Gene mining and functional analysis related to maize (Zea mays L.) seed size

Authors

  • Syed F.A. GILLANI Gansu Agricultural University, College of Agronomy, Lanzhou 730070; Gansu Provincial Key Lab of Arid Land Crop Science, Lanzhou 730070 (CN)
  • Adnan RASHEED Jiangxi Agricultural University, Ministry of Education/ College of Agronomy, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang 330045 (CN)
  • Yasir MAJEED Gansu Agricultural University, College of Agronomy, Lanzhou 730070 (CN)
  • Shamshad S. BUKHARI Nuclear Atomic Energy Institute of Agriculture, Tandojam Sindh (PK)
  • Huma TARIQ University of Poonch Rawalakot Ajk Pakistan, Laboratory of Plant Breeding and Molecular Genetics, Azad, Kashmir (PK)
  • Shafiq-Ur-REHMAN University of Poonch Rawalakot Ajk Pakistan, Laboratory of Plant Breeding and Molecular Genetics, Azad, Kashmir (PK)
  • Zhan-Wu GAO Baicheng Normal University, Tourism and Geographical Science Institute, Baicheng 137000 (CN)

DOI:

https://doi.org/10.15835/nbha51312659

Keywords:

functional analysis, gene mining, maize, polymorphisms, Rhizobacteria

Abstract

Maize has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9P. The strains, together with 26 other sequenced Maize were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9P. The strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. The distinction among people and different creatures can be gotten by relative examinations. This study reveals that both maize and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.

References

Achard P, Herr A, Baulcombe DC, Harberd NP (2014). Modulation of floral development by a gibberellin-regulated micro-RNA. Development 131:3357-3365. https://doi.org/10.1242/dev.01206

Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2018). Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology 18:758-762. https://doi.org/10.1016/j.cub.2008.04.042

Ahmadi J, Fotokian MH (2011). Identification and mapping of quantitative trait loci associated with salinity tolerance in rice (Oryza sativa) using SSR markers. Iran Journal of Biotechnology 9:21-30. https://doi.org/10.5897/AJB2018.16661

Akagi T, Ikegami A, Yonemori K (2012). DkMyb2 wound-induced transcription factor of persimmon (Diospyros kaki Thunb.), contributes to proanthocyanidin regulation. Planta 232:1045-1059. https://doi.org/10.1007/s00425-010-1241-7

Alexa A, Rahnenfuhrer J (2010). TopGO: enrichment analysis for gene ontology. R Package Version 2:2010. https://doi.org/10.1038/s41467-022-31280-w

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E (2011). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29:37-40.

Aya K, Ueguchi-Tanaka M, Kondo M, Hamada K, Yano K (2019). Gibberellin modulates anther development in rice via the transcriptional regulation of GAMYB. Plant Cell 21:1453-1472. https://doi.org/10.1105/tpc.108.062935

Bailey TL, Gribskov M (2018). Combining evidence using p–values: application to sequence homology searches. Bioinformatics 14:48-54. https://doi.org/10.1093

Bailey TL, Williams N, Misleh C, Li WW (2016). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research 34:W369-W373. https://doi.org/10.1093/nar/gkl198

Ballester AR, Molthoff J, de Vos R, Hekkert BL, Orzaez D (2010). Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. Plant Physiology 152:71-84. https://doi.org/10.1104/pp.109.147322

Balsalobre TWA., da Silva Pereira G, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Carneiro MS (2017). GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC genomics 18(1):1-19. https://doi.org/10.1186/s12864-016-3383-x

Baumann K, Perez–Rodriguez M, Bradley D, Venail J, Bailey P (2017). Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development 134:1691-1701. https://doi.org/10.1242/dev.02836

Bazzo BR, de Carvalho LM, Carazzolle MF, Pereira GAG, Colombo CA (2018). Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species. BMC Plant Biology 18:276. https://doi.org/10.1186/s12870-018-1509-9

