Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication relate...

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Main Authors: Yong-Chao Xu, Jie Zhang, Dong-Yan Zhang, Ying-Hui Nan, Song Ge, Ya-Long Guo
Format: Article
Language:English
Published: BMC 2021-06-01
Series:BMC Genomics
Subjects:
Online Access:https://doi.org/10.1186/s12864-021-07754-4
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author Yong-Chao Xu
Jie Zhang
Dong-Yan Zhang
Ying-Hui Nan
Song Ge
Ya-Long Guo
author_facet Yong-Chao Xu
Jie Zhang
Dong-Yan Zhang
Ying-Hui Nan
Song Ge
Ya-Long Guo
author_sort Yong-Chao Xu
collection DOAJ
description Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. O. nivara inhabits swampy areas with a seasonally dry climate, which is an ideal material to discover drought tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1246 lncRNAs were identified, including 1091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes enriched in stress responsive GO terms; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.
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spelling doaj.art-1e55c150871342cea06d7de9f6327b5f2022-12-21T20:25:31ZengBMCBMC Genomics1471-21642021-06-0122111110.1186/s12864-021-07754-4Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)Yong-Chao Xu0Jie Zhang1Dong-Yan Zhang2Ying-Hui Nan3Song Ge4Ya-Long Guo5State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesAbstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. O. nivara inhabits swampy areas with a seasonally dry climate, which is an ideal material to discover drought tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1246 lncRNAs were identified, including 1091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes enriched in stress responsive GO terms; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.https://doi.org/10.1186/s12864-021-07754-4Drought stressLong noncoding RNAO. nivaraStrand-specific RNA-seqWild rice
spellingShingle Yong-Chao Xu
Jie Zhang
Dong-Yan Zhang
Ying-Hui Nan
Song Ge
Ya-Long Guo
Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
BMC Genomics
Drought stress
Long noncoding RNA
O. nivara
Strand-specific RNA-seq
Wild rice
title Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
title_full Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
title_fullStr Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
title_full_unstemmed Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
title_short Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
title_sort identification of long noncoding natural antisense transcripts lncnats correlated with drought stress response in wild rice oryza nivara
topic Drought stress
Long noncoding RNA
O. nivara
Strand-specific RNA-seq
Wild rice
url https://doi.org/10.1186/s12864-021-07754-4
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