Adli H M. 2018. The CRISPR tool kit for genome editing and beyond. Nature Communications, 9, 1911.

Akagi H, Sakamoto M, Shinjyo C, Shimada H, Fujimura T. 1994. A unique sequence located downstream from the rice mitochondrial atp6 may cause male sterility. Current Genetics, 25, 52–58.

Ali A, Li Y, Chen H, Xu P, Zhang H, Chen X, Liao Y X, Fu S, Wu T, Iqbal M Z, Farooq M U, Wu X. 2019. Effect of male sterile and fertile cytoplasm on nuclear DNA methylation in hybrid rice. Acta Physiologiae Plantarum, 41, 81.

Ali G S, Palusa S G, Golovkin M, Prasad J, Manley J L, Reddy A S N. 2007. Regulation of plant developmental processes by a novel splicing factor. PLoS ONE, 2, e471.

Ali G S, Reddy A S N. 2006. ATP, phosphorylation and transcription regulate the mobility of plant splicing factors. Journal of Cell Science, 119, 3527–3538.

Arbuthnot P. 2015. Engineering sequence-specific DNA binding proteins for antiviral gene editing. In: Arbuthnot P, ed., Gene Therapy for Viral Infections. Elsevier, Amsterdam. pp. 63–94.

Ba Q S, Wang R, Zhang P F, Zhang L L, Li G P, Fu Z L. 2022. DNA methylation of TaACS2 gene involved in regulating formation of starch in pollen grain of S-type cytoplasmic male sterile lines in wheat (Triticum aestivum). Crop and Pasture Science, 73, 627–635.

Ba Q S, Zhang G S, Wang J S, Niu N, Ma S C, Wang J W. 2014. Gene expression and DNA methylation alterations in chemically induced male sterility anthers in wheat (Triticum aestivum L.). Acta Physiologiae Plantarum, 36, 503–512.

Bender J. 2004. DNA methylation and epigenetics. Annual Review of Plant Biology, 55, 41–68.

Bentolila S, Stefanov S. 2012. A reevaluation of rice mitochondrial evolution based on the complete sequence of male-fertile and male-sterile mitochondrial genomes. Plant Physiology, 158, 996–1017.

Bernstein D L, Le Lay J E, Ruano E G, Kaestner K H. 2015. TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts. Journal of Clinical Investigation, 125, 1998–2006.

Bisne R, Motiramani N K. 2011. Identification of maintainers and restorers using WA source cytoplasmic male sterile lines in rice. International Rice Research Notes, 30, 14.

Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard C S. 2015. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife, 4, p.e09591.

Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science, 326, 1509–1512.

Bohra A, Jha R, Singh I P, Pandey G, Pareek S, Basu P S, Chaturvedi S K, Singh N P. 2017. Novel CMS linesin pigeonpea [Cajanus cajan (L.) Millspaugh] derived from cytoplasmic substitutions, and their effective restoration and deployment in hybrid breeding. Crop Journal, 5, 89–94.

Brown G G. 1999. Unique aspects of cytoplasmic male sterility and fertility restoration in Brassica napus. Journal of Heredity, 90, 351–356.

Brown G G, Li X Q, Jean M, Landry B S. 1998. Restorer genes for different forms of Brassica cytoplasmic male sterility map to a single nuclear locus that modifies transcripts of several mitochondrial genes. Proceedings of the National Academy of Sciences of the United States of America, 95, 10032–10037.

Bueno C S, Pasuquin E M, Tubana B S, Lafarge T. 2010. Improving sink regulation, and searching for promising traits associated with hybrids, as a key avenue to increase yield potential of the rice crop in the tropics. Field Crops Research, 118, 199–207.

Campos-Rivero G, Osorio-Montalvo P, Sánchez-Borges R, Us-Camas R, Duarte-Aké F, De-la-Peña C. 2017. Plant hormone signaling in flowering: An epigenetic point of view. Journal of Plant Physiology, 214, 16–27.

Chaikind B, Ostermeier M. 2014. Directed evolution of improved zinc finger methyltransferases. PLoS ONE, 9, p.e96931.

Chase C D, Gabay-Laughnan S. 2004. Cytoplasmic male sterility and fertility restoration by nuclear genes. In: Daniell H, Chase C, eds., Molecular Biology and Biotechnology of Plant Organelles. Springer, Dordrecht. pp. 593–621.

Chen B, Zhang Y, Lu Y, Wang J, Zhang S, Lan H, Rong T, Cao M. 2016. DNA methylation analysis of sterile and fertile CMS-C hybrids and their parents in maize. Journal of Plant Biochemistry and Biotechnology, 25, 3–11.

Chen P, Shi Q, Liang Z, Lu H, Li R, Deynze A E V. 2019. Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line. Genome, 62, 455–466.

