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Zhang B, Liu G, Song J, Jia B, Yang S, Ma J, Liu J, Shahzad K, Wang W, Pei W, Wu M, Zhang J, Yu J. Analysis of the MIR396 gene family and the role of MIR396b in regulating fiber length in cotton. PHYSIOLOGIA PLANTARUM 2022; 174:e13801. [PMID: 36258652 DOI: 10.1111/ppl.13801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Cotton fiber is one of the most important natural raw materials in the world textile industry. Improving fiber yield and quality has always been the main goal. MicroRNAs, as typical small noncoding RNAs, could affect fiber length during different stages of fiber development. Based on differentially expressed microRNA in the two interspecific backcross inbred lines (BILs) with a significant difference in fiber length, we identified the miR396 gene family in the two tetraploid cotton genomes and found MIR396b_D13 as the functional precursor to produce mature miR396 during the fiber elongation stage. Among 46 target genes regulated by miR396b, the GROWTH-REGULATING FACTOR 5 gene (GRF5, Gh_A10G0492) had a differential expression level in the two BILs during fiber elongation stage. The expression patterns indicated that the miR396b-GRF5 regulatory module has a critical role in fiber development. Furthermore, virus-induced gene silencing (VIGS) of miR396b significantly produced longer fiber than the wild type, and the expression level of GRF5 showed the reverse trends of the miR396b expression level. The analysis of co-expression network for the GRF5 gene suggested that a cytochrome P450 gene functions as an allene oxide synthase (Gh_D06G0089, AOS), which plays a critical role in jasmonate biosynthetic pathway. In conclusion, our results revealed that the miR396b-GRF5 module has a critical role in fiber development. These findings provide a molecular foundation for fiber quality improvement in the future.
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Affiliation(s)
- Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoyuan Liu
- School of Life Science, Nantong University, Nantong, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxian Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianjiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenkui Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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Ayubov MS, Mirzakhmedov MH, Sripathi VR, Buriev ZT, Ubaydullaeva KA, Usmonov DE, Norboboyeva RB, Emani C, Kumpatla SP, Abdurakhmonov IY. Role of MicroRNAs and small RNAs in regulation of developmental processes and agronomic traits in Gossypium species. Genomics 2019; 111:1018-1025. [PMID: 30026106 DOI: 10.1016/j.ygeno.2018.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 02/08/2023]
Abstract
Small RNAs (sRNAs) are short, non-coding, 17-24 nucleotides long RNA molecules that play vital roles in regulating gene expression in every known organism investigated to date including cotton (Gossypium ssp.). These tiny RNA molecules target diverse categories of genes from different bioliogical and metabolic processes and have been reported in the three domains of life. Small RNAs, including miRNAs, are involved in ovule and fiber development, biotic and abiotic stresses, fertility, and other biochemical processes in cotton species. Also, sRNAs are the critical components in RNA interference pathway. In this article, we have reviewed the research efforts related to the isolation and characterization of miRNAs using molecular and genomic approaches. The progress made in understanding the functional roles of miRNAs in regulation, alteration, and inactivation of fundamental plant processes and traits of importance in cotton are presented here.
