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Hemasai B, Kumbha DK, Modem VN, Gannavarapu SK, Bommaka RR, Mallapuram S, Chintala S, Sreevalli MD, Ramireddy E, Vemireddy LR. Development of miRNA-SSR and target-SSR markers from yield-associate genes and their applicability in the assessment of genetic diversity and association mapping in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:30. [PMID: 38634111 PMCID: PMC11018576 DOI: 10.1007/s11032-024-01462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/25/2024] [Indexed: 04/19/2024]
Abstract
The gene-derived functional markers are considered effective to use in marker-assisted breeding and genetic diversity analysis. As of now, no functional markers have been identified from miRNAs regulating yield traits. The miRNAs play a key role as regulators in controlling the candidate genes involved in grain yield improvement in rice. In this study, 13 miRNA-SSR and their target gene SSR markers were mined from 29 yield-responsive miRNA along with their 29 target genes in rice. The validation of these markers showed that four miRNA-SSRs and one target gene SSR markers had shown polymorphism among 120 diverse rice genotypes. The PIC values ranged from 0.25 (OsARF18-SSR) to 0.72 (miR408-SSR, miR172b-SSR, and miR396f-SSR) with an average value of 0.57. These polymorphic markers grouped 120 rice genotypes into 3 main clusters based on the levels of high genetic diversity. These markers also showed significant association with key yield traits. Among all, miR172b-SSR showed a strong association with plant height in two seasons. This investigation suggests that this new class of molecular markers has great potential in the characterization of rice germplasm by genetic diversity and population structure and in marker-assisted breeding for the development of high-yielding varieties. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01462-z.
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Affiliation(s)
- Bavisetti Hemasai
- Dept. of Genetics and Plant Breeding, S. V. Agricultural College, Acharya N.G. Ranga Agricultural University (ANGRAU), Tirupati, 517 502 Andhra Pradesh India
| | - Dinesh K. Kumbha
- Dept. of Genetics and Plant Breeding, S. V. Agricultural College, Acharya N.G. Ranga Agricultural University (ANGRAU), Tirupati, 517 502 Andhra Pradesh India
| | - Vinodkumar Naik Modem
- Dept. of Genetics and Plant Breeding, S. V. Agricultural College, Acharya N.G. Ranga Agricultural University (ANGRAU), Tirupati, 517 502 Andhra Pradesh India
| | - Srividya K. Gannavarapu
- Dept. of Molecular Biology and Biotechnology, S. V. Agricultural College, ANGRAU, Tirupati, 517 502 Andhra Pradesh India
| | - Rupeshkumar R. Bommaka
- Dept. of Genetics and Plant Breeding, S. V. Agricultural College, Acharya N.G. Ranga Agricultural University (ANGRAU), Tirupati, 517 502 Andhra Pradesh India
| | - Shanthipriya Mallapuram
- Dept. of Genetics and Plant Breeding, Agricultural Research Station, ANGRAU, Perumallapalle, Tirupati, 517 502 Andhra Pradesh India
| | | | - Muga D. Sreevalli
- Dept. of Genetics and Plant Breeding, S. V. Agricultural College, Acharya N.G. Ranga Agricultural University (ANGRAU), Tirupati, 517 502 Andhra Pradesh India
| | - Eswarayya Ramireddy
- Department of Biology, Indian Institutes of Science Education and Research, Tirupati, 517507 Andhra Pradesh India
| | - Lakshminarayana R. Vemireddy
- Dept. of Molecular Biology and Biotechnology, S. V. Agricultural College, ANGRAU, Tirupati, 517 502 Andhra Pradesh India
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Wu X, Wang X, Chen W, Liu X, Lin Y, Wang F, Liu L, Meng Y. A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:958520. [PMID: 36131801 PMCID: PMC9484463 DOI: 10.3389/fpls.2022.958520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
To adapt to variable natural conditions, plants have evolved several strategies to respond to different environmental stresses. MicroRNA (miRNA)-mediated gene regulation is one of such strategies. Variants, e.g., single nucleotide polymorphisms (SNPs) within the mature miRNAs or their target sites may cause the alteration of regulatory networks and serious phenotype changes. In this study, we proposed a novel approach to construct a miRNA-miRNA crosstalk network in Arabidopsis thaliana based on the notion that two cooperative miRNAs toward common targets are under a strong pressure to be inherited together across ecotypes. By performing a genome-wide scan of the SNPs within the mature miRNAs and their target sites, we defined a "regulation fate profile" to describe a miRNA-target