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Cao Y, Qu J, Yu H, Yang Q, Li W, Fu F. Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:3242. [PMID: 36501283 PMCID: PMC9739999 DOI: 10.3390/plants11233242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Elite inbred line 18-599 was developed via triple test cross from introduced hybrid P78599 and used as parents of dozens of maize hybrids adapting to the diverse ecological conditions of the maize ecological region in Southwest China. In this study, its genomic DNA was resequenced and aligned with the B73 genome sequence to identify single nucleotide polymorphism (SNP), and insertion (In) and deletion (Del) loci. These loci were aligned with those between B73 and 1020 inbred lines in the HapMap database to identify specific variation loci of 18-599. The results showed that there were 930,439 specific SNPs and 358,750 InDels between 18-599 and the 1020 lines. In total, 21,961 of them showed significant impacts on the functions of 12,297 genes, such as frameshift, change of splicing site, stop gain, change of start site, and stop loss. Phylogenetic analysis showed that 18-599 was closely related to inbred lines ZEAxujRAUDIAAPE and 2005-4, but far from some inbred lines directly isolated from P78599. This result indicated that 18-599 not only pyramided the elite genes of P78599, but also acquired genetic divergence during the repetitive backcrosses of triple test cross to confer its elite agronomic characteristics. Subsequently, the RNA of 18-599 was sequenced. The aligned 9713 and 37,528 of the 165,098 unigenes were screened and aligned with annotated transcripts of the B73 genome differentially expressed under drought and low-temperature stress, respectively, and their functions were involved in the responses to these stresses. The quantitative PCR results of fourteen random genes verified the RNA sequencing results. These findings suggest that the transcriptional responses of many resistance-related genes were an important mechanism for 18-599 to adapt to diverse ecological conditions.
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Affiliation(s)
- Yang Cao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingtao Qu
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Haoqiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingqing Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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Gul Z, Barozai MYK, Din M. In-silico based identification and functional analyses of miRNAs and their targets in Cowpea ( Vigna unguiculata L.). AIMS GENETICS 2017; 4:138-165. [PMID: 31435506 PMCID: PMC6690248 DOI: 10.3934/genet.2017.2.138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022]
Abstract
Cowpea (Vigna unguiculata L.) is an important leguminous plant and a good diet due to presence of carbohydrate and high protein contents. Currently, only few cowpea microRNAs (miRNAs) are reported. This study is intended to identify and functionally analyze new miRNAs and their targets in cowpea. An in-silico based homology search approach was applied and a total of 46 new miRNAs belonging to 45 families were identified and functionally annotated from the cowpea expressed sequence tags (ESTs). All these potential miRNAs are reported here for the first time in cowpea. The 46 new miRNAs were also observed with stable hairpin structures with minimum free energy, ranging from -10 to -132 kcal mol-1 with an average of -40 kcal mol-1. The length of new cowpea miRNAs are ranged from 18 to 26 nt with an average of 21 nt. The cowpea miRNA-vun-mir4414, is found as pre-miRNA cluster for the first time in cowpea. Furthermore, a set of 138 protein targets were also identified for these newly identified 46 cowpea miRNAs. These targets have significant role in various biological processes, like metabolism, transcription regulation as transcription factor, cell transport, signal transduction, growth & development and structural proteins. These findings are the significant basis to utilize and manage this important leguminous plant-cowpea for better nutritional properties and tolerance for biotic and abiotic stresses.
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Affiliation(s)
- Zareen Gul
- Department of Botany, University of Balochistan, Sariab Road, Quetta, Pakistan
| | | | - Muhammad Din
- Department of Botany, University of Balochistan, Sariab Road, Quetta, Pakistan
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Din M, Barozai MYK, Baloch IA. Profiling and annotation of microRNAs and their putative target genes in chilli ( Capsicum annuum L.) using ESTs. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Deeplanaik N, Kumaran RC, Venkatarangaiah K, Shivashankar SKH, Doddamani D, Telkar S. Expression of drought responsive genes in pigeonpea and in silico comparison with soybean cDNA library. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s12892-013-0069-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Din M, Barozai MYK. Profiling and characterization of eggplant (Solanum melongena L.) microRNAs and their targets. Mol Biol Rep 2014; 41:889-94. [PMID: 24390233 DOI: 10.1007/s11033-013-2932-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/20/2013] [Indexed: 11/26/2022]
Abstract
MicroRNAs (miRNAs) are small, non-protein coding and functional RNAs. They play negative regulatory role in gene regulation. They are endogenous in nature and are ~21 nucleotides in length. They are reported in many plant species, but still missing and need to be identified in other important plants like; eggplant. The comparative genomic methodology due to their conserved nature is a reasonable approach for the novel miRNAs discovery. In this research, total 76 novel miRNAs from 67 families were identified in the important vegetable eggplant (Solanum melongena L.). All precursor miRNAs form stable minimum free energy secondary structures and the mature miRNAs reside in the stem regions. Furthermore, eight miRNAs were randomly selected and experimentally validated through RT-PCR. A total of 345 putative targets were also identified for the novel 76 eggplant miRNAs. Their targets are involved in regulation, metabolism, transcription factors, growth and development and other physiological processes. These findings provide a baseline to unravel the miRNAs role in eggplant and utilize them for the improvement of the plant biology.
