title: Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid.
abstract: We performed a genetic analysis of sRNA abundance in flag leaf from an immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining 80,362 sRNA clusters, 22,263 sRNA cluster QTLs (scQTLs) were recovered for 20,249 of all the 50,139 sRNA cluster expression traits (sc-traits). The expression levels for most of s-traits from the same genes or the same sRNA clusters were slightly positively correlated. While genetic co-regulation between sRNAs from the same mother genes and between sRNAs and their mother genes was observed for a portion of the sRNAs, most of the sRNAs and their mother genes showed little co-regulation. Some sRNA biogenesis genes were located in distant-sQTL hotspots and showed correspondence with specific length classes of sRNAs suggesting their important roles in the regulation and biogenesis of the sRNAs.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Yao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D002678:Chimera / Q000235:genetics; D003433:Crosses, Genetic; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics*; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D058727:RNA, Small Untranslated / Q000235:genetics*
chemical_list: D058727:RNA, Small Untranslated
keywords: evolutionary biology; genetics; genomics; plant biology; rice; sRNA
references.citation: Plant Mol Biol. 2006 Nov;62(4-5):579-91
references.pmid: 16941221
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1708-13
references.pmid: 17237218
references.citation: Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):12040-5
references.pmid: 22778444
references.citation: Nat Biotechnol. 2013 Sep;31(9):848-52
references.pmid: 23873084
references.citation: Nature. 2004 Mar 4;428(6978):84-8
references.pmid: 14999285
references.citation: Trends Genet. 2013 Dec;29(12):684-90
references.pmid: 23953922
references.citation: Biomolecules. 2013 Apr 09;3(2):287-302
references.pmid: 24970168
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Annu Rev Plant Biol. 2013;64:137-59
references.pmid: 23330790
references.citation: Genetics. 2002 Dec;162(4):1885-95
references.pmid: 12524357
references.citation: Plant J. 2008 Jul;55(1):131-51
references.pmid: 18363789
references.citation: Genome Res. 2014 May;24(5):850-9
references.pmid: 24482540
references.citation: PLoS Genet. 2012;8(5):e1002704
references.pmid: 22589741
references.citation: Biochim Biophys Acta. 2011 Aug;1809(8):427-37
references.pmid: 21459171
references.citation: Cell. 2009 Feb 20;136(4):642-55
references.pmid: 19239886
references.citation: Nat Rev Genet. 2007 Nov;8(11):884-96
references.pmid: 17943195
references.citation: Nat Rev Genet. 2013 Feb;14(2):100-12
references.pmid: 23329111
references.citation: Nat Genet. 2003 Sep;35(1):57-64
references.pmid: 12897782
references.citation: Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15847-52
references.pmid: 23019369
references.citation: BMC Genomics. 2008 Oct 01;9:451
references.pmid: 18826656
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7
references.pmid: 22684630
references.citation: Am J Hum Genet. 2012 Jun 8;90(6):1046-63
references.pmid: 22658545
references.citation: PLoS One. 2013 May 22;8(5):e63938
references.pmid: 23717514
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Plant Cell. 2010 Jan;22(1):17-33
references.pmid: 20086188
references.citation: Genes Dev. 2008 Nov 15;22(22):3172-83
references.pmid: 19056895
references.citation: Nature. 2004 Aug 12;430(7001):743-7
references.pmid: 15269782
references.citation: Plant Physiol. 2012 Aug;159(4):1488-500
references.pmid: 22715111
references.citation: Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2574-9
references.pmid: 12604771
references.citation: Genes Dev. 2005 Oct 1;19(19):2301-6
references.pmid: 16204182
references.citation: Annu Rev Plant Biol. 2009;60:93-114
references.pmid: 19012536
references.citation: PLoS One. 2011 Mar 03;6(3):e17595
references.pmid: 21390234
references.citation: Nat Rev Genet. 2009 Feb;10(2):94-108
references.pmid: 19148191
references.citation: Eur J Hum Genet. 2012 Jan;20(1):97-101
references.pmid: 21847142
references.citation: J Exp Bot. 2014 Mar;65(4):1069-79
references.pmid: 24420573
references.citation: Biochim Biophys Acta. 2008 Nov;1779(11):743-8
references.pmid: 18457682
references.citation: Curr Opin Plant Biol. 2013 May;16(2):170-9
references.pmid: 23466255
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10578-83
references.pmid: 20498060
references.citation: J Exp Bot. 2011 Jan;62(2):487-95
references.pmid: 20952628
references.citation: Genetics. 2009 Mar;181(3):1077-86
references.pmid: 19104078
references.citation: Heredity (Edinb). 1992 Oct;69(4):315-24
references.pmid: 16718932
references.citation: J Genet Genomics. 2013 May 20;40(5):205-10
references.pmid: 23706295
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2617-22
references.pmid: 21266545
references.citation: RNA. 2010 Mar;16(3):495-505
references.pmid: 20075166
references.citation: Plant J. 2010 Sep;63(6):1063-74
references.pmid: 20626655
references.citation: Bioinformatics. 2011 Jun 1;27(11):1571-2
references.pmid: 21493656
references.citation: Annu Rev Plant Biol. 2010;61:421-42
references.pmid: 20192739
references.citation: Nat Genet. 2010 Jun;42(6):545-9
references.pmid: 20495564
references.citation: Nat Genet. 2010 Jun;42(6):541-4
references.pmid: 20495565
references.citation: Genome Res. 2011 Jan;21(1):68-73
references.pmid: 21147911
references.citation: Hum Mol Genet. 2013 Aug 1;22(15):3023-37
references.pmid: 23562819
references.citation: Int J Mol Sci. 2013 Jul 24;14(8):15233-59
references.pmid: 23887650
references.citation: Annu Rev Cell Dev Biol. 2009;25:21-44
references.pmid: 19575669
references.citation: Elife. 2015 Mar 30;4:e04250
references.pmid: 25821986