regulation being static (kept) or dynamic (gained or lost) across 1,135 ecotypes compared with the reference genome of Col-0. The cooperative miRNA pairs were identified by estimating the similarity of their regulation fate profiles toward the common targets. The reliability of the cooperative miRNA pairs was supported by solid expressional correlation, high PPImiRFS scores, and similar stress responses. Different combinations of static and dynamic miRNA-target regulations account for the cooperative miRNA pairs acting on various biological characteristics of miRNA conservation, expression, homology, and stress response. Interestingly, the targets that are co-regulated dynamically by both cooperative miRNAs are more likely to be responsive to stress. Hence, stress-related genes probably bear selective pressures in a certain group of ecotypes, in which miRNA regulations on the stress genes reprogram. Finally, three case studies showed that reprogramming miRNA-miRNA crosstalk toward the targets in specific ecotypes was associated with these ecotypes' climatic variables and geographical locations. Our study highlights the potential of miRNA-miRNA crosstalk as a genetic basis underlying environmental adaptation in natural populations.
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Affiliation(s)
- Xiaomei Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wei Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xunyan Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yibin Lin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Fengfeng Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Lulu Liu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Xu Y, Lu JH, Zhang JD, Liu DK, Wang Y, Niu QD, Huang DD. Transcriptome revealed the molecular mechanism of Glycyrrhiza inflata root to maintain growth and development, absorb and distribute ions under salt stress. BMC PLANT BIOLOGY 2021; 21:599. [PMID: 34915868 PMCID: PMC8675533 DOI: 10.1186/s12870-021-03342-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/11/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Soil salinization extensively hampers the growth, yield, and quality of crops worldwide. The most effective strategies to counter this problem are a) development of crop cultivars with high salt tolerance and b) the plantation of salt-tolerant crops. Glycyrrhiza inflata, a traditional Chinese medicinal and primitive plant with salt tolerance and economic value, is among the most promising crops for improving saline-alkali wasteland. However, the underlying molecular mechanisms for the adaptive response of G. inflata to salinity stress remain largely unknown. RESULT G. inflata retained a high concentration of Na+ in roots and maintained the absorption of K+, Ca2+, and Mg2+ under 150 mM NaCl induced salt stress. Transcriptomic analysis of G. inflata roots at different time points of salt stress (0 min, 30 min, and 24 h) was performed, which resulted in 70.77 Gb of clean data. Compared with the control, we detected 2645 and 574 differentially expressed genes (DEGs) at 30 min and 24 h post-salt-stress induction, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that G. inflata response to salt stress post 30 min and 24 h was remarkably distinct. Genes that were differentially expressed at 30 min post-salt stress induction were enriched in signal transduction, secondary metabolite synthesis, and ion transport. However, genes that were differentially expressed at 24 h post-salt-stress induction were enriched in phenylpropane biosynthesis and metabolism, fatty acid metabolism, glycerol metabolism, hormone signal transduction, wax, cutin, and cork biosynthesis. Besides, a total of 334 transcription factors (TFs) were altered in response to 30 min and 24 h of salt stress. Most of these TFs belonged to the MYB, WRKY, AP2-EREBP, C2H2, bHLH, bZIP, and NAC families. CONCLUSION For the first time, this study elucidated the salt tolerance in G. inflata at the molecular level, including the activation of signaling pathways and genes that regulate the absorption and distribution of ions and root growth in G. inflata under salt stress conditions. These findings enhanced our understanding of the G. inflata salt tolerance and provided a theoretical basis for cultivating salt-tolerant crop varieties.
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Affiliation(s)
- Ying Xu
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Jia-Hui Lu
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China.
- Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, 832003, Xinjiang, China.
