Transcriptomic analysis of maize kernel row number-associated miRNAs between a single segment substitution line and its receptor parent

Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18(10):758–762 Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25(1):130–131 Bartel B, Bartel DP (2003) MicroRNAs: at the root of plant development? Plant Physiol 132(2):709–717 Bennetzen J, Hake S (2009) Handbook of maize: its biology. Springer, Berlin Bommert P, Nagasawa NS, Jackson D (2013) Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet 45:334–338. doi:10.1038/ng.2534 Bortiri E, Chuck G, Vollbrecht E et al (2006) ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize. Plant Cell Online 18(3):574–585 Bowman JL (2004) Class III HD-Zip gene regulation, the golden fleece of ARGONAUTE activity? BioEssays 26(9):938–942 Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Sci Signal 320(5880):1185 Busov VB, Brunner AM, Strauss SH (2008) Genes for control of plant stature and form. New Phytol 177(3):589–607 Chen J, Lin HJ, Pan GT et al (2010) Identification of known microRNAs in root and leaf of maize by deep sequencing. Yi Chuan 32(11):1175 Chuck G, Muszynski M, Kellogg E et al (2002) The control of spikelet meristem identity by the branched silkless1 gene in maize. Science 298(5596):1238–1241 Chuck G, Cigan AM, Saeteurn K et al (2007a) The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat Genet 39(4):544–549 Chuck G, Meeley R, Irish E, Sakai H, Hake S (2007b) The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat Genet 39(12):1517–1521 Chuck G, Whipple C, Jackson D et al (2010) The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development 137(8):1243–1250 Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y (2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot 103:29–38 Ding D, Wang Y, Han M, Fu Z, Li W, Liu Z, Hu Y, Tang J (2012) MicroRNA transcriptomic analysis of heterosis during maize seed germination. PLoS ONE 7(6):e39578. doi:10.1371/journal.pone.0039578 Douglas RN, Wiley D, Sarkar A et al (2010) ragged seedling2 encodes an ARGONAUTE7-like protein required for mediolateral expansion, but not dorsiventrality, of maize leaves. Plant Cell Online 22(5):1441–1451 Hobert O (2008) Gene regulation by transcription factors and microRNAs. Sci Signal 319(5871):1785 Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53 Kellogg EA (2000) The grasses: a case study in macroevolution. Annu Rev Ecol Syst 31:217–238 Kulcheski FR, de Oliveira LFV, Molina LG et al (2011) Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genom 12(1):307 Li XY, Mantovani R, Hooft van Huijsduijnen R et al (1992) Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res 20(5):1087–1091 Liu PP, Montgomery TA, Fahlgren N et al (2007) Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J 52(1):133–146 Liu R, Jia H, Cao X, Huang J, Li F, Tao Y, Qiu F, Zheng Y, Zhang Z (2012a) Fine mapping and candidate gene prediction of a pleiotropic quantitative trait locus for yield-related trait in Zea mays. PLoS ONE 7(11):e49836 Liu Z, Kumari S, Zhang L, Zheng Y, Ware D (2012b) Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PLoS ONE 7(6):e39786. doi:10.1371/journal.pone.0039786 Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25(4):402–408 Marin E, Jouannet V, Herz A et al (2010) miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell Online 22(4):1104–1117 Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell Online 17(3):705–721 Millar AA, Waterhouse PM (2005) Plant and animal microRNAs: similarities and differences. Funct Integr Genomics 5(3):129–135 Nag A, King S, Jack T (2009) miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc Natl Acad Sci 106(52):22534–22539 Nogueira FTS, Chitwood DH, Madi S et al (2009) Regulation of small RNA accumulation in the maize shoot apex. PLoS Genet 5(1):e1000320 Schauer SE, Jacobsen SE, Meinke DW et al (2002) DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci 7(11):487–491 Shen Y, Jiang Z, Lu S, Lin H, Gao S, Peng H, Yuan G, Liu L, Zhang Z, Zhao M, Rong T, Pan G (2013) Combined small RNA and degradome sequencing reveals microRNA regulation during immature maize embryo dedifferentiation. Biochem Biophys Res Commun 441(2):425–430 Song JB, Huang SQ, Dalmay T et al (2012) Regulation of leaf morphology by microRNA394 and its target LEAF CURLING RESPONSIVENESS. Plant Cell Physiol 53(7):1283–1294 Stone JM, Liang X, Nekl ER et al (2005) Arabidopsis AtSPL14, a plant-specific SBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1. Plant J 41(5):744–754 Wang QQ, Liu F, Chen XS et al (2010) Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96(6):369–376 Wang L, Zhang Z, Teng F et al (2012) Application of chromosomal segment introgression line (CSIL) in crop genetics and breeding. J Plant Genet Resour 1:014 Warpeha KM, Upadhyay S, Yeh J et al (2007) The GCR1, GPA1, PRN1, NF-Y signal chain mediates both blue light and abscisic acid responses in Arabidopsis. Plant Physiol 143(4):1590–1600 Xi ZY, He FH, Zeng RZ, Zhang ZM, Ding XH, Li WT, Zhang GQ (2006) Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49:476–484. doi:10.1139/G06-005 Xie F, Wang Q, Sun R, Zhang B (2014) Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton. J Exp Bot. doi:10.1093/jxb/eru437 Yang J, Liu X, Xu B, Zhao N, Yang X, Zhang M (2013a) Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea. BMC Genom 14(1):9 Yang X, Wang L, Yuan D, Lindsey K, Zhang X (2013b) Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. J Exp Bot 64(6):1521–1536 Zhang BH, Pan XP, Cox SB et al (2006) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63(2):246–254 Zhang Y, Schwarz S, Saedler H, Huijser P (2007) SPL8, a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol Biol 63(3):429–439 Zhang L, Chia JM, Kumari S et al (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genet 5(11):e1000716 Zhao B, Ge L, Liang R et al (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10(1):29