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3. Genome-wide identification and comparative analysis of drought-related microRNAs in two maize inbred lines with contrasting drought tolerance by deep sequencing

Author

Luyang Hao, Chunhui Li, Yu Li, Xuyang Liu, Yunsu Shi, Baocheng Sun, Xie Xiaoqing, Tang Huaijun, Tianyu Wang, Yanchun Song, Dengfeng Zhang, Xiaojing Zhang, Cheng Liu, and Yongxiang Li

Subjects
0106 biological sciences, 0301 basic medicine, Leaves, Molecular biology, Acclimatization, Plant genetics, Plant Science, 01 natural sciences, Plant Roots, Biochemistry, chemistry.chemical_compound, Sequencing techniques, Inbred strain, Gene Expression Regulation, Plant, Plant Resistance to Abiotic Stress, Abscisic acid, Plant Proteins, Cellular Stress Responses, Abiotic component, Regulation of gene expression, Multidisciplinary, Ecology, Plant Anatomy, High-Throughput Nucleotide Sequencing, Eukaryota, food and beverages, RNA sequencing, Plants, Adaptation, Physiological, Droughts, Nucleic acids, Experimental Organism Systems, Cell Processes, Plant Physiology, Medicine, Genome, Plant, Research Article, Drought Adaptation, Science, Drought tolerance, Biology, Research and Analysis Methods, Zea mays, Deep sequencing, 03 medical and health sciences, Model Organisms, Stress, Physiological, Plant and Algal Models, Plant-Environment Interactions, parasitic diseases, Genetics, Plant Defenses, Grasses, Non-coding RNA, Natural antisense transcripts, Biology and life sciences, business.industry, Plant Ecology, Ecology and Environmental Sciences, fungi, Organisms, Cell Biology, Plant Pathology, Biotechnology, Gene regulation, Maize, Plant Leaves, MicroRNAs, 030104 developmental biology, Molecular biology techniques, chemistry, Animal Studies, RNA, Gene expression, Rice, Adaptation, business, 010606 plant biology & botany, Genome-Wide Association Study
Abstract

Drought has become one of the most serious abiotic stresses influencing crop production worldwide. Understanding the molecular regulatory networks underlying drought adaption and tolerance in crops is of great importance for future breeding. microRNAs (miRNAs), as important components of post-transcriptional regulation, play crucial roles in drought response and adaptation in plants. Here, we report a miRNome analysis of two maize inbred lines with contrasting levels of drought tolerance under soil drought in the field. Differential expression analysis showed 11 and 34 miRNAs were uniquely responded to drought in H082183 (drought tolerant) and Lv28 (drought sensitive), respectively, in leaves. In roots, 19 and 23 miRNAs uniquely responded to drought in H082183 and Lv28, respectively. Expression analysis of these drought-responsive miRNA-mRNA modules revealed miR164-MYB, miR164-NAC, miR159-MYB, miR156-SPL and miR160-ARF showed a negative regulatory relationship. Further analysis showed that the miR164-MYB and miR164-NAC modules in the tolerant line modulated the stress response in an ABA (abscisic acid)-dependent manner, while the miR156-SPL and miR160-ARF modules in the sensitive line participated in the inhibition of metabolism in drought-exposed leaves. Together, our results provide new insight into not only drought-tolerance-related miRNA regulation networks in maize but also key miRNAs for further characterization and improvement of maize drought tolerance.