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Affiliation(s)
- Mirzakamol S Ayubov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Mukhammad H Mirzakhmedov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan; Faculty of Agricultural Science, University of Hohenheim, Germany
| | - Venkateswara R Sripathi
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama A and M University, AL, USA
| | - Zabardast T Buriev
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | | | - Dilshod E Usmonov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Risolat B Norboboyeva
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
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Fausto AKS, Silva TDF, Romanel E, Vaslin MFS. microRNAs as reference genes for quantitative PCR in cotton. PLoS One 2017; 12:e0174722. [PMID: 28414734 PMCID: PMC5393557 DOI: 10.1371/journal.pone.0174722] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/14/2017] [Indexed: 11/18/2022] Open
Abstract
Cotton (Gossypium hirsutum) is the most important non-food plant in the world. Studies concerning the fiber quality and plant fitness of cotton at molecular level depend on high sensitive and reproducible gene-expression assays. However, only a few reports have described genes suitable for normalizing gene expression data. In this study, we report for the first time that microRNAs (miRNAs) are reliable reference genes (RGs) for cotton gene expression normalization in quantitative real-time reverse transcription (RT)-PCR. The stability of cotton miRNAs was assayed in root, stem, leaf and flower samples from three different cultivars [FiberMax (FM966), Delta Opal (DO) and Cedro] and under conditions of biotic stress caused by infection with Cotton leafroll dwarf virus (CLRDV). The stability of mRNAs already described as reference genes in cotton was also assessed. The geNorm, NormFinder, BestKeeper and ΔCt algorithms were used to select the best reference genes. In 8 of the 12 sets tested, miRNAs (miR172, 168 and 390) were found to be the best RGs. To validate the best selected RGs, miR159, miR164, miR2118, miR2910, miR3476, GhDCL2 and GhDCL4 expression levels were evaluated under biotic stress conditions, and miR164 and a putative myo-inositol oxigenase gene (GhMIOX) were assessed in leaves and flowers. The RGs selected in this work proved to be excellent reference genes in the two cases studied. Our results support the use of miRNAs as reference genes for miRNA and protein-coding genes.
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Affiliation(s)
- Anna Karoline Silva Fausto
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
| | - Tatiane da Franca Silva
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brasil
| | - Elisson Romanel
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brasil
| | - Maite F. S. Vaslin
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
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MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development. Sci Rep 2017; 7:44454. [PMID: 28327647 PMCID: PMC5361117 DOI: 10.1038/srep44454] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/08/2017] [Indexed: 12/24/2022] Open
Abstract
The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield.
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Zhang T, Hu S, Yan C, Li C, Zhao X, Wan S, Shan S. Mining, identification and function analysis of microRNAs and target genes in peanut (Arachis hypogaea L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 111:85-96. [PMID: 27915176 DOI: 10.1016/j.plaphy.2016.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/03/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
In the present investigation, a total of 60 conserved peanut (Arachis hypogaea L.) microRNA (miRNA) sequences, belonging to 16 families, were identified using bioinformatics methods. There were 392 target gene sequences, identified from 58 miRNAs with Target-align software and BLASTx analyses. Gene Ontology (GO) functional analysis suggested that these target genes were involved in mediating peanut growth and development, signal transduction and stress resistance. There were 55 miRNA sequences, verified employing a poly (A) tailing test, with a success rate of up to 91.67%. Twenty peanut target gene sequences were randomly selected, and the 5' rapid amplification of the cDNA ends (5'-RACE) method were used to validate the cleavage sites of these target genes. Of these, 14 (70%) peanut miRNA targets were verified by means of gel electrophoresis, cloning and sequencing. Furthermore, functional analysis and homologous sequence retrieval were conducted for target gene sequences, and 26 target genes were chosen as the objects for stress resistance experimental study. Real-time fluorescence quantitative PCR (qRT-PCR) technology was applied to measure the expression level of resistance-associated miRNAs and their target genes in peanut exposed to Aspergillus flavus (A. flavus) infection and drought stress, respectively. In consequence, 5 groups of miRNAs & targets were found accorded with the mode of miRNA negatively controlling the expression of target genes. This study, preliminarily determined the biological functions of some resistance-associated miRNAs and their target genes in peanut.
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Affiliation(s)
- Tingting Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Shuhao Hu
- Shandong Peanut Research Institute, Qingdao, 266100, China; Shandong University, Weihai, 264200, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Shubo Wan
- Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, 266100, China.
