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Articles

Uncovering ceRNA integrated networks that associate with fertility in a photoperiod and temperature sensitive male sterile wheat line

ORCID Icon, , , , , , , , , , & ORCID Icon show all
Pages 1317-1330 | Received 05 May 2021, Accepted 26 Aug 2021, Published online: 18 Oct 2021

References

  • Wang Z, Li J, Chen S, et al. Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat. Proc Natl Acad Sci U S A. 2017; 114(47):12614–12619.
  • Xu S, Zhu D, Zhang Q. Predicting hybrid performance in rice using genomic best linear unbiased prediction. Proc Natl Acad Sci U S A. 2014; 111(34):12456–12461.
  • Longin C, Mühleisen J, Maurer H, et al. Hybrid breeding in autogamous cereals. Theor Appl Genet. 2012; 125(6):1087–1096.
  • Titan P, Iskra J. Interspecific crosses involving Rf3 gene carriers as potential sources of R lines for D2 type cytoplasm based hybrid wheat system. Cereal Res Commun. 2021;:1–10.
  • Chang Z, Chen Z, Wang N, et al. Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene. Proc Natl Acad Sci U S A. 2016; 113(49):14145–14150.
  • Ru ZG, Zhang LP, Hu TZ, et al. Genetic analysis and chromosome mapping of a thermo-sensitive genic male sterile gene in wheat. Euphytica. 2015; 201(3):321–327.
  • Bai JF, Wang YK, Wang P, et al.. Uncovering male fertility transition responsive mirna in a wheat photo-thermosensitive genic male sterile line by deep sequencing and degradome analysis. Front Plant Sci. 2017; 8:1370.
  • Heo JB, Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science. 2011;331(6013):76–79. doi:10.1126/science.1197349. 21127216
  • Liu J, Wang H, Chua N-H. Long noncoding RNA transcriptome of plants. Plant Biotechnol J. 2015;13(3):319–328. doi:10.1111/pbi.12336. 25615265
  • Huang L, Dong H, Zhou D, et al. Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. Plant J. 2018; 96(1):203–222.
  • Sablok G, Zhao H, Sun X. Plant circular RNAs (circRNAs): transcriptional regulation beyond miRNAs in plants. Mol Plant. 2016;9(2):192–194.
  • Pan T, Sun X, Liu Y, et al. Heat stress alters genome-wide profiles of circular RNAs in arabidopsis. Plant Mol Biol. 2018; 96(3):217–229.
  • Kaneko M, Inukai Y, Ueguchi-Tanaka M, et al. Loss-of-function mutations of the rice GAMYB gene impair alpha-amylase expression in aleurone and flower development. Plant Cell. 2004;16(1):33–44.
  • Ding J, Lu Q, Ouyang Y, et al. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A. 2012; 109(7):2654–2659.
  • Yuan SH, Bai JF, Guo HY, et al. QTL mapping of male sterility-related traits in a photoperiod and temperature-sensitive genic male sterile wheat line BS366. Plant Breed. 2020; 139(3):498–507.
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4):357–360.
  • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105–1111.
  • Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562–578.
  • Kong L, Zhang Y, Ye Z-Q, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35(Web Server issue):W345–349.
  • Sun L, Luo H, Dechao B, et al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;41(17):e166.
  • Wang L, Park HJ, Dasari S, et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013; 41(6):e74.
  • Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015;16:4.
  • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44–57.
  • Liu S, Wu L, Qi H, et al. LncRNA/circRNA–miRNA–mRNA networks regulate the development of root and shoot meristems of Populus. Ind Crop Prod. 2019; 133:333–347.
  • Pasquinelli AE. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet. 2012; 13(4):271–282.
  • Livak KJ, Schmittgen TD . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001; 25(4):402–408.
  • Xiang L, Cai C, Cheng J, et al. Identification of circularRNAs and their targets in gossypium under verticillium wilt stress based on RNA-seq. Peer J. 2018; 6:e4500.
  • Liu T, Zhang L, Chen G, et al. Identifying and characterizing the circular RNAs during the lifespan of arabidopsis leaves. Front Plant Sci. 2017; 8:1278.
  • Wang J, Yang Y, Jin L, et al. Re-analysis of long non-coding RNAs and prediction of circRNAs reveal their novel roles in susceptible tomato following TYLCV infection. BMC Plant Biol. 2018;18(1):104.
  • Chen M, Chory J. Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol. 2011; 21(11):664–671.
  • Solís MT, Chakrabarti N, Corredor E, et al. Epigenetic changes accompany developmental programmed cell death in tapetum cells. Plant Cell Physiol. 2014; 55(1):16–29.
  • Baxter A, Mittler R, Suzuki N. ROS as key players in plant stress signalling. J Exp Bot. 2014; 65(5):1229–1240.
  • Shadel GS, Horvath TL. Mitochondrial ROS signaling in organismal homeostasis. Cell. 2015; 163(3):560–569.
  • Liu Z, Shi X, Li S, et al. Oxidative stress and aberrant programmed cell death are associated with pollen abortion in isonuclear alloplasmic male-sterile wheat. Front Plant Sci. 2018; 9:595.
  • Sun W, Hui XX, Lu X, et al. The rice phytochrome genes, PHYA and PHYB, have synergistic effects on anther development and pollen viability. Sci Rep. 2017;7(1):6439.
  • Yang K-Z, Xia C, Liu X-L, et al. A mutation in thermosensitive male sterile 1, encoding a heat shock protein with DNAJ and PDI domains, leads to thermosensitive gametophytic male sterility in arabidopsis. Plant J. 2009; 57(5):870–882.
  • Takano M, Inagaki N, Xie X, et al. Distinct and cooperative functions of phytochromes A, B, and C in the control of deetiolation and flowering in rice. Plant Cell. 2005; 17(12):3311–3325.
  • Gu J-W, Liu J, Xue Y-J, et al. Functions of phytochrome in rice growth and development. Rice Sci. 2011; 18(3):231–237.
  • Sheoran IS, Saini HS. Drought-induced male sterility in rice: Changes in carbohydrate levels and enzyme activities associated with the inhibition of starch accumulation in pollen. Sexual Plant Reprod. 1996; 9(3):161–169.
  • Castro AJ, Clément C. Sucrose and starch catabolism in the anther of Lilium during its development: a comparative study among the anther wall, locular fluid and microspore/pollen fractions. Planta. 2007; 225(6):1573–1582.
  • Li WL, Liu Y, Douglas CJ . Role of glycosyl transferases in pollen wall primexine formation and exine patterning. Plant Physiol. 2017; 173(1):167–182. 02016.
  • Ariizumi T, Toriyama K. Genetic regulation of sporopollenin synthesis and pollen exine development. Annu Rev Plant Biol. 2011; 62(1):437–460.
  • Quilichini TD, Grienenberger E, Douglas CJ. The biosynthesis, composition and assembly of the outer pollen wall: a tough case to crack. Phytochemistry. 2015;113(2):170–182.