Chen X, Hu J, Zhang H, Ding Y. 2014. DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions. Gene, 537, 143–148. Cheng Y, Zhao Y. 2007. A role for auxin in flower development. Journal of Integrated Plant Biology, 49, 99–104.

Choi H, Jin J Y, Choi S, Hwang J U, Kim Y Y, Suh M C, Lee Y. 2011. An ABCG/WBC-type ABC transporter is essential for transport of sporopollenin precursors for exine formation in developing pollen. Plant Journal, 65, 181–193.

Damodaran T, Kumar N, Kavino M. 2009. Breeding and evaluation of Musa hybrids resistant to Fusarium oxysporum f. sp. cubense race 1. Fruits, 64, 3–12.

Das S, Sen S, Chakraborty A, Chakraborti P, Maiti M K, Basu A, Basu D, Sen S K. 2010. An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of Oryza sativa L. subsp. indica. BMC Plant Biology, 10, 39.

Datta R, Chamusco K C, Chourey P S. 2002. Starch biosynthesis during pollen maturation is associated with altered patterns of gene expression in maize. Plant Physiology, 130, 1645–1656.

Deng S, Dai H, Arenas C, Wang H, Niu Q W, Chua N H. 2014. Transcriptional silencing of Arabidopsis endogenes by single-stranded RNAs targeting the promoter region. Plant Cell Physiology, 55, 823–833.

Dewey R E, Timothy D H, Levings C S. 1987. A mitochondrial protein associated with cytoplasmic male sterility in the T cytoplasm of maize. Proceedings of the National Academy of Sciences of the United States of America, 84, 5374–5378.

Van Dijken A J H, Schluepmann H, Smeekens S C M. 2004. Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering. Plant Physiology, 135, 969–977.

Ding J, Shen J, Mao H, Xie W, Li X, Zhang Q. 2012. RNA- directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Molecular Plant, 5, 1210–1216.

Dowen R H, Pelizzola M, Schmitz R J, Lister R, Dowen J M, Nery J R, Dixon J E, Ecker J R. 2012. Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences of the United States of America, 109, E2183–E2191.

Du J, Johnson L M, Jacobsen S E, Patel D J. 2015. DNA methylation pathways and their crosstalk with histone

methylation. Nature Reviews Molecular Cell Biology, 16, 519–532.

Du J, Zhong X, Bernatavichute Y V, Stroud H, Feng S, Caro E, Vashisht A A, Terragni J, Chin H G, Tu A, Hetzel J, Wohlschlegel J A, Pradhan S, Patel D J, Jacobsen S E. 2012. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell, 151, 167–180.

Du K, Liu Q, Wu X, Jiang J, Wu J, Fang Y, Li A, Wang Y. 2016. Morphological structure and transcriptome comparison of the cytoplasmic male sterility line in Brassica napus (SaNa- 1A) derived from somatic hybridization and its maintainer line saNa-1B. Frontiers in Plant Science, 7, 1–13.

Duan J E, Jiang Z C, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani S L, Chen J, Tian X C. 2019. Methylome dynamics of bovine gametes and in vivo early embryos. Frontiers in Genetics, 10, 1–14.

Ducos E, Touzet P, Boutry M. 2001. The male sterile G cytoplasm of wild beet displays modified mitochondrial respiratory complexes. Plant Journal, 26, 171–180.

Ebbs M L, Bartee L, Bender J. 2005. H3 Lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Molecular Cell Biology, 25, 10507–10515.

Elina H. 2008. Expression of a Brassica napus mitochondrial gene region associated with cytoplasmic male sterility: Transcript initiation, editing, splicing and nuclease processing. Ph D thesis, Philosophy, Department of Biology, McGill University, Canada.

Elkonin L A, Kozhemyakin V V, Tsvetova M I. 2009. Epigenetic control of the expression of fertility-restoring genes for the ‘9E’ CMS-inducing cytoplasm of sorghum. Maydica, 54, 243–251.

Engelke T, Hirsche J, Roitsch T. 2010. Anther-specific carbohydrate supply and restoration of metabolically engineered male sterility. Journal of Experimental Botany, 61, 2693–2706.

Eveland A L, Jackson D P. 2012. Sugars, signalling, and plant development. Journal of Experimental Botany, 63, 3367–3377.

Formanová N, Stollar R, Geddy R, Mahé L, Laforest M, Landry B S, Brown G G. 2010. High-resolution mapping of the Brassica napus Rfp restorer locus using Arabidopsis- derived molecular markers. Theoretical and Applied Genetics, 120, 843–851.

Gallego-Bartolomé J. 2020. DNA methylation in plants: Mechanisms and tools for targeted manipulation. New Phytologist, 227, 38–44.

Garcia-Aguilar M, Michaud C, Leblanc O, Grimanelli D. 2010. Inactivation of a DNA methylation pathway in maize reproductive organs results in apomixis-like phenotypes. Plant Cell, 22, 3249–3267.