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6
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Sun R, Li C, Zhang J, Li F, Ma L, Tan Y, Wang Q, Zhang B. Differential expression of microRNAs during fiber development between fuzzless-lintless mutant and its wild-type allotetraploid cotton. Sci Rep 2017; 7:3. [PMID: 28127052 PMCID: PMC5428375 DOI: 10.1038/s41598-017-00038-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/07/2016] [Indexed: 11/30/2022] Open
Abstract
Cotton is one of the most important textile crops but little is known how microRNAs regulate cotton fiber development. Using a well-studied cotton fiberless mutant Xu-142-fl, we compared 54 miRNAs for their expression between fiberless mutant and its wildtype. In wildtype Xu-142, 26 miRNAs are involved in cotton fiber initiation and 48 miRNAs are related to primary wall synthesis and secondary wall thickening. Thirty three miRNAs showed different expression in fiber initiation between Xu-142 and Xu-142-fl. These miRNAs potentially target 723 protein-coding genes, including transcription factors, such as MYB, ARF, and LRR. ARF18 was newly predicted targets of miR160a, and miR160a was expressed at higher level in −2DPA of Xu-142-fl compared with Xu-142. Furthermore, the result of Gene Ontology-based term classification (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows that miRNA targets were classified to 222 biological processes, 64 cellular component and 42 molecular functions, enriched in 22 KOG groups, and classified into 28 pathways. Together, our study provides evidence for better understanding of miRNA regulatory roles in the process of fiber development, which is helpful to increase fiber yield and improve fiber quality.
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Affiliation(s)
- Runrun Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
| | - Chengqi Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
| | - Jinbao Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
| | - Fei Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
| | - Liang Ma
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
| | - Yangguang Tan
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
| | - Qinglian Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China.
| | - Baohong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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7
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Zahid KR, Ali F, Shah F, Younas M, Shah T, Shahwar D, Hassan W, Ahmad Z, Qi C, Lu Y, Iqbal A, Wu W. Response and Tolerance Mechanism of Cotton Gossypium hirsutum L. to Elevated Temperature Stress: A Review. FRONTIERS IN PLANT SCIENCE 2016; 7:937. [PMID: 27446165 PMCID: PMC4927942 DOI: 10.3389/fpls.2016.00937] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/13/2016] [Indexed: 05/23/2023]
Abstract
Cotton is an important multipurpose crop which is highly sensitive to both biotic and abiotic stresses. Proper management of this cash crop requires systematic understanding of various environmental conditions that are vital to yield and quality. High temperature stress can severely affect the viability of pollens and anther indehiscence, which leads to significant yield losses. Cotton can respond to withstand adverse environmental condition in several phases among which the accumulation of chemicals is extremely vital. Calcium, kinases, reactive oxygen species, carbohydrate, transcription factors, gene expression regulation, and plant hormones signaling pathways are playing a handy role in activating the major genes responsible to encounter and defend elevated temperature stress. The production of heat shock proteins is up-regulated when crops are unleashed to high temperature stress. Molecular breeding can play a functional role to identify superior genes for all the important attributes as well as provide breeder ready markers for developing ideotypes. The development of high-temperature resistant transgenic cultivars of cotton can grant a stability benefit and can also ameliorate the production capacity in response to elevated temperature.
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Affiliation(s)
- Kashif Rafiq Zahid
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal UniversityWuhan, China
| | - Farhan Ali
- Cereal Crops Research InstitutePirsabak, Nowshera, Pakistan
| | - Farooq Shah
- Department of Agriculture, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - Muhammad Younas
- Department of Biotechnology, Mohi-ud-Din Islamic UniversityAzad Jammu and Kashmir, Pakistan
| | - Tariq Shah
- Department of Agricultural Economics and Management, Huazhong Agricultural UniversityWuhan, China
| | - Durri Shahwar
- Department of Plant Breeding and Genetics, University of SwabiKhyber Pakhtunkhwa, Pakistan
| | - Waseem Hassan
- Department of Soil and Environmental Sciences, Muhammad Nawaz Shareef University of AgricultureMultan, Pakistan
| | - Zahoor Ahmad
- Key Lab of Crop Disease Monitoring and Safety Control, Huazhong Agricultural UniversityWuhan, China
| | - Chao Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal UniversityWuhan, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural UniversityWenjian Sichuan, China
| | - Amjad Iqbal
- Department of Agriculture, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - Wei Wu
- College of Agronomy, Northwest A&F UniversityYangling, China
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Wang Q, Zhang B. MicroRNAs in cotton: an open world needs more exploration. PLANTA 2015; 241:1303-12. [PMID: 25841643 DOI: 10.1007/s00425-015-2282-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/13/2015] [Indexed: 05/28/2023]
Abstract
This paper reviews the progress and current problems in the field of cotton microRNAs. Cotton is not only one of the most important crops in terms of fiber usage and economic value, but also a model species for investigating cell wall and cellulose biosynthesis as well plant polyploidization. Compared with model plant species, such as Arabidopsis and rice, the research on cotton microRNAs (miRNAs) is lagging, although great progress has been made in the past decade. Since the first reports on identifying miRNAs in cotton in 2007, hundreds of miRNAs have been identified using an in silico comparative genome-based approach and direct cloning. Next-generation deep sequencing has opened the door for cotton miRNA research. In cotton, miRNAs are associated with many biological and metabolic processes, including fiber initiation and development, floral development, embryogenesis, and response to biotic and abiotic stresses. However, the majority of current research is focused on miRNA identification. Although several targets have been predicted using computational approaches and degradome sequencing, more functional studies should be performed in the next couple of years to elucidate the roles of miRNAs in cotton fiber development and response to different environmental stresses using transgenic technology. This paper reviews the history, identification, and function of cotton miRNAs as well as future directions for this research.
