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A modified CTAB and Trizol® protocol for high-quality RNA extraction from whole wheat seedlings, including rhizosphere

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Abstract

The RNA extraction was performed from foliar (F) and whole wheat plants (including rhizosphere) (WP) samples by (1) the standard TRIzol® protocol, and (2) a modified CTAB and TRIzol® protocol. The modified CTAB and TRIzol® protocol was able to extract high-quality RNA (205.96 ± 18.7 ng/µL for F, and 231.76 ± 66.8 ng/µL for WP; RIN > 8.0), compared to the standard TRIzol® protocol (92.73 ± 24.2 ng/µL for F, and WP completely degraded, RIN < 8.0). Real-time RT-PCR assay was carried out for 6-SFT1 (target) and 18S rRNA (housekeeping) genes, which showed a PCR efficiency of 111% and 118%, respectively, and a no significant relative expression (3773 ± 1383.8 for F and 2847 ± 1037.5 for WP) was observed from RNA extracted by the modified protocol. The modified CTAB and TRIzol® protocol was able to produce high-quality RNA (yield, purity, and integrity) from foliar and whole wheat plants (including rhizosphere with recalcitrant properties).

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Acknowledgements

The authors acknowledge support by the CONACyT Project 257246 “Interacción trigo x microorganismos promotores del crecimiento vegetal: identificando genes con potencial agro-biotecnológico”, and the Instituto Tecnológico de Sonora (ITSON) Project PROFAPI 2020_0013 “Bacillus sp. TSO9: afiliación taxonómica a nivel del genoma e identificación de genes asociados a la promoción del crecimiento en el trigo”. Luis Abraham Chaparro-Encinas and Guillermo Luis Arellano-Wattenbarger were supported by CONACYT fellowships 292582 and 626633, respectively.

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Authors and Affiliations

  1. Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, Col. Centro, C.P. 85000, Ciudad Obregón, Sonora, Mexico

    L. A. Chaparro-Encinas, G. L. Arellano-Wattenbarger & S. de los Santos-Villalobos

  2. Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Norman E. Borlaug Km. 12, C.P. 85000, Ciudad Obregón, Sonora, Mexico

    F. I. Parra-Cota

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  1. L. A. Chaparro-Encinas
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  2. G. L. Arellano-Wattenbarger
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  3. F. I. Parra-Cota
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  4. S. de los Santos-Villalobos
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Correspondence to S. de los Santos-Villalobos.

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Communicated by K. Posta.

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Chaparro-Encinas, L.A., Arellano-Wattenbarger, G.L., Parra-Cota, F.I. et al. A modified CTAB and Trizol® protocol for high-quality RNA extraction from whole wheat seedlings, including rhizosphere. CEREAL RESEARCH COMMUNICATIONS 48, 275–282 (2020). https://doi.org/10.1007/s42976-020-00046-9

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  • DOI: https://doi.org/10.1007/s42976-020-00046-9

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