Glazkova D V, Shipulin G A. 2014. TALE nucleases as a new tool for genome editing. Molecular Biology, 48, 305–318.

Goetz M, Godt D E, Guivarc’h A, Kahmann U, Chriqui D, Roitsch T. 2001. Induction of male sterility in plants by metabolic engineering of the carbohydrate supply. Proceedings of the National Academy of Sciences of the United States of America, 98, 6522–6527.

Han F, Zhang X, Liu X, Su H, Kong C, Fang Z, Yang L, Zhuang M, Zhang Y, Liu Y, Li Z, Lv H. 2017. Comparative analysis of genome wide DNA methylation profiles for the genic male sterile cabbage line 01–20S and its maintainer line. Genes, 8, 159.

Han S, Li Y, Li J, Zhang H, Ding X, He T, Gai J, Yang S. 2018. Genome-wide analysis of DNA methylation to identify genes and pathways associated with male sterility in soybean. Molecular Breeding, 38, 118.

Hanson M R, Bentolila S. 2004. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. The Plant Cell, 16(Suppl 1), S154–S169.

He X J, Chen T, Zhu J K. 2011. Regulation and function of DNA methylation in plants and animals. Cell Research, 21, 442–465.

Henderson I R, Jacobsen S E. 2007. Epigenetic inheritance in plants. Nature, 447, 418–424.

Heng S, Gao J, Wei C, Chen F, Li X, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. 2018. Transcript levels of orf288 are associated with the hau cytoplasmic male sterility system and altered nuclear gene expression in Brassica juncea. Journal of Experimental Botany, 69, 455–466.

Hilton I B, D’Ippolito A M, Vockley C M, Thakore P I, Crawford G E, Reddy T E, Gersbach C A. 2015. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nature Biotechnology, 33, 510–517.

Hirai S, Kodama H. 2008. RNAi vectors for manipulation of gene expression in higher plants. Open Plant Science Journal, 2, 21–30.

Hofacker D, Broche J, Laistner L, Adam S, Bashtrykov P, Jeltsch A. 2020. Engineering of effector domains for targeted DNA methylation with reduced off-target effects. International Journal of Molecular Sciences, 21, 502.

Horn R, Gupta K J, Colombo N. 2014. Mitochondrion role in molecular basis of cytoplasmic male sterility. Mitochondrion, 19, 198–205.

Hu J, Chen, X, Zhang H, Ding Y. 2015. Genome-wide analysis of DNA methylation in photoperiod- and thermo-sensitive male sterile rice Peiai 64S. BMC Genomics, 16, 102.

Hu J, Huang W, Huang Q, Qin X, Dan Z, Yao G, Zhu R, Zhu Y. 2013. The mechanism of ORFH79 suppression with the artificial restorer fertility gene Mt-GRP162. New Phytologist, 199, 52–58.

Hu J, Huang W, Huang Q, Qin X, Yu C, Wang L, Li S, Zhu R, Zhu Y. 2014. Mitochondria and cytoplasmic male sterility in plants. Mitochondrion, 19, 282–288.

Hu J, Wang K, Huang W, Liu G, Gao Y, Wang J, Huang Q, Ji Y, Qin X, Wan L, Zhu R. 2012. The rice pentatricopeptide repeat protein RF5 restores fertility in Hong-Lian cytoplasmic male-sterile lines via a complex with the glycine-rich protein GRP162. Plant Cell, 24, 109–122.

Jackson J P, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh P B, Cheng X, Schubert I, Jenuwein T, Jacobsen S E. 2004. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma, 112, 308–315.

Jackson J P, Lindroth A M, Cao X, Jacobsen S E. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature, 416, 556–560.

Jankele R, Svoboda P. 2014. TAL effectors: Tools for DNATargeting. Briefings in Functional Genomics, 13, 409–419.

Ji J, Huang W, Yin C, Gong Z. 2013. Mitochondrial cytochrome c oxidase and F1Fo-ATPase dysfunction in peppers (Capsicum annuum L.) with cytoplasmic male sterility and its association with orf507 and Ψatp6-2 genes. International Journal of Molecular Sciences, 14, 1050–1068.

Jiang H, Lu Q, Qiu S, Yu H, Wang Z, Yu Z, Lu Y, Wang L, Xia F, Wu Y, Li F. 2022. Fujian cytoplasmic male sterility and the fertility restorer gene OsRf19 provide a promising breeding system for hybrid rice. Proceedings of the National Academy of Sciences of the United States of America, 119, e2208759119.

Jin B, Li Y, Robertson K D. 2011. DNA methylation: Superior or subordinate in the epigenetic hierarchy? Genes and Cancer, 2, 607–617.

Josipović G, Tadić V, Klasić M, Zanki V, Bečeheli I, Chung F, Ghantous A, Keser T, Madunić J, Bošković M, Lauc G, Herceg Z, Vojta A, Zoldoš V. 2019. Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system. Nucleic Acids Research, 47, 9637–9657.