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi University, Shihezi, 832003, Xinjiang, China.
| | - Jia-de Zhang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Deng-Kui Liu
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Yue Wang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Qing-Dong Niu
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Dan-Dan Huang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
- Licorice Research Institute of Shihezi University, Shihezi, 832003, Xinjiang, China
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Kong W, Zhang C, Zhang S, Qiang Y, Zhang Y, Zhong H, Li Y. Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq. RICE (NEW YORK, N.Y.) 2021; 14:93. [PMID: 34778931 PMCID: PMC8590990 DOI: 10.1186/s12284-021-00535-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/06/2021] [Indexed: 05/07/2023]
Abstract
Salinity is a major abiotic stress that limits plant growth and crop productivity. Indica rice and japonica rice show significant differences in tolerance to abiotic stress, and it is considered a feasible method to breed progeny with stronger tolerance to abiotic stress by crossing indica and japonica rice. We herein developed a high-generation recombinant inbred lines (RILs) from Luohui 9 (indica) X RPY geng (japonica). Based on the high-density bin map of this RILs population, salt tolerance QTLs controlling final survival rates were analyzed by linkage mapping and RTM-GWAS methods. A total of seven QTLs were identified on chromosome 3, 4, 5, 6, and 8. qST-3.1, qST-5.1, qST-6.1, and qST-6.2 were novel salt tolerance QTLs in this study and their function were functionally verified by comparative analysis of parental genotype RILs. The gene aggregation result of these four new QTLs emphasized that the combination of the four QTL synergistic genotypes can significantly improve the salt stress tolerance of rice. By comparing the transcriptomes of the root tissues of the parents' seedlings, at 3 days and 7 days after salt treatment, we then achieved fine mapping of QTLs based on differentially expressed genes (DEGs) identification and DEGs annotations, namely, LOC_Os06g01250 in qST-6.1, LOC_Os06g37300 in qST-6.2, LOC_Os05g14880 in qST-5.1. The homologous genes of these candidate genes were involved in abiotic stress tolerance in different plants. These results indicated that LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 were the candidate genes of qST-5.1, qST-6.1, and qST-6.2. Our finding provided novel salt tolerance-related QTLs, candidate genes, and several RILs with better tolerance, which will facilitate breeding for improved salt tolerance of rice varieties and promote the exploration tolerance mechanisms of rice salt stress.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Yalin Qiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Yue Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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de Sousa MAP, de Athayde FRF, Maldonado MBC, de Lima AO, Fortes MRS, Lopes FL. Single nucleotide polymorphisms affect miRNA target prediction in bovine. PLoS One 2021; 16:e0249406. [PMID: 33882076 PMCID: PMC8059806 DOI: 10.1371/journal.pone.0249406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) can have significant effects on phenotypic characteristics in cattle. MicroRNAs (miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators by binding them to target mRNAs. In the present study, we scanned ~56 million SNPs against 1,064 bovine miRNA sequences and analyzed, in silico, their possible effects on target binding prediction, primary miRNA formation, association with QTL regions and the evolutionary conservation for each SNP locus. Following target prediction, we show that 71.6% of miRNA predicted targets were altered as a consequence of SNPs located within the seed region of the mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE), which represents the capacity to alter molecule stability and, consequently, miRNA maturation. A total of 48.6% of the sequences analyzed showed values within those previously reported as sufficient to alter miRNA maturation. We have also found 131 SNPs in 46 miRNAs, with altered target prediction, occurring in QTL regions. Lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to affect bovine phenotypes and could be of great value for genetic improvement studies, as well as production.
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Affiliation(s)
- Marco Antônio Perpétuo de Sousa
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Flavia Regina Florêncio de Athayde
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Marina Rufino S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Flavia Lombardi Lopes
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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Kanzana G, Zhang Y, Ma T, Liu W, Wu F, Yan Q, Min X, Yan Z, Muvunyi BP, Li J, Zhang Z, Zhao Y, Zhang J. Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica and analysis of their transferability to Gramineae/non-Gramineae species. J Appl Genet 2020; 61:367-377. [PMID: 32507975 DOI: 10.1007/s13353-020-00561-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/28/2020] [Accepted: 05/07/2020] [Indexed: 11/24/2022]
Abstract
Simple sequence repeat (SSR) markers are commonly used for many genetic applications, such as map construction, fingerprinting, and genetic diversity analyses, due to their high reproducibility, polymorphism, and abundance. Endogenous miRNAs play essential roles in plant development and gene expression under diverse biotic and abiotic stress conditions. In the present study, we predicted 110 miRNA-SSR primer pairs from 287 precursor miRNAs. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other Gramineae and non-Gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. Furthermore, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. In conclusion, the results showed that an miRNA-based microsatellite marker system can be applicable for genetic diversity and marker-assisted breeding studies.