Boddu J, Jiang C, Sangar V, Olson T, Peterson T (2016). Comparative structural and functional characterization of sorghum and maize duplications containing orthologous myb transcription regulators of 3-deoxyflavonoid biosynthesis. Plant Molecular Biology 60:185-199. https://doi.org/10.1007/s11103-005-3568-1

Busson-Le Coniat M, Salomon-Nguyen F, Hillion J, Bernard OA, Berger R (2019). MLL-AF1q fusion resulting from t(1;11) in acute leukemia. Leukemia 13:302-306. https://doi.org/10.1038/sj.leu.2401299

Byrne ME, Barley R, Curtis M, Arroyo JM, Dunham M (2018). Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature 408:967-971. https://doi.org/10.1038/35050091

Cai H, Tian S, Dong H (2012). Large scale in silico identification of MYB family genes from wheat expressed sequence tags. Molecular Biotechnology. https://doi.org/10.1007/s12033-011-9486-3

Cannon SB, Shu H, Baumgarten AM, Spangler R, May G, Cook DR, Young ND (2012). Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. Journal of Molecular Evolution 54:548-562. https://doi.org/10.1007/s0023901-0057-2

Carine AT, Wang BB, Majesta SO, Shweta D, Zhu HY, Bruce R, Nevin DY, Steven BC (2018). Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiology 146:5-21. https://doi.org/10.1104/pp.107.104588

Ceasar SA, Ignacimuthu S (2018). Efficient somatic embryogenesis and plant regeneration from shoot apex explants of different Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn.). In Vitro Cell Devision Biology Plant 44:427-435. https://doi.org/10.1007/s11627-008-9153-y

Celenza JL, Quiel JA, Smolen GA, Merrikh H, Silvestro AR (2015). The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Plant Physiology 137:253-262. https://doi.org/10.1104/pp.104.054395

Chen C, Zhou P, Choi YA, Huang S, Gmitter FG Jr (2016). Mining and characterizing microsatellites from citrus ESTs. Theoretical and Applied Genetics 112:1248-1257. https://doi.org/10.1007/s00122-006-0226-1

Chen DM, Kang H, Liu CJ (2011). An overview on the potential quaternary glacial refugia of plants in China mainland. Bulletin of Botanical Research 31:623-632. https://doi.org/10.7525/j.issn.1673-5102.2011.05.019

Chen LY, Cao YN, Yuan N, Nakamura K, Wang GM, Qiu YX (2015). Characterization of transcriptome and development of novel EST-SSR makers based on next-generation sequencing technology in Neolitsea sericea (Lauraceae) endemic to East Asian land-bridge islands. Molecular Breeding 35:187. https://doi.org/10.1007/s11032-015-0379-1

Chen SY, Dong ML, Zhang Y, Qi SZ, Liu XZ, Zhang JF (2020). Development and characterization of simple sequence repeat markers for, and genetic diversity analysis of Liquidambar formosana. Forests 11:203. https://doi.org.10.3390/f11020203

Chennaveeraiah MS, Hiremath SC (2011). Cytogenetics of minor millets. In: Tsuchiya T, Gupta PK (Eds). Chromosome Engineering in Plants Genetics Breeding and Evolution. Elsevier, Amsterdam, pp 613-627. https://doi.org/10.1016/B978-0-444-88259-2.50034-5

Chilingaryan A, Gevorgyan N, Vardanyan A, Jones D, Szabo A (2002). Multivariate approach for selecting sets of differentially expressed genes. Math Bioscience 176:59-69. https://doi.org/10.1016/S0025-5564(01)00105-5

Cho SJ, Hermsmeier MA (2002). Genetic algorithm guided selection: variable selection and subset selection. Journal of Chemical Information and Computer Sciences 42:927-936. https://doi.org/10.1021/ci010247v

Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, … Cartinhour S (2010). Diversity of microsatellites derived from genomic libraries and Gen Bank sequences in rice (Oryza sativa). Theoretical and Applied Genetics 100:713-722. https://doi.org/10.1007/s001220051343