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Affiliation(s)
- Qinglian Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
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Selection and validation of reliable reference genes in Gossypium raimondii. Biotechnol Lett 2015; 37:1483-93. [PMID: 26003093 DOI: 10.1007/s10529-015-1810-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To identify reliable reference genes for gene expression analysis in Gossypium raimondii. RESULTS Five different software tools, geNorm, NormFinder, BestKeeper, ReFinder and ∆Ct method were employed to analyze the qRT-PCR data systematically of 12 housekeeping genes. SAD and TUA11 showed relatively stable expression levels in all tissues (i.e. leaves, shoots, buds, and sepals). We then limited our analysis to each plant part and identified tissue-specific reference genes. Our results showed TUA11, TUB6 and EF1a, EF1a, MZA and GAPC2, MZA, GAPC2, SAD and TUA11, and UBQ and MZA were reliable reference genes in leaves, shoots, buds, and sepals, respectively. CONCLUSION Some genes were commonly identified as candidate reference genes in more than two tissue, while others were tissue-specific. Thus, our study allows choosing an appropriate control gene based on sampling for gene expression analysis.
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Sun R, Wang K, Guo T, Jones DC, Cobb J, Zhang B, Wang Q. Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii. Funct Integr Genomics 2015; 15:481-93. [PMID: 25809690 DOI: 10.1007/s10142-015-0437-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/02/2015] [Accepted: 03/09/2015] [Indexed: 12/17/2022]
Abstract
Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In this study, a total of 35 ARF genes, named as GrARFs, were identified in a diploid cotton species Gossypium raimondii. The 35 ARF genes were located in 12 of the 13 cotton chromosomes; the intron/exon distribution of the GrARF genes was similar among sister pairs, whereas the divergence of some GrARF genes suggests the possibility of functional diversification. Our results show that the middle domains of nine GrARF proteins rich in glutamine (Q) are activators, while 26 other GrARF proteins rich in proline (P), serine (S), and threonine (T) are repressors. Our results also show that the expression of GrARF genes is diverse in different tissues. The expression of GrARF1 was significantly higher in leaves, whereas GrARF2a had higher expression level in shoots, which implicates different roles in the tested tissues. The GrARF11 has a higher expression level in buds than that in leaves, while GrARF19.2 shows contrasting expression patterns, having higher expression in leaves than that in buds. This suggests that they play different roles in leaves and buds. During long-term evolution of G. raimondii, some ARF genes were lost and some arose. The identification and characterization of the ARF genes in G. raimondii elucidate its important role in cotton that ARF genes regulate the development of flower buds, sepals, shoots, and leaves.