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Affiliation(s)
- Muhammad Din
- Department of Botany, University of Balochistan, Sariab Road, Quetta, Pakistan
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Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT. RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 2013; 8:e82634. [PMID: 24324815 PMCID: PMC3855774 DOI: 10.1371/journal.pone.0082634] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.
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Affiliation(s)
- Megan J. Bowman
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
- Clemson University Pee Dee Research and Education Center, Florence, South Carolina, United States of America
| | - Philip J. Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Joshua A. Udall
- Brigham Young University, Provo, Utah, United States of America
| | - Justin T. Page
- Brigham Young University, Provo, Utah, United States of America
| | - Joshua Raney
- Brigham Young University, Provo, Utah, United States of America
| | | | - Don. C. Jones
- Cotton Incorporated, Agricultural and Environmental Research, Cary, North Carolina, United States of America
| | - B. Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
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Din M, Barozai MYK. Profiling microRNAs and their targets in an important fleshy fruit: tomato (Solanum lycopersicum). Gene 2013; 535:198-203. [PMID: 24315821 DOI: 10.1016/j.gene.2013.11.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 12/11/2022]
Abstract
Tomato (Solanum lycopersicum) is an important and the most useful plant based diet. It is widely used for its antioxidant property. Presently, only two digits, tomato microRNAs (miRNAs) are reported in miRBase: a miRNA database. This study is aimed to profile and characterize more miRNAs and their targets in tomato. A comprehensive comparative genomic approach is applied and a total of 109 new miRNAs belonging to 106 families are identified and characterized from the tomato expressed sequence tags (ESTs). All these potential miRNAs are profiled for the first time in tomato. The profiled miRNAs are also observed with stable stem-loop structures (Precursor-miRNAs), whose length ranges from 45 to 329 nucleotides (nt) with an average of 125 nt. The mature miRNAs are found in the stem of pre-miRNAs and their length ranges from 19 to 24 nt with an average of 21 nt. Furthermore, twelve miRNAs are randomly selected and experimentally validated through RT-PCR. A total of 406 putative targets are also predicted for the newly 109 tomato miRNAs. These targets are involved in structural protein, metabolism, transcription factor, growth & development, stress related, signaling pathways, storage proteins and other vital processes. Some important proteins like; 9-cisepoxycarotenoid dioxygenase (NCED), transcription factor MYB, ATP-binding cassette transporters, terpen synthase, 14-3-3 and TIR-NBS proteins are also predicted as putative targets for tomato miRNAs. These findings improve a baseline data of miRNAs and their targets in tomato. This baseline data can be utilized to fine tune this important fleshy fruit for nutritional & antioxidant properties and also under biotic & abiotic stresses.
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Affiliation(s)
- Muhammad Din
- Department of Botany, University of Balochistan, Sariab Road Quetta, Pakistan
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Barozai MYK, Din M, Baloch IA. Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags. ACTA ACUST UNITED AC 2013; 14:11-8. [PMID: 23605779 DOI: 10.1007/s10969-013-9152-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 04/01/2013] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small, 18-26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.
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mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage. PLoS One 2013; 8:e54762. [PMID: 23382961 PMCID: PMC3557298 DOI: 10.1371/journal.pone.0054762] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/14/2012] [Indexed: 02/06/2023] Open
Abstract
The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H2O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts’ response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.
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The novel 172 sheep (Ovis aries) microRNAs and their targets. Mol Biol Rep 2012; 39:6259-66. [PMID: 22302387 DOI: 10.1007/s11033-012-1446-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/23/2012] [Indexed: 10/14/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about ≈22 nucleotides in length. The comparative genomics approach due to their conserved nature is a good source for the novel miRNAs discovery. In this study, total 172 novel miRNAs from 140 precursor sequences belonging to 114 families were identified in sheep (Ovis aries), the most important livestock animal. All the miRNA families (oar-mir-95, 129, 130, 186, 214, 219, 223, 324, 339, 423, 450, 499, 544, 562, 568, 584, 669, 671, 763, 935, 1281, 1282, 1306, 1552, 1584, 1587, 1603, 1607, 1706, 1711, 1718, 1732, 1738, 1761, 1771, 1777, 1778, 1780, 1807, 1843, 1895, 1930, 2127, 2139, 2182, 2284, 2287, 2295, 2296, 2310, 2311, 2314, 2315, 2316, 2320, 2359, 2378, 2381, 2382, 2395, 2400, 2404, 2410, 2412, 2423, 2426, 2435, 2470, 2477, 2482, 2487, 2881, 2883, 2885, 2888, 2889, 2896, 2901, 2904, 2917, 2964, 3063, 3064, 3074, 3080, 3432, 3529, 3533, 3613, 3649, 3654, 3658, 3661, 3662, 3940, 3960, 4273, 4426, 4447, 4459, 4468, 4493, 4507, 4647, 4680, 4785, 4788, 4800, 5102, 5105, 5109, 5115, 5125 and 5132) are found for the first time in Sheep. All 140 miRNA precursors form stable minimum free energy stem loop and the mature miRNAs reside in the stem portion of the stem loop structure. Their putative targets are involved in transcription factors (26%), signaling (19%), metabolism (18%), transportation (10%), immunity (9%), cancer and tumor related (5%), growth and development (5%), stress related (4%), and structural proteins (3%).