Colquhoun TA, Kim JY, Wedde AE, Levin LA, Schmitt KC (2012). PhMYB4 fine-tunes the floral volatile signature of Petunia x hybrida through PhC4H. Journal of Experimental Botany 62:1133-1143. https://doi.org/10.1093/jxb/erq342

Cone KC, Cocciolone SM, Burr FA, Burr B (2013). Maize anthocyanin regulatory gene pl is a duplicate of c1 that functions in the plant. Plant Cell 5:1795-1805. https://doi.org/10.1105/tpc.5.12.1795

Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2015). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676. https://doi.org/10.1093/bioinformatics/bti610

Czemmel S, Stracke R, Weisshaar B, Cordon N, Harris NN (2019). The grapevine R2R3-MYB transcription factor VvMYBF1 regulates flavonol synthesis in developing grape berries. Plant Physiology 151:1513-1530. https://doi.org/10.1104/pp.109.142059

Dang ZH, Huang L, Jia YY, Lockhart PJ, Fong Y, Jan YY (2020). Identification of genic SSRs provide a perspective for studying environmental adaptation in the endemic shrub Tetraena mongolica. Genes 11:322. https://doi.org/10.3390/genes11030322

Dong, ML, Wang ZW, He QW, Zhao J, Fan ZR, Zhang, JF (2018). Development of EST-SSR markers in Larix principis-rupprechtii Mayr and evaluation of their polymorphism and cross-species amplification. Trees 32:1559-1571. https://doi.org/10.1007/s00468-018-1733-9

Dubos C, Le Gourrierec J, Baudry A, Huep G, Lanet E (2018). MYBL2 is a new regulator of flavonoid biosynthesis in Arabidopsis thaliana. The Plant Journal 55:940-953. https://doi.org/10.1111/j.1365-313X.2008.03564.x

Durand J, Catherine B, Emilie C, Frigerio JM (2010). A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11:570-583. https://doi.org/10.1186/1471-2164-11-570

Dutta S, Kumawat G, Singh BP,Gupta DK., Singh S, Dogra V (2011). Development of genic-SSR markers by deep transcriptome sequencing in pigeon pea Cajanus cajan (L.) Millspaugh. BMC Plant Biology 11:17. https://doi.org/10.1186/1471-2229-11-17

Engqvist M, Yatusevich R, Müller C, Flügge UI (2018). HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. New Phytology 177:627-642. https://doi.org/10.1111/j.1469-8137.2007.02295.x

Eujayl I, Sledge MK., Wang L, May GD, Chekhovskiy K., Zwonitzer JC (2014). Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theoretical and Applied Genetics 108:414-422. https://doi.org/10.1007/s00122-003-1450-6

Feng C, Andreasson E, Maslak A, Mock HP, Mattsson O (2014). Arabidopsis MYB68 in development and responses to environmental cues. Plant Science 167:1099-1107. https://doi.org/10.1016/j.plantsci.2004.06.014

Fornalé S, Sonbol FM, Maes T, Capellades M, Puigdomènech P (2016). Down-regulation of the maize and Arabidopsis thaliana caffeic acid O-methyl-transferase genes by two new maize R2R3-MYB transcription factors. Plant Molecular Biology 62:809-823. https://doi.org/10.1007/s11103-006-9058-2

Fu LG, Jin JM (2012). Red List of Endangered Plants in China. Vol. 1. Science Press.

