Benavente E, Giménez E (2021) Modern Approaches for the Genetic Improvement of Rice, Wheat and Maize for Abiotic Constraints-Related Traits: A Comparative Overview. Agronomy 11:376. https://doi.org/10.3390/agronomy11020376
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinforma Oxf Engl 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Chico JM, Lechner E, Fernandez-Barbero G, Canibano E, Garcia-Casado G, Franco-Zorrilla JM, Hammann P, Zamarreno AM, Garcia-Mina JM, Rubio V et al (2020) CUL3(BPM) E3 ubiquitin ligases regulate MYC2, MYC3, and MYC4 stability and JA responses. Proc Natl Acad Sci U S A 117:6205–6215
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. https://doi.org/10.4161/fly.19695
Darvasi A, Soller M, Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic-mapping. Genetics 141:1199–1207. https://doi.org/10.1093/genetics/141.3.1199
Article PubMed PubMed Central CAS Google Scholar
Deb S, Sankaranarayanan S, Wewala G, Widdup E, Samuel MA (2014) The S-domain receptor kinase arabidopsis receptor Kinase2 and the U Box/Armadillo repeat-containing E3 ubiquitin Ligase9 module mediates lateral root development under phosphate starvation in Arabidopsis. Plant Physiol 165:1647–1656
Article PubMed PubMed Central CAS Google Scholar
Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464:1039–1042. https://doi.org/10.1038/nature08923
Article PubMed PubMed Central CAS Google Scholar
Fattorini L, Hause B, Gutierrez L, Veloccia A, Rovere FD, Piacentini D, Falasca G, Altamura MM (2018) Jasmonate promotes auxin-induced adventitious rooting in dark-grown Arabidopsis thaliana seedlings and stem thin cell layers by a cross-talk with ethylene signalling and a modulation of xylogenesis. BMC Plant Biol 18:1–18
des Georges A, Dhote V, Kuhn L, Hellen CUT, Pestova TV, Frank J, Hashem Y (2015) Structure of mammalian eIF3 in the context of the 43S preinitiation complex. Nature 525(7570):491–495. https://doi.org/10.1038/nature14891
Article PubMed PubMed Central CAS Google Scholar
Giovannoni JJ, Wing RA, Ganal MW, Tanksley SD (1991) Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Res 19:6553–6568. https://doi.org/10.1093/nar/19.23.6553
Article PubMed PubMed Central CAS Google Scholar
Hentrich M, Böttcher C, Düchting P, Cheng Y, Zhao Y, Berkowitz O, Masle J, Medina J, Pollmann S (2013) The jasmonic acid signaling pathway is linked to auxin homeostasis through the modulation of YUCCA8 and YUCCA9 gene expression. Plant J 74(4):626-37. https://doi.org/10.1111/tpj.12152
Jung C, Zhao P, Seo JS, Mitsuda N, Deng S, Chua NH (2015) PLANT U-BOX PROTEIN10 regulates MYC2 stability in Arabidopsis. Plant Cell 27:2016–2031
Article PubMed PubMed Central CAS Google Scholar
Kim M-S, Kang K-K, Cho Y-G (2021) Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice (Oryza sativa). Int J Mol Sci 22(21):12088. https://doi.org/10.3390/ijms222112088
Article PubMed PubMed Central CAS Google Scholar
Kim T-H, Kim B-H, Yahalom A, Chamovitz DA, von Arnim AG (2004) Translational Regulation via 5′ mRNA Leader Sequences Revealed by Mutational Analysis of the Arabidopsis Translation Initiation Factor Subunit eIF3h. Plant Cell 16(12):3341–3356. https://doi.org/10.1105/tpc.104.026880
Article PubMed PubMed Central CAS Google Scholar
Lakehal A, Dob A, Rahneshan Z, Novák O, Escamez S, Alallaq S, Strnad M, Tuominen H, Bellini C (2020) Ethylene response factor 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in Arabidopsis. New Phytol. 228(5):1611–1626. https://doi.org/10.1111/nph.16794
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma Oxf Engl 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Muthayya S, Sugimoto JD, Montgomery S, Maberly GF (2014) An overview of global rice production, supply, trade, and consumption. Ann N Y Acad Sci 1324(1):7–14. https://doi.org/10.1111/nyas.12540
Nubankoh P, Wanchana S, Saensuk C et al (2020) QTL-seq reveals genomic regions associated with spikelet fertility in response to a high temperature in rice (Oryza sativa L.). Plant Cell Rep 39:149–162. https://doi.org/10.1007/s00299-019-02477-z
Article PubMed CAS Google Scholar
Ou Y, Kui H, Li J (2021J 4) Receptor-like kinases in root development: current progress and future directions. Mol Plant 14(1):166–185. https://doi.org/10.1016/j.molp.2020.12.004
Article PubMed CAS Google Scholar
Sugihara Y, Young L, Yaegashi H, Natsume S, Shea DJ, Takagi H, Booker H, Innan H, Terauchi R, Abe A (2022) High-performance pipeline for MutMap and QTL-seq. PeerJ 10:e13170. https://doi.org/10.7717/peerj.13170
Article PubMed PubMed Central Google Scholar
Sun C, He Y, Chen G, Rao Y, Zhang G, Gao Z, Liu J, Ju P, Hu J, Guo L, Qian Q, Zeng D (2010) A Simple Method for Preparation of Rice Genomic DNA. Rice Sci 17:326–329. https://doi.org/10.1016/S1672-6308(09)60034-2
Sun J, Xu Y, Ye S et al (2009) Arabidopsis ASA1 Is Important for Jasmonate-Mediated Regulation of Auxin Biosynthesis and Transport during Lateral Root Formation. Plant Cell Online 21:1495–1511
Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. https://doi.org/10.1111/tpj.12105
Article PubMed CAS Google Scholar
To HTM, Nguyen HT, Dang NTM et al (2019) Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study. Rice 12:69. https://doi.org/10.1186/s12284-019-0327-5
Article PubMed PubMed Central Google Scholar
To HTM, Pham DT, Le Thi VA, Nguyen TT, Tran TA, Ta AS, Chu HH, Do PT (2022N) The Germin-like protein OsGER4 is involved in promoting crown root development under exogenous jasmonic acid treatment in rice. Plant J 112(3):860–874. https://doi.org/10.1111/tpj.15987
Article PubMed CAS Google Scholar
Vij S, Giri J, Dansana PK, Kapoor S, Tyagi AK (2008) The receptor-like cytoplasmic kinase (OsRLCK) gene family in rice: organization, phylogenetic relationship, and expression during development and stress. Mol Plant 1(5):732–750. https://doi.org/10.1093/mp/ssn047
Article PubMed CAS Google Scholar
Wang Y, Liu J, Meng Y, Liu H, Liu C, Ye G (2021) Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis. Front Genet 12:713446. https://doi.org/10.3389/fgene.2021.713446
Article PubMed PubMed Central CAS Google Scholar
Zeng LR, Park CH, Venu RC, Gough J, Wang GL (2008) Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins. Mol Plant 1(5):800–815. https://doi.org/10.1093/mp/ssn044
Article PubMed CAS Google Scholar
Zhao FY, Hu F, Zhang SY, Wang K, Zhang CR, Liu T (2013) MAPKs regulate root growth by influencing auxin signaling and cell cycle-related gene expression in cadmium-stressed rice. Environ Sci Pollut Res 20(8):5449–5460. https://doi.org/10.1007/s11356-013-1559-3
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