Jurkowska R Z, Jeltsch A. 2010. Silencing of gene expression by targeted DNA methylation: Concepts and approaches. Methods in Molecular Biology, 649, 149–161.

Kalia P, Mangal M, Singh S, Chugh C, Mishra S, Chaudhary S. 2019. Morphological and molecular changes on cytoplasmic male sterility (CMS) introgression in Asiatic carrot (Daucus carota L.). Planta, 250, 507–518.

Kankel M W, Ramsey D E, Stokes T L, Flowers S K, Haag J R, Jeddeloh J A, Riddle N C, Verbsky M L, Richards E J. 2003. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics, 163, 1109–1122.

Kazama T, Toriyama K. 2003. A pentatricopeptide repeat- containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice. FEBS Letters, 544, 99–102.

Koizuka N, Imai R, Iwabuchi M, Sakai T, Imamura J. 2000. Genetic analysis of fertility restoration and accumulation of ORF125 mitochondrial protein in the kosena radish (Raphanus sativus cv. Kosena) and a Brassica napus restorer line. Theoretical and Applied Genetics, 100, 949–955.

Klose R J, Bird A. 2006. Genomic DNA methylation: the mark and its mediators. Trends in Biochemical Sciences, 312, 89–97.

Komori T, Ohta S, Murai N, Takakura Y, Kuraya Y, Suzuki S, Hiei Y, Imaseki H, Nitta N. 2004. Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). Plant Journal, 37, 315–325.

Kon T, Yoshikawa N. 2014. Induction and maintenance of DNA methylation in plant promoter sequences by apple latent spherical virus-induced transcriptional gene silencing. Frontiers in Microbiology, 5, 595.

Konate M, Wilkinson M J, Taylor J, Scott E S, Berger B, Rodriguez Lopez C M. 2020. Greenhouse spatial effects detected in the barley (Hordeum vulgare L.) epigenome underlie stochasticity of DNA methylation. Frontiers in Plant Science, 11, 553907.

Kong X, Khan A, Li B, Zheng J, Dawar F U, Li M, You J, Li Z, Zhou R. 2020. Deviant DNA methylation play a key role in the pollen abortion of Gossypium barbadense L. cytoplasmic male sterility. Industrial Crops and Products, 154, 112622.

Kovaleva L V, Voronkov A S, Zakharova E V, Andreev I M. 2018. ABA and IAA control microsporogenesis in Petunia hybrida L. Protoplasma, 255, 751–759.

Krizek B A. 2011. Auxin regulation of Arabidopsis flower development involves members of the AINTEGUMENTA- LIKE/PLETHORA (AIL/PLT) family. Journal of Experimental Botany, 62, 3311–3319.

Kuang Z, Yao S, Xu Y, Lewis R S, Low A, Masters S L, Willson T A, Kolesnik T B, Nicholson S E, Garrett T J, Norton R S. 2009. SPRY domain-containing SOCS box protein 2: Crystal structure and residues critical for protein binding. Journal of Molecular Biology, 386, 662–674.

Law J A, Jacobsen S E. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics, 11, 204–220.

L’Homme Y, Stahl R J, Li X Q, Hameed A, Brown G G. 1997. Brassica nap cytoplasmic male sterility is associated with expression of a mtDNA region containing a chimeric gene similar to the pol CMS-associated orf224 gene. Current Genetics, 31, 325–335.

Lei Y, Huang Y H, Goodell M A. 2018. DNA methylation and de-methylation using hybrid site-targeting proteins. Genome Biology, 19, 187.

Lewis J, Bird A. 1991. DNA methylation and chrolmatim structure. FEBS Letters, 285, 155–159.

Li C, Zhang C, Rong T, Lu Y, Wang J, Lan H, Cao M. 2017. Insight into the maize CMS-associated mitochondrial- nuclear interaction at the DNA methylation level. Canadian Journal of Plant Science, 97, 665–673.

Li M, Chen L, Tang D, Liao X, Kong X, Li B, You J, Zhou R. 2020. Discovery of four novel ORFs responsible for cytoplasmic male sterility (CMS) in cotton (Gossypium hirsutum L.) through comparative analysis of the mitochondrial genomes of four isoplasmic lines. Agronomy, 10, 1–17.

Li S, Chen Z, Zhao N, Wang Y, Nie H, Hua J. 2018. The comparison of four mitochondrial genomes reveals cytoplasmic male sterility candidate genes in cotton. BMC Genomics, 19, 1–15.

Li X, Yu H, Jiao Y, Shahid M Q, Wu J, Liu X. 2018. Genome- wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice. PLoS ONE, 13, 1–25.

