Cargando…
Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing
Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, freezing tolerance is a complex trait that is determined by many genes. To unders...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777136/ https://www.ncbi.nlm.nih.gov/pubmed/26801649 http://dx.doi.org/10.1534/g3.115.025981 |
_version_ | 1782419260167946240 |
---|---|
author | Shu, Yongjun Liu, Ying Li, Wei Song, Lili Zhang, Jun Guo, Changhong |
author_facet | Shu, Yongjun Liu, Ying Li, Wei Song, Lili Zhang, Jun Guo, Changhong |
author_sort | Shu, Yongjun |
collection | PubMed |
description | Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°) and freezing (−8°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. Our results provide valuable information to help determine the molecular mechanisms of freezing tolerance in alfalfa, which will aid the application of these miRNAs and their targets in the improvement of freezing tolerance in alfalfa and related plants. |
format | Online Article Text |
id | pubmed-4777136 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-47771362016-03-03 Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing Shu, Yongjun Liu, Ying Li, Wei Song, Lili Zhang, Jun Guo, Changhong G3 (Bethesda) Investigations Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°) and freezing (−8°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. Our results provide valuable information to help determine the molecular mechanisms of freezing tolerance in alfalfa, which will aid the application of these miRNAs and their targets in the improvement of freezing tolerance in alfalfa and related plants. Genetics Society of America 2016-01-20 /pmc/articles/PMC4777136/ /pubmed/26801649 http://dx.doi.org/10.1534/g3.115.025981 Text en Copyright © 2016 Shu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Shu, Yongjun Liu, Ying Li, Wei Song, Lili Zhang, Jun Guo, Changhong Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing |
title | Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing |
title_full | Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing |
title_fullStr | Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing |
title_full_unstemmed | Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing |
title_short | Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing |
title_sort | genome-wide investigation of micrornas and their targets in response to freezing stress in medicago sativa l., based on high-throughput sequencing |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777136/ https://www.ncbi.nlm.nih.gov/pubmed/26801649 http://dx.doi.org/10.1534/g3.115.025981 |
work_keys_str_mv | AT shuyongjun genomewideinvestigationofmicrornasandtheirtargetsinresponsetofreezingstressinmedicagosativalbasedonhighthroughputsequencing AT liuying genomewideinvestigationofmicrornasandtheirtargetsinresponsetofreezingstressinmedicagosativalbasedonhighthroughputsequencing AT liwei genomewideinvestigationofmicrornasandtheirtargetsinresponsetofreezingstressinmedicagosativalbasedonhighthroughputsequencing AT songlili genomewideinvestigationofmicrornasandtheirtargetsinresponsetofreezingstressinmedicagosativalbasedonhighthroughputsequencing AT zhangjun genomewideinvestigationofmicrornasandtheirtargetsinresponsetofreezingstressinmedicagosativalbasedonhighthroughputsequencing AT guochanghong genomewideinvestigationofmicrornasandtheirtargetsinresponsetofreezingstressinmedicagosativalbasedonhighthroughputsequencing |