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Affiliation(s)
- Runrun Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
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11
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Sun R, Wang Q, Ma J, He Q, Zhang B. Differentiated expression of microRNAs may regulate genotype-dependent traits in cotton. Gene 2014; 547:233-8. [PMID: 24971502 DOI: 10.1016/j.gene.2014.06.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/03/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
Abstract
miRNA is an exogenous non-coding RNA with 21-24nt in length, which plays a crucial role in almost all biological processes. In plants, miRNAs regulate organ development, phase change, signal transduction and response to different biotic and abiotic stresses at the post-transcriptional levels. Although there are many studies on plant miRNAs, no studies have been focused on the genotype dependence. Genotype-dependent traits may be controlled by the differential expression of certain miRNAs. To test this hypothesis, we investigated the expression profile patterns of 11 selected miRNAs in 5 different organs in 5 different cotton cultivars and their implication on plant development. Our results demonstrate that miRNAs have different expression patterns in different plant organs in different genotypes, which implicate their different traits, including early flowering. miR172 is a miRNA controlling floral development and phase change; our results show that miR172 has a higher expression level in the flower bud than in any other organ, our results also show that Baimian cultivars have a higher expression of miR172 than TM-1. This suggests that Baimian cultivars have an earlier transition from vegetable growth to reproductive growth, which is confirmed by our development data on floral branch development. Our result also shows that several miRNAs, including miR159 and miR162, were highly expressed in Baimian cultivars. The results obtained in this study would provide new insight for improving cotton using miRNA-based biotechnology.
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Affiliation(s)
- Runrun Sun
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qinglian Wang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China
| | - Jun Ma
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qiuling He
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Baohong Zhang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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12
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He Q, Zhu S, Zhang B. MicroRNA-target gene responses to lead-induced stress in cotton (Gossypium hirsutum L.). Funct Integr Genomics 2014; 14:507-15. [PMID: 24879091 DOI: 10.1007/s10142-014-0378-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/27/2014] [Accepted: 05/12/2014] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) play key roles in plant responses to various metal stresses. To investigate the miRNA-mediated plant response to heavy metals, cotton (Gossypium hirsutum L.), the most important fiber crop in the world, was exposed to different concentrations (0, 25, 50, 100, and 200 µM) of lead (Pb) and then the toxicological effects were investigated. The expression patterns of 16 stress-responsive miRNAs and 10 target genes were monitored in cotton leaves and roots by quantitative real-time PCR (qRT-PCR); of these selected genes, several miRNAs and their target genes are involved in root development. The results show a reciprocal regulation of cotton response to lead stress by miRNAs. The characterization of the miRNAs and the associated target genes in response to lead exposure would help in defining the potential roles of miRNAs in plant adaptation to heavy metal stress and further understanding miRNA regulation in response to abiotic stress.
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Affiliation(s)
- Qiuling He
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
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13
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Xie F, Stewart CN, Taki FA, He Q, Liu H, Zhang B. High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:354-66. [PMID: 24283289 DOI: 10.1111/pbi.12142] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/22/2013] [Accepted: 10/03/2013] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are an important class of small regulatory RNAs. The goal of this study was to analyse stress-responsive miRNAs in switchgrass (Panicum virgatum), the emerging biofuel crop, to facilitate choosing gene targets for improving biomass and biofuel yield. After sequencing three small RNA libraries constructed from control, salt- and drought-treated switchgrass using Illumina sequencing technology, we identified 670 known miRNA families from a total of more than 50 million short reads. A total of 273 miRNAs were identified with precursors: 126 conserved miRNAs and 147 novel miRNAs. Of them, 265 miRNAs were found to have their opposite sequences (miRNA*) with 2-nt overhang on the 3' end. Of them, 194 were detected in switchgrass transcriptome sequences generated from 31 high-throughput RNA sequencing (RNA-Seq) data sets in NCBI. Many miRNAs were differentially or uniquely expressed during salinity or drought stress treatment. We also discovered 11 miRNA clusters containing 29 miRNAs. These identified miRNAs potentially targeted 28549 genes with a various function, including transcription factors, stress-response proteins and cellulose biosynthesis-related proteins. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the identified miRNAs and their targets were classified to 3779 GO terms including 1534 molecular functions, 1851 biological processes and 394 cellular components and were enriched to 147 KEGG pathways. Interestingly, 195 miRNA families and 450 targets were involved in the biosynthesis pathways of carbon, glucose, starch, fatty acid and lignin and in xylem formation, which could aid in designing next-generation switchgrass for biomass and biofuel.