Published
2019

4. Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance

Author

Xuyang Liu, Tang Huaijun, Baocheng Sun, Luyang Hao, Yunsu Shi, Yongxiang Li, Chunhui Li, Yu Li, Xie Xiaoqing, Dengfeng Zhang, Cheng Liu, Tianyu Wang, Yanchun Song, and Xiaojing Zhang

Subjects
0106 biological sciences, 0301 basic medicine, Gene Expression, lcsh:Medicine, Plant Science, 01 natural sciences, Genome, Biochemistry, Transcriptome, Inbred strain, Gene Expression Regulation, Plant, Plant Resistance to Abiotic Stress, Gene expression, Inbreeding, lcsh:Science, Plant Proteins, Cellular Stress Responses, Regulation of gene expression, Multidisciplinary, Ecology, food and beverages, Plants, Adaptation, Physiological, Droughts, Experimental Organism Systems, Cell Processes, Plant Physiology, Genome, Plant, Research Article, Drought Adaptation, Drought tolerance, Biology, Research and Analysis Methods, Zea mays, 03 medical and health sciences, Model Organisms, Stress, Physiological, Plant and Algal Models, Plant-Environment Interactions, DNA-binding proteins, parasitic diseases, Genetics, Plant Defenses, Gene Regulation, Grasses, Transcription factor, Gene, Drought, business.industry, Plant Ecology, Ecology and Environmental Sciences, fungi, lcsh:R, Organisms, Biology and Life Sciences, Proteins, Cell Biology, Plant Pathology, Biotechnology, Maize, Regulatory Proteins, 030104 developmental biology, lcsh:Q, business, 010606 plant biology & botany, Transcription Factors
Abstract

Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement.

Published
2017

5. Genome-wide identification and comparative analysis of drought-related microRNAs in two maize inbred lines with contrasting drought tolerance by deep sequencing.

Author

Liu, Xuyang, Zhang, Xiaojing, Sun, Baocheng, Hao, Luyang, Liu, Cheng, Zhang, Dengfeng, Tang, Huaijun, Li, Chunhui, Li, Yongxiang, Shi, Yunsu, Xie, Xiaoqing, Song, Yanchun, Wang, Tianyu, and Li, Yu

Subjects
ABSCISIC acid, DROUGHT tolerance, CORN breeding, CORN, PLANT adaptation, MICRORNA, BOTANY
Abstract

Drought has become one of the most serious abiotic stresses influencing crop production worldwide. Understanding the molecular regulatory networks underlying drought adaption and tolerance in crops is of great importance for future breeding. microRNAs (miRNAs), as important components of post-transcriptional regulation, play crucial roles in drought response and adaptation in plants. Here, we report a miRNome analysis of two maize inbred lines with contrasting levels of drought tolerance under soil drought in the field. Differential expression analysis showed 11 and 34 miRNAs were uniquely responded to drought in H082183 (drought tolerant) and Lv28 (drought sensitive), respectively, in leaves. In roots, 19 and 23 miRNAs uniquely responded to drought in H082183 and Lv28, respectively. Expression analysis of these drought-responsive miRNA-mRNA modules revealed miR164-MYB, miR164-NAC, miR159-MYB, miR156-SPL and miR160-ARF showed a negative regulatory relationship. Further analysis showed that the miR164-MYB and miR164-NAC modules in the tolerant line modulated the stress response in an ABA (abscisic acid)-dependent manner, while the miR156-SPL and miR160-ARF modules in the sensitive line participated in the inhibition of metabolism in drought-exposed leaves. Together, our results provide new insight into not only drought-tolerance-related miRNA regulation networks in maize but also key miRNAs for further characterization and improvement of maize drought tolerance. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
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6. Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance.

Author

Zhang, Xiaojing, Liu, Xuyang, Zhang, Dengfeng, Tang, Huaijun, Sun, Baocheng, Li, Chunhui, Hao, Luyang, Liu, Cheng, Li, Yongxiang, Shi, Yunsu, Xie, Xiaoqing, Song, Yanchun, Wang, Tianyu, and Li, Yu

Subjects
DROUGHTS & the environment, CORN farming, DROUGHT tolerance of corn, GENOTYPE-environment interaction, TRANSCRIPTION factors, AGRICULTURE & the environment, THERAPEUTICS
Abstract

Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement. [ABSTRACT FROM AUTHOR]

Published
2017
Full Text
View/download PDF

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