Fu LG, Li N, Mill RR (2019). Taxaceae. In: Wu ZY, Raven PH (Eds). Flora of China. Beijing: Science Press, pp 89-98. https://doi.org/10.3389/fgene.2019.01014

Fu LM, Niu BF, Zhu ZW, Wu ST, Li WZ (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150-3152. https://doi.org/10.1093/bioinformatics/bts565

Gao CH, Ren XD, Mason AS, Li J, Wang W, Xiao ML (2013). Revisiting an important component of plant genomes: microsatellites. Functional Plant Biology 40:645-661. https://doi.org/10.1071/12325

Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, … Shape JW (2010). An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 53:1-13. https://doi.org/10.1139/g09-079

Gupta PK, Varshney RK (2020). The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163-185. https://doi.org/10.1023/A:1003910819967

Hancock JM (2015). The contribution of slippage-like processes to genome evolution. Journal of Molecular Evolution 41:1038-1047. https://doi.org/10.1007/BF00173185

Haseman JK. Elston RC (2012). The investigation of linkage between a quantitative trait and a marker locus. Behavioral Genetics 2:3-19. https://doi.org/10.1007/BF01066731

He L, Du C, Covaleda L, Xu Z, Robinson AF, Yu JZ, Kohel RJ, Zhang HB (2014). Cloning, characterization, and evolution of the NBSLRR-encoding resistance gene analogue family in polyploidy cotton (Gossypium hirsutum L.). Molecular Plant Microbe Interaction 17:1234-1241. https://doi.org/10.1094/MPMI.2004.17.11.1234

Jia XP, Shi YS, Song YC (2017). Development of EST–SSR in foxtail millet (Setaria italica) [J]. Genetic Resource and Crop Evolution 54:233-236.

Jiang C, Gu X, Peterson T (2014). Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biology 5:R46. https://doi.org/10.1186/gb-2004-5-7-r46

Jin H, Cominelli E, Bailey P, Parr A, Mehrtens F (2015). Transcriptional repression by AtMYB4 controls production of UV–protecting sunscreens in Arabidopsis. EMBO Journal 19:6150-6161.

Kaneko M, Inukai Y, Ueguchi-Tanaka M, Itoh H, Izawa T (2014). Loss-of-function mutations of the rice GAMYB gene impair alpha-amylase expression in aleurone and flower development. Plant Cell 16:33-44.

Kantety RV, La Rota M, Matthews DE, Sorrells ME (2012). Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Molecular Biology 48:501-510.

Keller T, Abbott J, Moritz T, Doerner P (2016). Arabidopsis REGULATOR OF AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative development. Plant Cell 18:598-611.

Koltai H, Bird DM (2011). Epistatic repression of PHANTASTICA and class 1 KNOTTED genes is uncoupled in tomato. The Plant Journal 22:455-459.

Latha MA, Venkateswara Rao K, Dashavantha Reddy V (2015). Production of transgenic plants resistant to leaf blast disease in finger millet (Eleusine coracana (L.) Gaertn.). Plant Science 169:657-667.

Laurent, P, Elduque C, Hayes H, Saunier K., Eggen A, Levéziel H (2012). Assignment of 60 human ESTs in cattle Mammal. Genome 11:748-754.

Legay S, Sivadon P, Blervacq AS, Pavy N, Baghdady A (2012). EgMYB1, an R2R3 MYB transcription factor from eucalyptus negatively regulates secondary cell wall formation in Arabidopsis and poplar. New Phytology 188:774-786.

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T (2014). SMART 4.0: towards genomic data integration. Nucleic Acids Research 32:D142-D144.

Li L, Darden TA., Weinberg CR, Levine AJ, Pedersen LG (2001). Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. Comb. Chem. High Throughput Screening 4:727-739.

Li SF, Milliken ON, Pham H, Seyit R, Napoli R (2019). The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis. Plant Cell 21:72-89.

Li ZG, Wu MY, Zhao W, Li B, Yang ZP, Hu YM (2003). Detection of 29 types of fusion gene in leukemia by multiplex RT-PCR [in Chinese]. Zhonghua Xue Ye Xue Za Zhi 24:256-258.

