QTL-seq identifies genomic region associated with the crown root development under Jasmonic acid response

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  Google Scholar 

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

Article  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  PubMed  Google Scholar 

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

Article  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

Comments (0)

No login
gif