Li X Q, Jean M, Landry B S, Brown G G. 1998. Restorer genes for different forms of Brassica cytoplasmic male sterility map to a single nuclear locus that modifies transcripts of several mitochondrial genes. Proceedings of the National Academy of Sciences of the United States of America, 95, 10032–10037.

Li Y, Ding X, Wang X, He T, Zhang H, Yang L, Wang T, Chen L, Gai J, Yang S. 2017. Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male- sterile line NJCMS5A and its maintainer NJCMS5B. BMC Genomics, 18, 1–16.

Li Z, Luo D, Tang M, Cao S, Pan J, Zhang W, Hu Y, Yue J, Huang Z, Li R, Chen P. 2022. Integrated methylome and transcriptome analysis provides insights into the DNA methylation underlying the mechanism of cytoplasmic male sterility in kenaf (Hibiscus cannabinus L.). International Journal of Molecular Sciences, 23, 6864.

Lim H, Cho M H, Jeon J S, Bhoo S H, Kwon Y K, Hahn T R. 2009. Altered expression of pyrophosphate: Fructose- 6-phosphate 1-phosphotransferase affects the growth of transgenic Arabidopsis plants. Molecular Cells, 27, 641–649.

Lin C, Peng B, Li Y, Wang P, Zhao G, Ding X, Li R, Zhao L, Zhang C. 2020. Cytoplasm types affect DNA methylation among different cytoplasmic male sterility lines and their maintainer line in soybean (Glycine max L.). Plants, 9, 385.

Lin S C, Yuan L. 1980. Hybrid rice breeding in China. In: Innovative Approaches to Rice Breeding. International Rice Research Institute, Los Banos, Philippines. pp. 35–51.

Linke B, Börner T. 2005. Mitochondrial effects on flower and pollen development. Mitochondrion, 5, 389–402.

Lister R, Mukamel E A, Nery J R, Urich M, Puddifoot C A, Johnson N D, Lucero J, Huang Y, Dwork A J, Schultz M D, Yu M. 2013. Global epigenomic reconfiguration during mammalian brain development. Science, 80, 341.

Liu C. 2018. Cytoplasmic male sterility (CMS) in hybrid breeding in field crops. Euphytica, 214, 967–993.

Liu G, Tian H, Huang Y Q, Hu J, Ji Y X, Li S Q, Feng Y Q, Guo L, Zhu Y G. 2012. Alterations of mitochondrial protein assembly and jasmonic acid biosynthesis pathway in honglian (HL)-type cytoplasmic male sterility rice. Journal of Biological Chemistry, 287, 40051–40060.

Lo C L, Choudhury S R, Irudayaraj J, Zhou F C. 2017. Epigenetic editing of ascl1 gene in neural stem cells by optogenetics. Scientific Reports, 7, 1–12.

Lu Y, Liu Y, Wang J, Cao M, Rong T. 2010. Variation and patterns of DNA methylation in maize C-type CMS lines and their maintainers. Journal of Plant Biochemistry and Biotechnology, 19, 43–50.

Lucibelli F, Valoroso M C, Aceto S. 2022. Plant DNA methylation: An epigenetic mark in development, environmental interactions, and evolution. International Journal of Molecular Sciences, 23, 8299.

Luo D, Xu H, Liu Z, Guo J, Li H, Chen L, Fang C, Zhang Q, Bai M, Yao N, Wu H. 2013. A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice. Nature Genetics, 45, 573–577.

Ma Y, Min L, Wang M, Wang C, Zhao Y, Li Y, Fang Q, Wu Y, Xie S, Ding Y, Su X. 2018. Disrupted genome methylation in response to high temperature has distinct effects on microspore abortion and anther indehiscence. Plant Cell, 30, 1387–1403.

Malagnac F, Bartee L, Bender J. 2002. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO Journal, 21, 6842–6852.

Matera J T, Monroe J, Smelser W, Gabay-Laughnan S, Newton K J. 2011. Unique changes in mitochondrial genomes associated with reversions of S-type cytoplasmic male sterility in Maizemar. PLoS ONE, 6, e23405.

Matzke M, Kanno T, Daxinger L, Huettel B, Matzke A J. 2009. RNA-mediated chromatin-based silencing in plants. Current Opinon in Cell Biology, 21, 367–376.

Matzke M A, Kanno T, Matzke A J M. 2015. RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Annual Review of Plant Biology, 66, 243–267.

Matzke M A, Mosher R A. 2014. RNA-directed DNA methylation: An epigenetic pathway of increasing complexity. Nature Reviews Genetics, 15, 394–408.

Mbichi R W, Wang Q F, Wan T. 2020. RNA directed DNA methylation and seed plant genome evolution. Plant Cell Report, 39, 983–996.

McDonald J I, Celik H, Rois L E, Fishberger G, Fowler T, Rees R, Kramer A, Martens A, Edwards J R, Challen G A. 2016. Reprogrammable CRISPR/Cas9-based system for inducing sitespecific DNA methylation. Biology Open, 5, 866–874.

