title: Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing.
abstract: BACKGROUND
  Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics have led to the identification of several genetic markers associated with genes affecting economic traits. Until recently, the identification of the causative genetic variants involved in the phenotypes of interest has remained a difficult task. The advent of novel sequencing technologies now offers a new opportunity for the identification of such variants. Despite sequencing costs plummeting, sequencing whole-genomes or large targeted regions is still too expensive for most laboratories. A transcriptomic-based sequencing approach offers a cheaper alternative to identify a large number of polymorphisms and possibly to discover causative variants. In the present study, we performed a gene-based single nucleotide polymorphism (SNP) discovery analysis in bovine Longissimus thoraci, using RNA-Seq. To our knowledge, this represents the first study done in bovine muscle.
  
  
  RESULTS
  Messenger RNAs from Longissimus thoraci from three Limousin bull calves were subjected to high-throughput sequencing. Approximately 36-46 million paired-end reads were obtained per library. A total of 19,752 transcripts were identified and 34,376 different SNPs were detected. Fifty-five percent of the SNPs were found in coding regions and ~22% resulted in an amino acid change. Applying a very stringent SNP quality threshold, we detected 8,407 different high-confidence SNPs, 18% of which are non synonymous coding SNPs. To analyse the accuracy of RNA-Seq technology for SNP detection, 48 SNPs were selected for validation by genotyping. No discrepancies were observed when using the highest SNP probability threshold. To test the usefulness of the identified SNPs, the 48 selected SNPs were assessed by genotyping 93 bovine samples, representing mostly the nine major breeds used in France. Principal component analysis indicates a clear separation between the nine populations.
  
  
  CONCLUSIONS
  The RNA-Seq data and the collection of newly discovered coding SNPs improve the genomic resources available for cattle, especially for beef breeds. The large amount of variation present in genes expressed in Limousin Longissimus thoracis, especially the large number of non synonymous coding SNPs, may prove useful to study the mechanisms underlying the genetic variability of meat quality traits.
authors: INRA, UMR 1313 GABI, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France.
authors: Anis
authors: A
authors: Djari
authors: Diane
authors: D
authors: Esquerré
authors: Bernard
authors: B
authors: Weiss
authors: Frédéric
authors: F
authors: Martins
authors: Cédric
authors: C
authors: Meersseman
authors: Mekki
authors: M
authors: Boussaha
authors: Christophe
authors: C
authors: Klopp
authors: Dominique
authors: D
authors: Rocha
mesh_terms: D000483:Alleles; D000818:Animals; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D005787:Gene Frequency; D005819:Genetic Markers; D005828:Genetics, Population; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D018482:Muscle, Skeletal / Q000378:metabolism*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
references: Bioinformatics. 2008 Aug 15;24(16):1757-64
references: 18567917
references: Nature. 2003 Oct 23;425(6960):832-6
references: 14574411
references: Gene Regul Syst Bio. 2012;6:67-80
references: 22654504
references: J Anim Sci. 2009 May;87(5):1576-81
references: 19213716
references: BMC Genomics. 2011 Feb 10;12:103
references: 21310019
references: Biochem Biophys Res Commun. 2004 Mar 12;315(3):525-31
references: 14975732
references: Nat Rev Genet. 2010 Aug;11(8):533-8
references: 20567245
references: J Hered. 2012 May-Jun;103(3):342-8
references: 22315242
references: Nat Genet. 1997 Sep;17(1):71-4
references: 9288100
references: Genome Res. 2009 Sep;19(9):1527-41
references: 19546169
references: Genetics. 2001 Nov;159(3):1151-62
references: 11729159
references: J Anim Breed Genet. 2011 Jun;128(3):201-8
references: 21554414
references: Bioinformatics. 2009 Jul 15;25(14):1754-60
references: 19451168
references: Vet Res. 2011 Nov 30;42:114
references: 22129081
references: Science. 2009 Apr 24;324(5926):528-32