Li B, Peng L, Sun X, Huang W, Wang N, He Y, Tang Z (2020). Organ-specific transcriptome sequencing and mining of genes involved in polyphyllin biosynthesis in Paris polyphylla. Industrial Crops and Products 156:112775. https://doi.org/10.1016/j.indcrop.2020.112775

Ma QH, Wang C, Zhu HH (2013). TaMYB4 cloned from wheat regulates lignin biosynthesis through negatively controlling the transcripts of both cinnamyl alcohol dehydrogenase and cinnamoyl-CoA reductase genes. Biochemistry 93:1179-1186. https://doi.org/10.1016/j.biochi.2011.04.012

Maia LC, Souza VQ, Kopp MM, Carvalho FIF, Oliveira AC (2019). Tandem repeat distribution of gene transcripts in three plant families. Genetic and Molecular Biology 32:1-12.

Marocco A, Wissenbach M, Becker D, Paz-Ares J, Saedler H (2019). Multiple genes are transcribed in Hordeum vulgare and Zea mays that carry the DNA binding domain of the myb oncoproteins. Molecular Genetics 216:183-187. https://doi.org/10.1007/BF00334354

Martienssen RA, Rabinowicz PD, O’Shaughnessy A, McCombie WR (2014). Sequencing the maize genome. Current Opinion in Plant Biology 7:102-107.

Martins WS, Lucas DCS, Neves KFS, Bertioli DJ (2019). WebSat-A Web Software for microsatellite marker development. Bioinformatics 3(6):28-283. https://doi.org/10.6026/97320630003282

Matus JT, Aquea F, Arce-Johnson P (2018). Analysis of the grape MYB R2R3 subgroup reveals expanded wine quality–related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biology 8:83-98. https://doi.org/10.1186/1471-2229-8-83

Mehrtens F, Kranz H, Bednarek P, Weisshaar B (2015). The Arabidopsis transcription factor MYB12 is a flavonol–specific regulator of phenylpropanoid biosynthesis. Plant Physiology 138:1083-1096. https://doi.org/10.1104/pp.104.058032

Mellway RD, Tran LT, Prouse MB, Campbell MM, Constabel CP (2019). The wound-, pathogen-, and ultraviolet B-responsive MYB134 gene encodes an R2R3 MYB transcription factor that regulates proanthocyanidin synthesis in poplar. Plant Physiology 150:924-941. https://doi.org/10.1104/pp.109.139071

Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (2019). Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. The Plant Journal 20:317-332. https://doi.org/10.1046/j.1365-313X.1999.00606.x

Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2013). Genome-wide analysis of NBS–LRR encoding genes in Arabidopsis. Plant Cell 15:809-834. https://doi.org/10.1105/tpc.009308

Millar AA, Gubler F (2015). The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705-721. https://doi.org/10.1105/tpc.104.027920

Mishra RK, Gangadhar BH, Jae Woong Yu, Doo Hwan Kim, Se Won Park (2011). Development and characterization of EST based SSR markers in Madagascar periwinkle (Catharanthus roseus) and their transferability in other medicinal plants. Plant Omics Journal 4(3):154-162.

Morimoto R, Nishioka E, Murai K, Takumi S (2019). Functional conservation of wheat orthologs of maize rough sheath1 and rough sheath2 genes. Plant Molecular Biology 69:273-285. https://doi.org/10.1007/s11103-008-9422-5

Müller D, Schmitz G, Theres K (2016). Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis. The Plant Cell 18:586-597. https://doi.org/10.1105/tpc.105.038745

Murray F, Kalla R, Jacobsen J, Gubler F (2013). A role for HvGAMYB in anther development. The Plant Journal 33:481-491. https://doi.org/10.1046/j.1365-313X.2003.01641.x

Murray MG, Thompson WF (2011). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8:4321-4326. https://doi.org/10.1093/nar/8.19.4321

Nesi N, Jond C, Debeaujon I, Caboche M, Lepiniec L (2018). The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. The Plant Cell 13:2099-2114. https://doi.org/10.1105/TPC.010098

Nicholas KB, Nicholas HBJ, Deerfield DWI (2017). Genedoc: analysis and visualization of genetic variation. Embnew News 4:14.

Noda K, Glover BJ, Linstead P, Martin C (2014). Flower colour intensity depends on specialized cell shape controlled by a Myb-related transcription factor. Nature 369:661-664.

