Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]

Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.
Original languageEnglish
Pages (from-to)163-172
Number of pages10
JournalJournal of Plant Physiology
Volume224-225
Publication statusPublished - 2018

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science
  • Agronomy and Crop Science

Cite this

Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z. (2018). Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]. Journal of Plant Physiology, 224-225, 163-172.

Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]. / Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z.

In: Journal of Plant Physiology, Vol. 224-225, 2018, p. 163-172.

Research output: Contribution to journalArticle

Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z. 2018, 'Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]', Journal of Plant Physiology, vol. 224-225, pp. 163-172.
Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z. Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]. Journal of Plant Physiology. 2018;224-225:163-172.
Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z. / Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]. In: Journal of Plant Physiology. 2018 ; Vol. 224-225. pp. 163-172.
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title = "Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]",
abstract = "Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.",
keywords = "Drought; Eragrostis tef; microRNA (miRNA); miRNA target; Tef; Eragrostis; Genotype; MicroRNAs; Plant Roots; Plant Shoots; RNA, Plant; Droughts; Physiology; Agronomy and Crop Science; Plant Science",
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T1 - Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]

AU - Cannarozzi, G.; Siegrist, F.; Weichert, A.; Blösch, R.; Tadele, Z.

AU - Martinelli, Federico

AU - Balan, Bipin

PY - 2018

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N2 - Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.

AB - Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.

KW - Drought; Eragrostis tef; microRNA (miRNA); miRNA target; Tef; Eragrostis; Genotype; MicroRNAs; Plant Roots; Plant Shoots; RNA, Plant; Droughts; Physiology; Agronomy and Crop Science; Plant Science

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