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Affiliation(s)
- Gisele Kanzana
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Yufei Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Tiantian Ma
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Qi Yan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xueyang Min
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Blaise Pascal Muvunyi
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Jie Li
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Yufeng Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
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7
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Omariba G, Xu F, Wang M, Li K, Zhou Y, Xiao J. Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome. Sci Rep 2020; 10:5789. [PMID: 32238847 PMCID: PMC7113310 DOI: 10.1038/s41598-020-62588-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs are widely referred to as gene expression regulators for different diseases. The integration between single nucleotide polymorphisms (SNPs) and miRNAs has been associated with both human and animal diseases. In order to gain new insights on the effects of SNPs on miRNA and their related sequences, we steadily characterized a whole mouse genome miRNA related SNPs, analyzed their effects on the miRNA structural stability and target alteration. In this study, we collected 73643859 SNPs across the mouse genome, analyzed 1187 pre-miRNAs and 2027 mature miRNAs. Upon mapping the SNPs, 1700 of them were identified in 702 pre-miRNAs and 609 SNPs in mature miRNAs. We also discovered that SNP densities of the pre-miRNA and mature miRNAs are lower than the adjacent flanking regions. Also the flanking regions far away from miRNAs appeared to have higher SNP density. In addition, we also found that transitions were more frequent than transversions in miRNAs. Notably, 841 SNPs could change their corresponding miRNA's secondary structure from stable to unstable. We also performed target gain and loss analysis of 163 miRNAs and our results showed that few miRNAs remained unchanged and many miRNAs from wild mice gained target site. These results outline the first case of SNP variations in the mouse whole genome scale. Those miRNAs with changes in structure or target could be of interest for further studies.
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Affiliation(s)
- Gideon Omariba
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Fuyi Xu
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Maochun Wang
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Kai Li
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Yuxun Zhou
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Junhua Xiao
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China.
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8
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Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species. Genomics 2020; 112:1554-1564. [DOI: 10.1016/j.ygeno.2019.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
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9
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Xu Y, Zhang T, Li Y, Miao Z. Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize ( Zea mays). Front Genet 2020; 11:51. [PMID: 32117460 PMCID: PMC7026458 DOI: 10.3389/fgene.2020.00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/16/2020] [Indexed: 01/15/2023] Open
Abstract
The evolutionary dynamics and tissue specificity of protein-coding genes are well documented in plants. However, the evolutionary consequences of small RNAs (sRNAs) on tissue-specific functions remain poorly understood. Here, we performed integrated analysis of 195 deeply sequenced sRNA libraries of maize B73, representing more than 10 tissues, and identified a comprehensive list of 419 maize microRNA (miRNA) genes, 271 of which were newly discovered in this study. We further characterized the evolutionary dynamics and tissue specificity of miRNA genes and corresponding miRNA isoforms (isomiRs). Our analysis revealed that tissue specificity of isomiR events tends to be associated with miRNA gene abundance and suggested that the frequencies of isomiR types are affected by the local genomic regions. Moreover, genome duplication (GD) events have dramatic effect on evolutionary dynamics of maize miRNA genes, and the abundance divergence for tissue-specific miRNA genes is associated with GD events. Further study indicated that duplicate miRNA genes with tissue-specific expression patterns, such as miR2275a, a phased siRNA (phasiRNA) trigger, contribute to phenotypic traits in maize. Additionally, our study revealed the expression preference of 21- and 24-nt phasiRNAs in relation to tissue specificity. This large-scale sRNAomic study depicted evolutionary implications of tissue-specific maize sRNAs, which coordinate genome duplication, isomiR modification, phenotypic traits and phasiRNAs differentiation.
