Long noncoding RNA: a new player of heart failure?J. Cardiovasc. Transl. Res. 6, 876–883.
Pearson J. C., Lemons D. and McGinnis W. 2005 Modulating Hox gene functions during animal body patterning. Nat. Rev. Genet. 6, 893–904.
Quinn J. J. and Chang, H. Y. 2016 Unique features of long non-coding RNA biogenesis and function. Nat. Rev. Genet. 17, 47–62.
Qureshi I. A. and Mehler M. F. 2012 Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat. Rev. Neurosci. 13, 528–541.
Rinn J. L. and Chang H. Y. 2012 Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166.
Rohrer G. A., Freking B. A. and Nonneman D. 2007 Single nucleotide polymorphisms for pig identification and parentage exclusion. Anim. Genet. 38, 253–258.
Schmittgen T. D. and Livak K. J. 2008 Analyzing real-time PCR data by the comparative C(t) method. Nat. Protoc. 3, 1101–1108.
Stephens M., Smith N. J. and Donnelly P. 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978–989.
Wan L. B. and Bartolomei M. S. 2008 Regulation of imprinting in clusters: noncoding RNAs versus insulators.Adv. Genet. 61, 207–223.
Wang K. C. and Chang H. Y. 2011 Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914.
Wapinski O. and Chang H. Y. 2011 Long noncoding RNAs and human disease. Trends Cell Biol. 21, 354–361.
Yeh F. C., Yang R. and Boyle T. 1999 Microsoft Windows-based freeware for population genetic analysis. POPGENE. Release 1.31. University of Alberta, Edmonton.
Zhao H., Nettleton D. and Dekkers J. C. M. 2007 Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Genet. Res. 89, 1–6.
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This work was supported by the project funded by China Postdoctoral Science Foundation (no. 2014M552004), Programme for Innovation Research Team of Ministry of Education (no. IRT16R23) and Key Science and Technology Research Project of Henan Province (no. 151100110800).
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Ren, T., Zhou, Y., Zhou, Y. et al. Identification and association of novel lncRNA pouMU1 gene mutations with chicken performance traits. J Genet 96, 941–950 (2017). https://doi.org/10.1007/s12041-017-0858-8
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DOI: https://doi.org/10.1007/s12041-017-0858-8