Prioritization of candidate genes regulating the dwarfness in rice by integration of whole-genome and transcriptome analyses

Abdullah-Zawawi M-R, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein Z-A (2022) Multi-omics approaches and resources for systems-level gene function prediction in the plant kingdom. Plants 11:2614

Article  PubMed  CAS  Google Scholar 

Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X (2018) High-density genetic map using whole‐genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnol J 16:1954–1967

Article  PubMed  CAS  Google Scholar 

Aoi Y, Hira H, Hayakawa Y, Liu H, Fukui K, Dai X, Tanaka K, Hayashi K-i, Zhao Y, Kasahara H (2020) UDP-glucosyltransferase UGT84B1 regulates the levels of indole-3-acetic acid and phenylacetic acid in Arabidopsis. Biochem Biophys Res Commun 532:244–250

Article  PubMed  CAS  Google Scholar 

Arite T, Umehara M, Ishikawa S, Hanada A, Maekawa M, Yamaguchi S, Kyozuka J (2009) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant Cell Physiol 50:1416–1424

Article  PubMed  CAS  Google Scholar 

Arunachalam P, Lalitha R, Vanniarajan C, Souframanien J (2022) Comparative analysis of gamma rays and electron beam in altering rice (Oryza sativa L.) grain size. Indian J Genet 82:355–358

Article  CAS  Google Scholar 

Ashikari M, Sasaki A, Ueguchi-Tanaka M, Itoh H, Nishimura A, Datta S, Ishiyama K, Saito T, Kobayashi M, Khush GS (2002) Loss-of-function of a rice gibberellin biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice ‘green revolution’. Breed Sci 52:143–150

Article  CAS  Google Scholar 

Bandumula N (2018) Rice production in Asia: Key to global food security. Proc Natl Acad Sci India Sect B: Biol Sci 88:1323–1328

Article  Google Scholar 

Bei X, Shahid MQ, Wu J, Chen Z, Wang L, Liu X (2019) Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neo-tetraploid rice. PLoS ONE 14:e0214953

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bin Rahman AR, Zhang J (2023) Trends in rice research: 2030 and beyond. Food Energy Secur 12:e390

Article  Google Scholar 

Bohra A, Chand Jha U, Godwin ID, Kumar Varshney R (2020) Genomic interventions for sustainable agriculture. Plant Biotechnol J 18:2388–2405

Article  PubMed  Google Scholar 

Bordoloi D, Sarma D, Sarma Barua N, Das BK (2023) Mutation induction in aromatic Joha rice of Assam for improvement of morpho-agronomic traits through M1 to M3 generation. Int J Radiat Biol 99:1760–1777

Article  PubMed  CAS  Google Scholar 

Chan AN, Wang L-L, Zhu Y-J, Fan Y-Y, Zhuang J-Y, Zhang Z-H (2021) Identification through fine mapping and verification using CRISPR/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice. Theor Appl Genet 134:327–337

Article  PubMed  CAS  Google Scholar 

Chen R, Cheng Y, Han S, Van Handel B, Dong L, Li X, Xie X (2017) Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar–sea rice 86. BMC Genet 18:1–11

Google Scholar 

Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. fly 6:80–92

Corchete LA, Rojas EA, Alonso-López D, De Las Rivas J, Gutiérrez NC, Burguillo FJ (2020) Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis. Sci Rep 10:19737

Article  PubMed  PubMed Central  CAS  Google Scholar 

de Saint Germain A, Bonhomme S, Boyer F-D, Rameau C (2013) Novel insights into strigolactone distribution and signalling. Curr Opin Plant Biol 16:583–589

Article  PubMed  Google Scholar 

Dong NQ, Sun Y, Guo T, Shi CL, Zhang YM, Kan Y, Xiang YH, Zhang H, Yang YB, Li YC (2020) UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nat Commun 11:2629

Article  PubMed  CAS  Google Scholar 

Du L, Li N, Chen L, Xu Y, Li Y, Zhang Y, Li C, Li Y (2014) The ubiquitin receptor DA1 regulates seed and organ size by modulating the stability of the ubiquitin-specific protease UBP15/SOD2 in Arabidopsis. Plant Cell 26:665–677