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Affiliation(s)
- Yu Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China.,Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yuchen Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Zhenyan Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China.,Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, China
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10
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Iquebal MA, Sharma P, Jasrotia RS, Jaiswal S, Kaur A, Saroha M, Angadi UB, Sheoran S, Singh R, Singh GP, Rai A, Tiwari R, Kumar D. RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat. Sci Rep 2019; 9:13917. [PMID: 31558740 PMCID: PMC6763491 DOI: 10.1038/s41598-019-49915-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 01/08/2023] Open
Abstract
Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Amandeep Kaur
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Monika Saroha
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
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11
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Sabzehzari M, Naghavi M. Phyto-miRNA: A molecule with beneficial abilities for plant biotechnology. Gene 2019; 683:28-34. [DOI: 10.1016/j.gene.2018.09.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022]
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12
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Singh I, Smita S, Mishra DC, Kumar S, Singh BK, Rai A. Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea. FRONTIERS IN PLANT SCIENCE 2017; 8:1943. [PMID: 29209340 PMCID: PMC5702422 DOI: 10.3389/fpls.2017.01943] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/30/2017] [Indexed: 05/30/2023]
Abstract
Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.
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Affiliation(s)
- Indra Singh
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shuchi Smita
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C. Mishra
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Binay K. Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Anil Rai
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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13
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Jasrotia RS, Iquebal MA, Yadav PK, Kumar N, Jaiswal S, Angadi UB, Rai A, Kumar D. Development of transcriptome based web genomic resources of yellow mosaic disease in Vigna mungo. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:767-777. [PMID: 29158627 PMCID: PMC5671452 DOI: 10.1007/s12298-017-0470-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 05/27/2023]
Abstract
Vigna mungo (Urdbean) is cultivated in the tropical and sub-tropical continental region of Asia. It is not only important source of dietary protein and nutritional elements, but also of immense value to human health due to medicinal properties. Yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus is known to incur huge loss to crop, adversely affecting crop yield. Contrasting genotypes are ideal source for knowledge discovery of plant defence mechanism and associated candidate genes for varietal improvement. Whole genome sequence of this crop is yet to be completed. Moreover, genomic resources are also not freely accessible, thus available transcriptome data can be of immense use. V. mungo Transcriptome database, accessible at http://webtom.cabgrid.res.in/vmtdb/ has been developed using available data of two contrasting varieties viz., cv. VM84 (resistant) and cv. T9 (susceptible). De novo assembly was carried out using Trinity and CAP3. Out of total 240,945 unigenes, 165,894 (68.8%) showed similarity with known genes against NR database, and remaining 31.2% were found to be novel. We found 22,101 differentially expressed genes in all datasets, 44,335 putative genic SSR markers, 4105 SNPs and Indels, 64,964 transcriptional factor, 546 mature miRNA target prediction in 703 differentially expressed unigenes and 137 pathways. MAPK, salicylic acid-binding protein 2-like, pathogenesis-related protein and NBS-LRR domain were found which may play an important role in defence against pathogens. This is the first web genomic resource of V. mungo for future genome annotation as well as ready to use markers for future variety improvement program.
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Affiliation(s)
- Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology & Sciences (SHUATS), Allahabad, 211007 India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology & Sciences (SHUATS), Allahabad, 211007 India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
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14
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Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0214-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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15
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Ganie SA, Debnath AB, Gumi AM, Mondal TK. Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species. BMC Genomics 2017; 18:711. [PMID: 28893199 PMCID: PMC5594537 DOI: 10.1186/s12864-017-4089-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species. Analysis of the nucleotide substitution rates indicated that the mature sequences show the least substitution rates among the different regions of miRNA genes, and also show a very much less substitution rates as compared to that of all protein-coding genes across the Oryza species. Evolution of miRNA genes was also found to be contributed by transposons. A non-neutral selection was observed at 80 different miRNA loci across Oryza species which were estimated to have lost ~87% of the sequence diversity during the domestication. The phylogenetic analysis revealed that O. longistaminata diverged first among the AA-genomes, whereas O. brachyantha and O. punctata appeared as the eminent out-groups. The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. Further, the expression analysis showed that 11 salt-responsive miRNAs were differentially regulated between O. coarctata and O. glaberrima. CONCLUSION Our study provides the evolutionary dynamics in the miRNA genes of 10 different Oryza species which will support more investigations about the structural and functional organization of miRNA genes of Oryza species.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Abubakar Mohammad Gumi
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
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16
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Wen M, Xie M, He L, Wang Y, Shi S, Tang T. Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa). Genome Biol Evol 2016; 8:3529-3544. [PMID: 27797952 PMCID: PMC5203789 DOI: 10.1093/gbe/evw252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Munan Xie
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | | | - Yushuai Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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17
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Chen B, Du Q, Chen J, Yang X, Tian J, Li B, Zhang D. Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus. Heredity (Edinb) 2016; 117:73-83. [PMID: 27118153 DOI: 10.1038/hdy.2016.26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/02/2016] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.