references: 19390050
references: Yi Chuan. 2012 Jul;34(7):872-8
references: 22805213
references: J Anim Sci. 1998 Sep;76(9):2331-9
references: 9781489
references: J Anim Sci. 2004;82 E-Suppl:E313-328
references: 15471812
references: Anim Genet. 2007 Oct;38(5):440-6
references: 17617213
references: Nat Biotechnol. 2010 May;28(5):511-5
references: 20436464
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6
references: 16845052
references: J Anim Sci. 2008 May;86(5):1038-46
references: 18245504
references: Genetics. 2003 Jan;163(1):253-66
references: 12586713
references: Meat Sci. 2010 Oct;86(2):270-5
references: 20510534
references: Genome Res. 2006 Mar;16(3):340-6
references: 16415109
references: Mamm Genome. 2006 Jan;17(1):83-92
references: 16416094
references: Mamm Genome. 2010 Dec;21(11-12):592-8
references: 21057797
references: Proc Natl Acad Sci U S A. 1997 Nov 11;94(23):12457-61
references: 9356471
references: Science. 1991 Jul 26;253(5018):448-51
references: 1862346
references: Nat Biotechnol. 2012 Feb 12;30(3):253-60
references: 22327324
references: Anim Genet. 2010 Dec;41(6):597-607
references: 20477797
references: Meat Sci. 2009 Jan;81(1):126-31
references: 22063972
references: Genetics. 1983 Nov;105(3):767-79
references: 17246175
references: BMC Genomics. 2012 Mar 28;13:118
references: 22452724
references: Genome Biol. 2009;10(4):R42
references: 19393038
references: Mamm Genome. 1998 Mar;9(3):210-3
references: 9501304
references: Science. 2009 Apr 24;324(5926):522-8
references: 19390049
references: Nat Methods. 2008 Jul;5(7):613-9
references: 18516046
references: BMC Genomics. 2012 Jan 25;13:45
references: 22276848
references: Anim Genet. 2000 Oct;31(5):306-9
references: 11105210
references: J Anim Sci. 2010 Feb;88(2):446-54
references: 19966162
references: PLoS One. 2009;4(4):e5350
references: 19390634
references: Anim Genet. 1998 Aug;29(4):273-82
references: 9745665
references: Genome Res. 2012 Apr;22(4):778-90
references: 22300768
references: Bioinformatics. 2011 Nov 1;27(21):2987-93
references: 21903627
references: Animal. 2010 Apr;4(4):530-4
references: 22444040
references: Nature. 2005 Sep 15;437(7057):376-80
references: 16056220
references: Genetics. 2001 Apr;157(4):1819-29
references: 11290733
references: J Anim Sci. 2002 Sep;80(9):2316-24
references: 12350008
references: Genome Res. 1997 Sep;7(9):910-6
references: 9314496
references: Nature. 2008 Nov 6;456(7218):53-9
references: 18987734
references: Science. 2008 Apr 4;320(5872):106-9
references: 18388294
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: Genome Res. 2001 May;11(5):863-74
references: 11337480
references: Bioinformatics. 2010 Aug 15;26(16):2069-70
references: 20562413
references: PLoS One. 2012;7(1):e30244
references: 22291923
references: Nat Methods. 2010 Apr;7(4):248-9
references: 20354512
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D604-9
references: 17135205
references: Genome Biol. 2009;10(8):R82
references: 19660108
references: BMC Genomics. 2011 Nov 15;12:559
references: 22085807
references: Science. 2010 Jan 1;327(5961):78-81
references: 19892942
references: Genome Res. 2002 Feb;12(2):222-31
references: 11827942
references: J Anim Breed Genet. 2005 Oct;122(5):294-301
references: 16191037
references: Mamm Genome. 2003 Jun;14(6):392-5
references: 12879361
references: Biometrics. 1992 Jun;48(2):361-72
references: 1637966
references: Science. 2000 May 19;288(5469):1248-51
references: 10818001
references: BMC Genomics. 2011 Nov 14;12:557
references: 22082336
references: Nat Rev Genet. 2004 Mar;5(3):202-12
references: 14970822
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: Genome Res. 2005 Jul;15(7):936-44
references: 15998908
references: Meat Sci. 2012 Oct;92(2):132-8
references: 22578477
references: Nat Genet. 2006 Jul;38(7):813-8
references: 16751773
references: Proc Natl Acad Sci U S A. 2012 May 15;109(20):7693-8
references: 22529356
references: Mamm Genome. 2003 Dec;14(12):853-8
references: 14724738
references: PLoS One. 2010 Sep 30;5(9):
references: 20927341
references: Nat Methods. 2008 Mar;5(3):247-52
references: 18297082
references: Biometrics. 1984 Mar;40(1):157-64
references: 6733226
references: Genet Sel Evol. 2003 Jan-Feb;35(1):103-18
references: 12605853