Ogata K, Morikawa S, Nakamura H, Hojo H, Yoshimura S (2014). Comparison of the free and DNA–complexed forms of the DNA–binding domain from c–Myb. Nature Structural Biology 2:309-320.

Okuyama Y, Kanzaki H, Abe A, Yoshida K, Tamiru M, Saitoh H, … Terauchi R (2011). A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes. The Plant Journal 66:467-479.

Palmer LE, Rabinowicz PD, O’Shaughnessy AL, Balija VS, Nascimento LU (2013). Maize genome sequencing by methylation filtration. Science 302:2115-2117.

Payne CT, Zhang F, Lloyd AM (2012). GL3 encodes a bHLH protein that regulates trichome development in Arabidopsis through interaction with GL1 and TTG1. Genetics 156:1349-1362.

Paz-Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H (2017). The regulatory c1 locus of maize encodes a protein with homology to myb proto–oncogene products and with structural similarities to transcriptional activators. EMBO Journal 6:3553-3558.

Rabinowicz PD, Braun EL, Wolfe AD, Bowen B, Grotewold E (2019). Maize R2R3 Myb genes: sequence analysis reveals amplification in the higher plants. Genetics 153:427-444.

Perez-Rodriguez M, Jaffe FW, Butelli E, Glover BJ, Martin C (2015). Development of three different cell types is associated with the activity of a specific MYB transcription factor in the ventral petal of Antirrhinum majus flowers. Development 132:359-370.

Pilu R, Piazza P, Petroni K, Ronchi A, Martin C (2013). pl-bol3, a complex allele of the anthocyanin regulatory pl1 locus that arose in a naturally occurring maize population. The Plant Journal 36:510-521.

Pletscher-Frankild S, Pallejà A. Tsafou K, Binder JX, Jensen LJ (2015). DISEASES: Text mining and data integration of disease–gene associations. Methods 74:83-89.

Pmaniatis T, Sambrook J, Fritsch EF (2019). Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, New York.

Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P (2016). SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus. Molecular Genetics and Genomics 276:436-449.

Preston J, Wheeler J, Heazlewood J, Li SF, Parish RW (2014). AtMYB32 is required for normal pollen development in Arabidopsis thaliana. The Plant Journal 40:979-995. https://doi.org/10.1111/j.1365-313X.2004.02280.x

Province MA, Shannon WD, Rao DC (2001). Classification methods for confronting heterogeneity. Advance Genetics 42:273-286. https://doi.org/10.1016/S0065-2660(01)42028-1

PS, Ware D, Fulton RS, Stein JC, Wei F (2019). The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115. https://doi.org/10.1126/science.1178534

Qi J, Zheng N, Zhang B, Sun P, Hu S, Xu W, Li X (2013). Mining genes involved in the stratification of Paris polyphylla seeds using high-throughput embryo Transcriptome sequencing. BMC Genomics 14(1):1-14. https://doi.org/10.1186/1471-2164-14-358

Reddy BLIN, Lakshmi NM, Sivaramakrishnan S (2012). Identification and characterization of EST–SSRs in finger millet (Eleusine coracana (L.) Gaertn.). Journal of Crop Science and Biotechnology 15(1):9-16. https://doi.org/10.1007/s12892-011-0064-9

Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B (2012). Prediction of plant microRNA targets. Cell 110:513-520. https://doi.org/10.1016/S0092-8674(02)00863-2

Saitoh K, Onishi K, Mikami I, Thidar K, Sano Y (2014). Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics 168:997-1007. https://doi.org/10.1534/genetics.103.018390

Schmitz G, Tillmann E, Carriero F, Fiore C, Cellini F (2012). The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems. Proceedings of the National Academy of Science 99:1064-1069. https://doi.org/10.1073/pnas.022516199

Senthilvel S, Jayashree B, Mahalakshmi V, Sathish Kumar P, Nakka S, Nepolean T, Hash CT (2018). Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biology 8:119. https://doi.org/10.1186/1471-2229-8-119

