Dataset Information

Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (Zea mays L.) Using High-throughput Sequencing and Degradome Analysis.

ABSTRACT: To identify the known and novel microRNAs (miRNAs) and their targets that are involved in the response and adaptation of maize (Zea mays) to salt stress, miRNAs and their targets were identified by a combined analysis of the deep sequencing of small RNAs (sRNA) and degradome libraries. The identities were confirmed by a quantitative expression analysis with over 100 million raw reads of sRNA and degradome sequences. A total of 1040 previously known miRNAs were identified from four maize libraries, with 762 and 726 miRNAs derived from leaves and roots, respectively, and 448 miRNAs that were common between the leaves and roots. A total of 37 potential new miRNAs were selected based on the same criteria in response to salt stress. In addition to known miR167 and miR164 species, novel putative miR167 and miR164 species were also identified. Deep sequencing of miRNAs and the degradome [with quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses of their targets] showed that more than one species of novel miRNA may play key roles in the response to salinity in maize. Furthermore, the interaction between miRNAs and their targets may play various roles in different parts of maize in response to salinity.

SUBMITTER: Fu R

PROVIDER: S-EPMC5445174 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Publications

Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (<i>Zea mays</i> L.) Using High-throughput Sequencing and Degradome Analysis.

Fu Rong R Zhang Mi M Zhao Yinchuan Y He Xuechuan X Ding Chenyun C Wang Shuangkuai S Feng Yan Y Song Xianliang X Li Ping P Wang Baohua B

Frontiers in plant science 20170526

To identify the known and novel microRNAs (miRNAs) and their targets that are involved in the response and adaptation of maize (<i>Zea mays</i>) to salt stress, miRNAs and their targets were identified by a combined analysis of the deep sequencing of small RNAs (sRNA) and degradome libraries. The identities were confirmed by a quantitative expression analysis with over 100 million raw reads of sRNA and degradome sequences. A total of 1040 previously known miRNAs were identified from four maize l ...[more]

PMID: 28603532

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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.

Project description:Soil salinization is a widely recognized global environmental concern that has a significant impact on the sustainable development of agriculture at a global scale. Maize, a major crop that contributes to the global agricultural economy, is particularly vulnerable to the adverse effects of salt stress, which can hinder its growth and development from germination to the seedling stage. This study aimed to screen highly salt-tolerant maize varieties by using four NaCl concentrations of 0, 60, 120, and 180 mMol/L. Various agronomic traits and physiological and biochemical indices associated with salt tolerance were measured, and salt tolerance was evaluated using principal component analysis, membership function method, and GGE biplot analysis. A total of 41 local maize varieties were assessed based on their D values. The results show that stem thickness, germ length, radicle length, leaf area, germination rate, germination index, salt tolerance index, and seed vigor all decreased as salt concentration increased, while electrical conductivity and salt injury index increased with the concentration of saline solution. Under the stress of 120 mMol/L and 180 mMol/L NaCl, changes in antioxidant enzymes occurred, reflecting the physiological response mechanisms of maize under salt stress. Principal component analysis identified six major components including germination vigor, peroxidase (POD), plant height, embryo length, SPAD chlorophyll and proline (PRO) factors. After calculating the comprehensive index (D value) of each variety's performance in different environments using principal component analysis and the membership function method, a GGE biplot analysis was conducted to identify maize varieties with good salt tolerance stability: Qun Ce 888, You Qi 909, Ping An 1523, Xin Nong 008, Xinyu 66, and Hong Xin 990, as well as varieties with poor salt tolerance: Feng Tian 14, Xi Meng 668, Ji Xing 218, Gan Xin 2818, Hu Xin 712, and Heng Yu 369. Furthermore, it was determined that a 120 mMol/L NaCl concentration was suitable for screening maize varieties during germination and seedling stages. This study further confirmed the reliability of GGE biplot analysis in germplasm selection, expanded the genetic resources of salt-tolerant maize, and provided theoretical references and germplasm utilization for the introduction of maize in saline-alkali areas. These research findings contribute to a better understanding of maize salt tolerance and promote its cultivation in challenging environments.

Dataset Information

Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (Zea mays L.) Using High-throughput Sequencing and Degradome Analysis.

Publications

Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (<i>Zea mays</i> L.) Using High-throughput Sequencing and Degradome Analysis.

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