McNamara A R, Hurd P J, Smith A E F, Ford K G. 2002. Characterisation of site-biased DNA methyltransferases: Specificity, affinity and subsite relationships. Nucleic Acids Research, 30, 3818–3830.

Melonek J, Duarte J, Martin J, Beuf L, Murigneux A, Varenne P, Comadran J, Specel S, Levadoux S, Bernath-Levin K, Torney F. 2021. The genetic basis of cytoplasmic male sterility and fertility restoration in wheat. Nature Communications, 12, 1036.

Menassa R, L’Homme Y, Brown G G. 1999. Post-transcriptional and developmental regulation of a CMS-associated mitochondrial gene region by a nuclear restorer gene. Plant Journal, 17, 491–499.

Moradpour M, Abdulah S N A. 2020. CRISPR/dCas9 platforms in plants: Strategies and applications beyond genome editing. Plant Biotechnology Journal, 18, 32–44.

Moscou M J, Bogdanove A J. 2009. A simple cipher governs DNA recognition by TAL effectors. Science, 326, 1501.

Mosher R A, Schwach F, Studholme D, Baulcombe D C. 2008. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proceedings of the National Academy of Sciences of the United States of America, 105, 3145–3150.

Nath A, Nath D, Santra C K, Dasgupta T. 2020. Identification of suitable restorers for WA-CMS lines of rice (Oryza sativa L.) through conventional and molecular breeding methods. Agricultural Science Digest, 40, 249–254.

Okazaki M, Kazama T, Murata H, Motomura K, Toriyama K. 2013. Whole mitochondrial genome sequencing and transcriptional analysis to uncover an RT102-Type cytoplasmic male sterility-associated candidate gene derived from Oryza rufipogon. Plant Cell Physiology, 54, 1560–1568.

Oliver S N, Dennis E S, Dolferus R. 2007. ABA regulates apoplastic sugar transport and is a potential signal for cold- induced pollen sterility in rice. Plant and Cell Physiology, 48, 1319–1330.

Pattanayak V, Ramirez C L, Joung J K, Liu D R. 2011. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nature Methods, 8, 765–772.

Peng X, Wang K, Hu C, Zhu Y, Wang T, Yang J, Tong J, Li S, Zhu Y. 2010. The mitochondrial gene orfH79 plays a critical role in impairing both male gametophyte development and root growth in CMS-Honglian rice.

BMC Plant Biology, 10, 125. Perez-Pinera P, Kocak D D, Vockley C M, Adler A F, Kabadi A M, Polstein L R, Thakore P I, Glass K A, Ousterout D G, Leong K W, Guilak F, Crawford G E, Reddy T E, Gersbach C A. 2013. RNA-guided gene activation by CRISPR-Cas9- based transcription factors. Nature Methods, 10, 973–976. Pérez-Villa A, Darvas M, Bussi G. 2015. ATP dependent NS3 helicase interaction with RNA: Insights from molecular simulations. Nucleic Acids Research, 43, 8725–8734.

Peter S, Goran K, Renata J, Tamir C, Felix K, Richard R, Wolf R, Albert J, Tomasz J. 2017. Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Research, 45, 1703–1713. Phillips T. 2008. The role of methylation in gene expression‎. Nature Education, 1, 116.

Pikaard C S, Haag J R, Pontes O M F, Blevins T, Cocklin R. 2012. A transcription fork model for pol IV- and pol V-dependent RNA-directed DNA methylation. In: Cold Spring Harbor Symposia on Quantitative Biology. vol.

77. Cold Spring Harbor Laboratory Press, New York. pp. 205–212.

Přibylová A, Čermák V, Tyč D, Fischer L. 2019. Detailed insight into the dynamics of the initial phases of de novo RNA- directed DNA methylation in plant cells. Epigenetics and Chromatin, 12, 54.

Roach H I, Hashimoto K. 2007. PCR-based methods to determine DNA methylation status at specific CpG sites using methylation-sensitive restriction enzymes. [2023-3- 11]. https://core.ac.uk/download/pdf/26666.pdf

Sakr S, Wang M, Dédaldéchamp F, Perez-Garcia M D, Ogé L, Hamama L, Atanassova R. 2018. The sugar-signaling hub: Overview of regulators and interaction with the hormonal and metabolic network. International Journal of Molecular Sciences, 19, 2506.

Sang S, Cheng H, Hao M, Ding B, Mei D, Wang H, Wang W, Liu J, Fu L, Liu K, Hu Q. 2021. Mitochondrial localization of ORF346 causes pollen abortion in alloplasmic male sterility. Crop Journal, 9, 1320–1329.

Saze H, Scheid O M, Paszkowski J. 2003. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nature Genetics, 34, 65–69.