Shannon WD, Province MA, Rao DC (2001). Tree-based recursive partitioning methods for subdividing sibpairs into relatively more homogeneous subgroups. Genetics Epidemiology 20:293-306. https://doi.org/10.1002/gepi.1

Sonbol FM, Fornale S, Capellades M, Encina A, Tourin S (2014). The maize ZmMYB42 represses the phenylpropanoid pathway and affects the cell wall structure, composition and degradability in Arabidopsis thaliana. Plant Molecular. Biology 70:283-296. https://doi.org/10.1007/s11103-009-9473-2

Sønderby IE, Hansen BG, Bjarnholt N, Ticconi C, Halkier BA (2017). A systems biology approach identifies a R2R3 MYB gene subgroup with distinct and overlapping functions in regulation of aliphatic glucosinolates. PLoS One 19:e1322. https://doi.org/10.1371/journal.pone.0001322

Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2013). How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology 12:1339-1348. https://doi.org/10.1046/j.1365-294X.2003.01825.x

Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Lancet D (2016). The GeneCards suite: from gene data mining to disease genome sequence analyses. Current Protocol in Bioinformatics 54(1):1-30. https://doi.org/10.1002/cpbi.5

Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F (2017). Differential regulation of closely related R2R3–MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. The Plant Journal 50:660-677. https://doi.org/10.1111/j.1365-313X.2007.03078.x

Szabo A, Boucher K, Jones D, Tsodikov AD, Klebanov LB, Yakovlev AY (2003). Multivariate exploratory tools for microarray data analysis. Biostatistics 4:555-567. https://doi.org/10.1093/biostatistics/4.4.555

Thiel T, Michalek W, Varshney RK, Graner A (2013). Exploiting EST database for the development and characterization of gen-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106:411-422. https://doi.org/10.1007/s00122-002-1031-0

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (2017). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25:4876-4882. https://doi.org/10.1093/nar/25.24.4876

Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J (2015a). Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. The Plant Journal 42:218-235. https://doi.org/10.1111/j.1365-313X.2005.02371.x

Tsamardinos I, Aliferis CF (2003). Towards principled feature selection: relevance, filters and wrappers. In: Ninth International Workshop on Artificial Intelligence and Statistics, Key West, FL.

Tsiantis M, Schneeberger R, Golz JF, Freeling M, Langdale JA (2020). The maize rough sheath2 gene and leaf development programs in monocot and dicot plants. Science 284:154-156. https://doi.org/10.1126/science.284.5411.154

Tsuji H, Aya K, Ueguchi-Tanaka M, Shimada Y, Nakazono M (2016). GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. The Plant Journal 47:427-444. https://doi.org/10.1111/j.1365-313X.2006.02795.x

Van Aalten DM, Grotewold E, Joshua-Tor L (2018). Essential dynamics from NMR clusters: dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant. Methods 14:318-328. https://doi.org/10.1006/meth.1998.0587

Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2012). In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cellular and Molecular Biology Letters 7:537-546.

Victoria FC, da Maia Luciano C, de Oliveira Antonio C (2011). In silico comparative analysis of SSR markers in plants. BMC Plant Biology 11:15–30. https://doi.org/10.1186/1471-2229-11-15

Vizir I, Twell D (2015). Male germ line development in Arabidopsis: duo pollen mutants reveal gametophytic regulators of generative cell cycle progression. Plant Physiology 137:297-307. https://doi.org/10.1104/pp.104.053165

Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Griffith OL (2016). DGIdb 2.0: mining clinically relevant drug–gene interactions. Nucleic Acids Research 44(D1): D1036-D 1044. https://doi.org/10.1093/nar/gkv1165

Waites R, Selvadurai HR, Oliver IR, Hudson A (2018). The PHANTASTICA gene encodes a MYB transcription factor involved in growth and dorsoventrality of lateral organs in Antirrhinum. Cell 93:779-789. https://doi.org/10.1016/S0092-8674(00)81439-7

Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N (2020). The Transparent Testa Glabra1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes aWD40 repeat protein. The Plant Cell 11:1337-1350. https://doi.org/10.1105/tpc.11.7.1337

Watanabe N, Kobayashi H, Ichiji O, Yoshida MA, Kikuta A, Komada Y, Sekine I, Ishida Y, Horiukoshi Y, Tsunematsu Y (2003). Cryptic insertion and translocation or nondividing leukemic cells disclosed by FISH analysis in infant acute leukemia with discrepant molecular and cytogenetic findings. Leukemia 17:876-882. https://doi.org/10.1038/sj.leu.2402900

Weising K, Nybom H, Wolff K, Kahl G (2015). Application of DNA fingerprinting in plant sciences. DNA Fingerprinting in plants-principles, methods, and applications. CRC Press, Boca Raton, pp 235-276. https://doi.org/10.1093/aob/mcj057

Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM (2019). Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiology 149:981-993. https://doi.org/10.1104/pp.108.132795

Williams CE, Grotewold E (2017). Differences between plant and animal Myb domains are fundamental for DNA binding activity, and chimeric Myb domains have novel DNA binding specificities. Journal of Biological Chemistry 272:563-571. https://doi.org/10.1074/jbc.272.1.563

Woodger FJ, Gubler F, Pogson BJ, Jacobsen JV (2013). A Mak-like kinase is a repressor of GAMYB in barley aleurone. The Plant Journal 33:707-717. https://doi.org/10.1046/j.1365-313X.2003.01663.x

Xiaoyuan Y, Kun H, Meihua L, Jigang L (2016). The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Molecular Biology 60:107-124. https://doi.org/10.1007/s11103-005-2910-y

Xu R, Wang Z, Su Y, Wang T (2020). Characterization and development of microsatellite markers in Pseudotaxus chienii (Taxaceae) based on transcriptome sequencing. Frontier in Genetics 11:1249. https://doi.org/10.3389/fgene.2020.574304

Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME (2014). Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805-818.

Zane L, Bargelloni L, Patarnello T (2012). Strategies for microsatellite isolation: a review. Molecular Ecology 11:1-16. https://doi.org/10.1046/j.0962-1083.2001.01418.x

Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Bruce A Roe, Wang Y (2010). Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) maxim. BMC Genomics 11:94-105. https://doi.org/10.1186/1471-2164-11-94

Zhang F, Gonzalez A, Zhao M, Payne CT, Lloyd A (2013). A network of redundant bHLH proteins functions in all TTG1-dependent pathways of Arabidopsis. Development 130:4859-4869. https://doi.org/10.1242/dev.00681

Zhang F, Peterson T (2015). Comparisons of maize pericarp color1 alleles reveal paralogous gene recombination and an organ-specific enhancer region. Plant Cell 17:903-914. https://doi.org/10.1105/tpc.104.029660

Zhang L, Chia JM, Kumari S, Stein JC, Liu Z (2019). A genome-wide characterization of microRNA genes in maize. PLoS Genetics 5:e1000716. https://doi.org/10.1371/journal.pgen.1000716

Zhang L, Zhao G, Jia J, Liu X, Kong X (2012). Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress. Journal of Experimental Botany 63:203-214. https://doi.org/10.1093/jxb/err264

Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF (2014). Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. The Plant Journal 40:22-34. https://doi.org/10.1111/j.1365-313X.2004.02183.x

Published

2023-08-31

How to Cite

GILLANI, S. F., RASHEED, A., MAJEED, Y., BUKHARI, S. S., TARIQ, H., Shafiq-Ur-REHMAN, & GAO, Z.-W. (2023). Gene mining and functional analysis related to maize (Zea mays L.) seed size. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51(3), 12659. https://doi.org/10.15835/nbha51312659

Issue

Section

Review Articles
CITATION
DOI: 10.15835/nbha51312659

Most read articles by the same author(s)

<< < 1 2