Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response

S. Esposito, R. Aversano, J. M. Bradeen, A. Di Matteo, C. Villano, D. Carputo

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.

Original languageEnglish (US)
Pages (from-to)133-142
Number of pages10
JournalPlant Biology
Volume22
Issue numberS1
DOIs
StatePublished - Jan 1 2020

Fingerprint

Solanum commersonii
RNA libraries
potato
RNA
potatoes
tolerance
breeding
stress change
cold stress
small interfering RNA
abiotic stress
phenotype
clone
genomics
temperature
genome
clones
resource
high-throughput nucleotide sequencing
cold shock response

Keywords

  • Cold stress conditions
  • TasiRNA
  • microRNA
  • smRNAseq
  • sncRNA
  • wild potato

Cite this

Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response. / Esposito, S.; Aversano, R.; Bradeen, J. M.; Di Matteo, A.; Villano, C.; Carputo, D.

In: Plant Biology, Vol. 22, No. S1, 01.01.2020, p. 133-142.

Research output: Contribution to journalArticle

Esposito, S. ; Aversano, R. ; Bradeen, J. M. ; Di Matteo, A. ; Villano, C. ; Carputo, D. / Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response. In: Plant Biology. 2020 ; Vol. 22, No. S1. pp. 133-142.
@article{6d15670cb8dd4917b44b0f9526b3f80a,
title = "Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response",
abstract = "Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.",
keywords = "Cold stress conditions, TasiRNA, microRNA, smRNAseq, sncRNA, wild potato",
author = "S. Esposito and R. Aversano and Bradeen, {J. M.} and {Di Matteo}, A. and C. Villano and D. Carputo",
year = "2020",
month = "1",
day = "1",
doi = "10.1111/plb.12955",
language = "English (US)",
volume = "22",
pages = "133--142",
journal = "Acta Botanica Neerlandica",
issn = "1435-8603",
publisher = "Wiley-Blackwell",
number = "S1",

}

TY - JOUR

T1 - Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response

AU - Esposito, S.

AU - Aversano, R.

AU - Bradeen, J. M.

AU - Di Matteo, A.

AU - Villano, C.

AU - Carputo, D.

PY - 2020/1/1

Y1 - 2020/1/1

N2 - Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.

AB - Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.

KW - Cold stress conditions

KW - TasiRNA

KW - microRNA

KW - smRNAseq

KW - sncRNA

KW - wild potato

UR - http://www.scopus.com/inward/record.url?scp=85061044079&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85061044079&partnerID=8YFLogxK

U2 - 10.1111/plb.12955

DO - 10.1111/plb.12955

M3 - Article

C2 - 30597710

AN - SCOPUS:85061044079

VL - 22

SP - 133

EP - 142

JO - Acta Botanica Neerlandica

JF - Acta Botanica Neerlandica

SN - 1435-8603

IS - S1

ER -