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Affiliation(s)
- B Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - Q Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - J Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - X Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - J Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - B Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Department of Forestry, North Carolina State University, Raleigh, NC, USA
| | - D Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
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18
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Tian J, Chen J, Li B, Zhang D. Association genetics in Populus reveals the interactions between Pto-miR160a and its target Pto-ARF16. Mol Genet Genomics 2016; 291:1069-82. [PMID: 26732268 DOI: 10.1007/s00438-015-1165-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) play important roles in the regulation of gene expression in various biological processes. However, the interactions between miRNAs and their targets are largely unknown in plants. As a powerful tool for identification of variation associated with traits, association genetics provides another strategy for exploration of interactions between miRNAs and their targets. Here, we conducted expression analysis and association mapping to evaluate the interaction between Pto-miR160a and its target Pto-ARF16 in Populus tomentosa. By examining the expression patterns of Pto-MIR160a and Pto-ARF16, we identified a significant, negative correlation between their expression levels, indicating that Pto-miR160a may affect the expression of Pto-ARF16. Among the single nucleotide polymorphisms (SNPs) identified in this study, one common SNP in the pre-miRNA region of Pto-miR160a altered its predicted secondary structure while another common SNP in the predicted miRNA target site changed the binding affinity of Pto-miR160a. Linkage disequilibrium (LD) analysis revealed low LD levels of Pto-MIR160a and Pto-ARF16, indicating that they are suitable for candidate gene-based association analysis. Single SNP-based association analysis identified 19 SNPs (false discovery rate Q < 0.05) in Pto-MIR160a and Pto-ARF16 associated with three phenotypic traits. Epistasis analysis further identified 36 SNP-SNP interactions between SNPs in Pto-MIR160a and SNPs in Pto-ARF16, reflecting the possible genetic interaction of Pto-miR160a and Pto-ARF16. Taking these results together, our study identified SNPs in Pto-MIR160a and Pto-ARF16 associated with tree growth and wood properties, providing SNPs with potential applications in marker-assisted breeding and evidence for the genetic interaction of Pto-miR160a and Pto-ARF16.
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Affiliation(s)
- Jiaxing Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Jinhui Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. .,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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19
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Chen J, Chen B, Yang X, Tian J, Du Q, Zhang D. Association genetics in Populus reveals the interactions between Pt-miR397a and its target genes. Sci Rep 2015; 5:11672. [PMID: 26115173 PMCID: PMC4481775 DOI: 10.1038/srep11672] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/02/2015] [Indexed: 12/29/2022] Open
Abstract
Recent studies have revealed associations between single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes and diseases. However, association studies to decipher the interactions between miRNAs and their target genes remain to be conducted. Here, we investigated the association of growth and wood traits with SNPs in Pt-miR397a and its targets, in 261 individuals from a natural population of Populus tomentosa. Of the 57 SNPs identified in Pt-miR397a, three strongly affect its secondary stability, and SNPs in target sites in Pt-LAC20 and Pt-HSP40 changed the binding affinity of Pt-miR397a. Single-SNP association analysis revealed that SNPs in Pt-miR397a significantly associated with α-cellulose content and stem volume, and SNPs in target genes also associated with growth and wood-property traits. Multi-SNP association analysis with additive and dominant models found that SNPs in six potential target genes associated with at least one trait in common with Pt-miR397a, revealing a possible genetic interaction between Pt-miR397a and its targets. Furthermore, epistasis analysis revealed epistatic interactions between SNPs in Pt-miR397a and its target genes. Thus, our study indicated that SNPs in Pt-miR397a and six target genes affect wood formation and that association studies can reveal the interactions between miRNAs and their target genes.