Schnable P S, Wise R P. 1998. The molecular basis of cytoplasmic male sterility and fertility restoration. Trends in Plant Science, 3, 175–180.

Schubert R, Grunewald S, Sivers L V, Hause B. 2019. Effects of jasmonate on ethylene function during the development of tomato stamens. Plants, 8, 277.

Scott R J, Spielman M, Dickinson H G. 2004. Stamen structure and function. Plant Cell, 16, 46–60.

Sharma R P, Grayson D R, Guidotti A, Costa E. 2005. Chromatin, DNA methylation and neuron gene regulation

- The purpose of the package. Journal of Psychiatry and Neuroscience, 30, 257–263.

Sheng P, Flood K A, Xie M. 2020. Short hairpin RNAs for strand-specific small interfering RNA production. Frontiers in Bioengineering and Biotechnology, 8, 940.

Shinada T, Kikuchi Y, Fujimoto R, Kishitani S. 2006. An alloplasmic male-sterile line of Brassica oleracea harboring the mitochondria from Diplotaxis muralis expresses a novel chimeric open reading frame, orf72. Plant Cell Physiology, 47, 549–553.

Shinjyo C. 1969. Cytoplasmic genetic male sterility in cultivated rice, Oryza sativa L. II. The inheritance of male sterility. The Japanese Journal of Genetics, 44, 149–156.

Singh S, Dey S S, Bhatia R, Kumar R, Behera T K. 2019. Current understanding of male sterility systems in vegetable Brassicas and their exploitation in hybrid breeding. Plant Reproduction, 32, 231–256.

Singh S P, Singh S P, Pandey T, Singh R R, Sawant S V. 2015. A novel male sterility-fertility restoration system in plants for hybrid seed production. Scientific Reports, 5, 1127.

Song J, Rechkoblit O, Bestor T H, Patel D J. 2011. Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science, 331, 1036–1040. Song Y, Ma K, Bo W, Zhang Z, Zhang D. 2012. Sex-specific DNA methylation and gene expression in andromonoecious poplar. Plant Cell Report, 31, 1393–1405.

Stepien P P, Margossian S P, Landsman D, Butow R A. 1992. The yeast nuclear gene suv3 affecting mitochondrial post-transcriptional processes encodes a putative ATP- dependent RNA helicase. Proceedings of the National Academy of Sciences of the United States of America, 89, 6813–6817.

Spillane C, McKeown P C. 2014. Plant Epigenetics and Epigenomics. Humana Press, New York, NY.

Stepper P, Kungulovski G, Jurkowska R Z, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A, Jurkowski T

P. 2017. Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Research, 45, 1703–1713.

Štorchová H. 2017. The role of non-coding RNAs in cytoplasmic male sterility in flowering plants. International Journal of Molecular Sciences, 18, 2429

Stratford S, Barnes W, Hohorst D L, Sagert J G, Cotter R, Golubiewski A, Showalter A M, Mccormick S, Bedinger P. 2001. A leucine-rich repeat region is conserved in pollen extensin-like (Pex) proteins in monocots and dicots. Plant Molecular Biology, 46, 43–56.

Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel D J, Jacobsen S E. 2014. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nature Structural & Molecular Biology, 21, 64–72.

Su A, Song W, Xing J, Zhao Y, Zhang R, Li C, Duan M, Luo M, Shi Z, Zhao J. 2016. Identification of genes potentially associated with the fertility instability of s-type cytoplasmic male sterility in maize via bulked segregant RNA-Seq. PLoS ONE, 11, e0163489.

Suzuki N, Miller G, Morales J, Shulaev V, Torres M A, Mittler R. 2011. Respiratory burst oxidases: the engines of ROS signaling. Current Opinion in Plant Biology, 14, 691–699.

Tadić V, Josipović G, Zoldoš V, Vojta A. 2019. CRISPR/Cas9- based epigenome editing: An overview of dCas9-based tools with special emphasis on off-target activity. Methods, 164, 109–119.

Urbano A, Smith J, Weeks R J, Chatterjee A. 2019. Gene- specific targeting of DNA methylation in the mammalian genome. Cancers, 11, 1515.

Vandevenne M, Jacques D A, Artuz C, Nguyen C D, Kwan A H, Segal D J, Matthews J M, Crossley M, Guss J M, Mackay J P. 2013. New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217. Journal of Biology and Chemistry, 288, 10616–10627.

Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P, Julg B, Klasić M, Zoldoš V. 2016. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Research, 44, 5615–5628.

Wang K, Gao F, Ji Y, Liu Y, Dan Z, Yang P, Zhu Y, Li S. 2013a. ORFH79 impairs mitochondrial function via interaction with a subunit of electron transport chain complex III in Honglian cytoplasmic male sterile rice. New Phytologist, 198, 408–418.

Wang K, Peng X, Ji Y, Yang P, Zhu Y, Li S. 2013b. Gene, protein, and network of male sterility in rice. Frontiers in Plant Science, 4, 92.