Article  PubMed  PubMed Central  CAS  Google Scholar 

Feng-hua H, Zhang-Ying X, Rui-zhen Z, Gui-quan TALUKDARA Z (2005) Identification of QTLs for plant height and its components by using single segment substitution lines in rice (Oryza sativa). Rice Sci 12:151

Google Scholar 

Garcia RS, Coronejo S, Concepcion J, Subudhi PK (2022) Whole-genome sequencing and RNA-seq reveal differences in genetic mechanism for flowering response between weedy rice and cultivated rice. Int J Mol Sci 23:1608

Article  PubMed  PubMed Central  CAS  Google Scholar 

Gautam V, Swaminathan M, Akilan M, Gurusamy A, Suresh M, Kaithamalai B, Joel AJ (2021) Early flowering, good grain quality mutants through gamma rays and EMS for enhancing per day productivity in rice (Oryza sativa L). Int J Radiat Biol 97:1716–1730

Article  PubMed  CAS  Google Scholar 

Gowthami R, Vanniarajan C, Souframanien J, Veni K, Renganathan V (2021) Efficiency of electron beam over gamma rays to induce desirable grain-type mutation in rice (Oryza sativa L). Int J Radiat Biol 97:727–736

Article  PubMed  CAS  Google Scholar 

Hake AA, Ballichatla S, Barbadikar KM, Magar N, Dutta S, Gokulan C, Awalellu K, Patel HK, Sonti RV, Phule AS (2023) Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice. Mol Breeding 43:69

Article  CAS  Google Scholar 

Hirano K, Okuno A, Hobo T, Ordonio R, Shinozaki Y, Asano K, Kitano H, Matsuoka M (2014) Utilization of stiff culm trait of rice smos1 mutant for increased lodging resistance. PLoS ONE 9:e96009

Article  PubMed  PubMed Central  Google Scholar 

Huang N, Courtois B, Khush GS, Lin H, Wang G, Wu P, Zheng K (1996) Association of quantitative trait loci for plant height with major dwarfing genes in rice. Heredity 77:130–137

Article  CAS  Google Scholar 

International Rice Genome Sequencing Project (2005) (2005) The map-based sequence of the rice genome. Nature 436:793–800

Ishikawa S, Maekawa M, Arite T, Onishi K, Takamure I, Kyozuka J (2005) Suppression of tiller bud activity in tillering dwarf mutants of rice. Plant Cell Physiol 46:79–86

Article  PubMed  CAS  Google Scholar 

Jia Y, Shen T, Wen Z, Chen J, Liu Q (2023) Combining transcriptome and whole genome re-sequencing to screen Disease Resistance genes for wheat dwarf bunt. Int J Mol Sci 24:17356

Article  PubMed  CAS  Google Scholar 

Jiang L, Liu X, Xiong G, Liu H, Chen F, Wang L, Meng X, Liu G, Yu H, Yuan Y (2013) DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature 504:401–405

Article  PubMed  CAS  Google Scholar 

Joshi R, Prashat R, Sharma PC, Singla-Pareek SL, Pareek A (2016) Physiological characterization of gamma-ray induced mutant population of rice to facilitate biomass and yield improvement under salinity stress. Indian J Plant Physiol 21:545–555

Article  Google Scholar 

Kato H, Li F, Shimizu A (2020) The selection of gamma-ray irradiated higher yield rice mutants by directed evolution method. Plants 9:1004

Article  PubMed  CAS  Google Scholar 

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S (2013) Improvement of the Oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice 6:1–10

Article  Google Scholar 

Kim C-K, Seol Y-J, Shin Y, Lim H-M, Lee G-S, Kim A-R, Lee T-H, Lee J-H, Park D-S, Yoo S (2015) Whole-genome resequencing and transcriptomic analysis to identify genes involved in leaf-color diversity in ornamental rice plants. PLoS ONE 10:e0124071

Article  PubMed  PubMed Central  Google Scholar 

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37:907–915

Article  PubMed  PubMed Central  CAS 

留言 (0)

沒有登入
gif