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Barozai MYK. The MicroRNAs and their targets in the channel catfish (Ictalurus punctatus). Mol Biol Rep 2012; 39:8867-72. [PMID: 22729904 DOI: 10.1007/s11033-012-1753-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding and negative regulatory RNAs about 22 nucleotides. They are mostly conserved among the organisms and this conservation makes them a good source for the identification of novel miRNAs by computational genomic homology. The miRNA repertoire of the major aquaculture species, channel catfish (Ictalurus punctatus), is unknown. This study is focused on computational search for novel miRNA homologs and their targets along with their characterization in channel catfish. Total 60 novel precursor miRNAs having 73 mature sequences belong to 45 families in channel catfish were identified and characterized. They belong to the miRNA families; ipu-let-7, miR-7, 10, 16, 24, 29, 32, 93, 99, 101, 105, 126, 127, 133, 135, 141, 142, 143, 144 145, 148, 150, 152, 153, 203, 210, 214, 221, 223, 293, 429, 430, 466, 682, 731, 737, 1388, 1594, 1642, 1701, 1782, 1814, 2145, 2182 and 3074 are reported for the first time in channel catfish. All the 73 mature miRNAs are observed in the stem portion of the stable minimum free energy stem-loop structures. Total 341 proteins targeted by the novel channel catfish miRNAs were also identified. They are involved in immune-related (32 %), signaling (15 %), transcription factors (15 %), metabolism (12 %), transportation (8 %), growth & development (5 %), structural (5 %) and others (8 %) proteins.
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Overexpression of the halophyte Kalidium foliatum H⁺-pyrophosphatase gene confers salt and drought tolerance in Arabidopsis thaliana. Mol Biol Rep 2012; 39:7989-96. [PMID: 22539184 DOI: 10.1007/s11033-012-1645-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 04/16/2012] [Indexed: 10/28/2022]
Abstract
According to sequences of H(+)-pyrophosphatase genes from GenBank, a new H(+)-pyrophosphatase gene (KfVP1) from the halophyte Kalidium foliatum, a very salt-tolerant shrub that is highly succulent, was obtained by using reverse transcription PCR and rapid amplification of cDNA ends methods. The obtained KfVP1 cDNA contained a 2295 bp ORF and a 242 bp 3'-untranslated region. It encoded 764 amino acids with a calculated molecular mass of 79.78 kDa. The deduced amino acid sequence showed high identity to those of H(+)-PPase of some Chenopodiaceae plant species. Semi-quantitative PCR results revealed that transcription of KfVP1 in K. foliatum was induced by NaCl, ABA and PEG stress. Transgenic lines of A. thaliana with 35S::KfVP1 were generated. Three transgenic lines grew more vigorous than the wild type (ecotype Col-0) under salt and drought stress. Moreover, the transgenic plants accumulated more Na(+) in the leaves compared to wild type plants. These results demonstrated that KfVP1 from K. foliatum may be a functional tonoplast H(+)-pyrophosphatase in contributing to salt and drought tolerance.
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Barozai MYK. Identification and characterization of the microRNAs and their targets in Salmo salar. Gene 2012; 499:163-8. [PMID: 22425976 DOI: 10.1016/j.gene.2012.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 03/04/2012] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about 18 to 26 nucleotides long. Their conserved nature among the various organisms makes them a good source of new miRNAs discovery by comparative genomics approach. The study resulted in novel 75 precursor miRNAs containing 102 mature sequences belonging to 46 families in an important aquatic environmental monitoring fish (Salmo salar). All the miRNA families (let-7, mir-1, 7, 9, 21, 22, 92, 96, 122, 126, 128, 129, 132, 133, 142, 144, 147, 148, 196, 202, 212, 223, 375, 429, 430, 449, 451, 457, 466, 682, 700, 1388, 1594, 1600, 1607, 1616, 1642, 1681, 1701, 1720, 1772, 1782, 1787, 1814, 2189 and 3540) are found for the first time in S. salar. All 75 miRNA precursors form stable minimum free energy stem loop and the mature miRNAs reside in the stem portion of the stem loop structure. Their target proteins are involved in transcription factors (28%), metabolism (23%), signaling (18%), transportation (9%), immunity (8%), stress related activity (5%), cancer and tumor related activity (5%), growth and development (3%), and cell division (1%).
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