Wang Y, Wang Q, Hao W, Li J, Qi M, Zhang L. 2020. Mitochondrial genome sequencing reveals orf463a may induce male sterility in NWB cytoplasm of radish. Genes, 11, 74.

Wang Z, Wu X, Wu Z, An H, Yi B, Wen J, Ma C, Shen J, Fu T, Tu J. 2018. Genome-wide DNA methylation comparison between Brassica napus genic male sterile line and restorer line. International Journal of Molecular Sciences, 19, 2689. Wang Z, Zou Y, Li X, Zhang Q, Chen L, Wu H, Su D, Chen Y, Guo J, Luo D, Long Y, Zhong Y, Liu Y G. 2006. Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. Plant Cell. 18, 676–687.

Xie M, Yu B. 2015. siRNA-directed DNA methylation in plants. Current Genomics, 16, 23–31.

Xu G L, Bestor T H. 1997. Cytosine methylation targetted to pre-determined sequences. Nature Genetics, 17, 378.

Xu J, Yang C, Yuan Z, Zhang D, Gondwe M Y, Ding Z, Liang W, Zhang D, Wilson Z A. 2010. The aborted microspores regulatory network is required for postmeiotic male reproductive development in Arabidopsis thaliana. Plant Cell, 22, 91–107.

Xu P, Yan W, He J, Li Y, Zhang H, Peng H, Wu X. 2013. DNA methylation affected by male sterile cytoplasm in rice (Oryza sativa L.). Molecular Breeding, 31, 719–727.

Yamagishi H, Hashimoto A, Fukunaga A, Bang S W, Terachi T. 2021a. Intraspecific variations of the cytoplasmic male sterility genes orf108 and orf117 in Brassica maurorum and Moricandia arvensis, and the specificity of the mRNA processing. Genome, 64, 1081–1089.

Yamagishi H, Jikuya M, Okushiro K, Hashimoto A, Fukunaga A, Takenaka M, Terachi T. 2021b. A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish. Molecular Genetics and Genomics, 296, 705–717.

Ye L X, Gan Z M, Wang W F, Ai X Y, Xie Z Z, Hu C G, Zhang J Z. 2020. Comparative analysis of the transcriptome, methylome, and metabolome during pollen abortion of a seedless citrus mutant. Plant Molecular Biology, 104, 151–171.

Yi P, Wang L, Sun Q, Zhu Y. 2002. Discovery of mitochondrial chimeric-gene associated with cytoplasmic male sterility of HL-rice. Chinese Science Bulletin, 47, 744–747.

You J, Li M, Li H, Bai Y, Zhu X, Kong X, Chen X, Zhou R. 2022. Integrated methylome and transcriptome analysis widen the knowledge of cytoplasmic male sterility in cotton (Gossypium barbadense L.). Frontiers in Plant Science, 13, 770098.

Zemach A, Kim M Y, Hsieh P H, Coleman-Derr D, Eshed- Williams L, Thao K, Harmer S L, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell, 153, 193–205.

Zhang H, Lang Z, Zhu J K. 2018. Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology, 19, 489–506.

Zhang H, Liang W, Yang X, Luo X, Jiang N, Ma H, Zhang D. 2010. Carbon starved anther encodes a MYB domain protein that regulates sugar partitioning required for rice pollen development. Plant Cell, 22, 672–689.

Zhang M, Guo L, Qi T, Zhang X, Tang H, Wang H, Qiao X, Zhang B, Feng J, Zuo Z, Li T. 2019. Integrated methylome and transcriptome analysis between the CMS-D2 line ZBA and its maintainer line ZB in Upland cotton. International Journal of Molecular Science, 20, 6070.

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan S W, Chen H, Henderson I R, Shinn P, Pellegrini M, Jacobsen S E, Ecker J R. 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell, 126, 1189–1201.

Zhang Y, Yi H, Fang M, Rong T, Cao M. 2014. Cytological observation and DNA methylation analysis of two new cytoplasmic male sterile lines of maize during microsporogenesis. Hereditas, 36, 1021–1026. (in Chinese)

Zhong S, Xu Y, Yu C, Zhang X, Li L, Ge H, Ren G, Wang Y, Ma J, Zheng Y, Zheng B. 2019. Anaphase-promoting complex/cyclosome regulates RdDM activity by degrading DMS3 in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 116, 3899–3908.

Zhu T, Li L, Feng L, Mo H, Ren M. 2020. Target of rapamycin regulates genome methylation reprogramming to control plant growth in Arabidopsis. Frontiers in Genetics, 11, 1–15. Zhuang J Y, Fan Y Y, Wu J L, Rao Z M, Xia Y W, Zheng K L. 2001. Mapping genes for rice CMS-WA fertility restoration. Acta Genetica Sinica, 28, 129–134. (in Chinese)