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Affiliation(s)
- Jinhui Chen
- 1] National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China [2] Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Beibei Chen
- 1] National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China [2] Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Xiaohui Yang
- 1] National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China [2] Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Jiaxing Tian
- 1] National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China [2] Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Qingzhang Du
- 1] National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China [2] Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Deqiang Zhang
- 1] National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China [2] Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
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20
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Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site in SmDCL1 from Salvia miltiorrhiza. Sci Rep 2015; 5:9891. [PMID: 25970825 PMCID: PMC4429486 DOI: 10.1038/srep09891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/23/2015] [Indexed: 11/08/2022] Open
Abstract
DCL1, the core component for miRNA biogenesis, is itself regulated by miR162 in Arabidopsis. MiRNA-mediated feedback regulation of AtDCL1 is important to maintain the proper level of DCL1 transcripts. However, it is unknown whether the miRNA-mediated regulation of DCL1 is conserved among plants. We analyzed the SmDCL gene family in Salvia miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies, using a comprehensive approach integrating genome-wide prediction, molecular cloning, gene expression profiling, and posttranscriptional regulation analysis. A total of five SmDCLs were identified. Comparative analysis of SmDCLs and AtDCLs showed an apparent enlargement of SmDCL introns in S. miltiorrhiza. The absence of miR162 in S. miltiorrhiza and the loss of miR162 target site in SmDCL1 were unexpectedly found. Further analysis showed that the miR162 target site was not present in DCL1 from ancient plants and was gained during plant evolution. The gained miR162 target site might be lost in a few modern plants through nucleotide mutations. Our results provide evidence for the gain and loss of miR162 and its target sites in Dicer-like genes during evolution. The data is useful for understanding the evolution of miRNA-mediated feedback regulation of DCLs in plants.
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Zhang W, Wang L, Zhou P, Song G, Shen M, Gan S, Shi G. Identification and analysis of genetic variations in pri-miRNAs expressed specifically or at a high level in sheep skeletal muscle. PLoS One 2015; 10:e0117327. [PMID: 25699993 PMCID: PMC4336289 DOI: 10.1371/journal.pone.0117327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/23/2014] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators in miRNA-mediated gene regulatory networks and play important roles in many biological processes, such as growth and development of mammals. In this study, we used microarrays to detect 261 miRNAs that are expressed in sheep skeletal muscle. We found 22 miRNAs that showed high levels of expression and equated to 89% of the total miRNA. Genetic variations in these 22 pri-miRNAs were further investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing. A total of 49 genetic variations, which included 41 single nucleotide polymorphisms (SNPs) and 8 deletions/insertions, were identified in four sheep breeds. Three variations were further researched in a larger sample set, including five sheep breeds with different meat production performances. We found that the genotype and allele frequencies of the CCC deletion/insertion in pri-miR-133a were significantly related to the sheep meat production trait. Finally, cell assays and quantitative reverse transcription PCR (qRT-PCR) were employed to investigate the effect of pri-miRNA genetic variation on the miRNA biogenesis process. The results confirmed that genetic variations can influence miRNA biogenesis and increase or decrease the levels of mature miRNAs, in accordance with the energy and stability change of hair-pin secondary structures. Our findings will help to further the understanding of the functions of genetic variations in sheep pri-miRNAs in skeletal muscle growth and development.
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Affiliation(s)
- Wei Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Limin Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Guangchao Song
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Shangquan Gan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- * E-mail: (SG); (GS)
| | - Guoqing Shi
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- * E-mail: (SG); (GS)
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Liu Q, Wang H, Hu H, Zhang H. Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice. Mol Genet Genomics 2014; 290:593-602. [DOI: 10.1007/s00438-014-0943-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 10/17/2014] [Indexed: 01/24/2023]
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