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Affiliation(s)
- Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC, USA
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miRNAs expression profile in bast of ramie elongation phase and cell wall thickening and end wall dissolving phase. Mol Biol Rep 2014; 41:901-7. [PMID: 24385297 DOI: 10.1007/s11033-013-2934-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/20/2013] [Indexed: 10/25/2022]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide long non-coding RNAs that play critical regulatory roles during plant development, organ morphogenesis, and cell fate determination and differentiation. In this study, miRNA microarray chips were used to explore the expression profile of ramie miRNAs between the bast of fiber elongation phase and those of cell wall thickening and end wall dissolving phase. There are 150 and 148 credible miRNAs in the bast of fiber elongation phase and cell wall thickening and end wall dissolving phase, respectively. These miRNAs distributed in 27 species and mainly concentrated in nine species. Analysis showed that 51 miRNAs were differentially expressed: 27 up-regulated (miR166, miR172, miR396, miR482, miR894 and miR2911 families) and 24 down-regulated (miR156, miR159, miR164, miR319 and miR1450 families) in the bast of fiber elongation phase compared with the bast of cell wall thickening and end wall dissolving phase. To further confirm our results, we examined the expression of three miRNAs (zma-miR172b*, pvu-miR482 and vvi-172a) by quantitative real-time reverse transcriptase-PCR. Our results will provide a molecular basis for future research miRNA function on ramie genetics and breeding.
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Wang M, Wang Q, Zhang B. Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.). Gene 2013; 530:26-32. [PMID: 23948080 DOI: 10.1016/j.gene.2013.08.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/15/2013] [Accepted: 08/03/2013] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are an important gene regulator, controlling almost all biological and metabolic processes, in both plants and animals. In this study, we investigated the effect of drought and salinity stress on the expression of miRNAs and their targets in cotton (Gossypium hirsutum L.). Our results show that the expression change of miRNAs and their targets were dose-dependent and tissue-dependent under salinity and drought conditions. The expression of miRNAs in leaf was down-regulated under higher salinity stress while shows variable patterns in other conditions. The highest fold-changes of miRNAs were miR398 in roots with 28.9 fold down-regulation under 0.25% NaCl treatment and miR395 in leaves with 7.6 fold down-regulation under 1% PEG treatment. The highest up-regulation of miRNA targets was AST in roots with 4.7 fold-change under 2.5% PEG and the gene with highest down-regulation was CUC1 in leaves with 25.6 fold-change under 0.25% NaCl treatment. Among seven miRNA-target pairs we studied, five pairs, miR156-SPL2, miR162-DCL1, miR159-TCP3, miR395-APS1 and miR396-GRF1, show significant regulation relationship in roots and leaves under salinity stress concentration.
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Affiliation(s)
- Min Wang
- Beijing Key Laboratory of Plant Resources Research and Development, Department of Biotechnology, School of Science, Beijing Technology and Business University, Haidian District, Beijing, China
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16
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MicroRNAs and their cross-talks in plant development. J Genet Genomics 2013; 40:161-70. [PMID: 23618399 DOI: 10.1016/j.jgg.2013.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 01/10/2023]
Abstract
Plant development is a complex process influenced by exogenous and endogenous elements. A series of postembryonic developmental events is involved to form the final architecture and contend with the changing environment. MicroRNA (miRNA) is one of endogenous non-coding RNAs, which plays an important role in plant developmental regulation. In this review, we summarized 34 miRNA families that are closely associated with plant development. Among these families, nine are expressed only in specific organs, whereas 20 families are expressed in at least two different organs. It is known that some miRNAs are expressed across most processes of plant growth, while some appear only at particular developmental stages or under special environmental conditions such as drought, waterlogging and short-day time. These miRNAs execute their diverse functions by regulating developmental gene expression levels, interacting with phytohormone signaling response, participating in the biogenesis of ta-siRNAs and affecting the production of miRNAs.
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Wang M, Wang Q, Wang B. Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). PLoS One 2012; 7:e33696. [PMID: 22493671 PMCID: PMC3320894 DOI: 10.1371/journal.pone.0033696] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 02/18/2012] [Indexed: 01/01/2023] Open
Abstract
To date, no miRNAs have been identified in the important diploid cotton species although there are several reports on miRNAs in upland cotton. In this study, we identified 73 miRNAs, belonging to 49 families, from Asiatic cotton using a well-developed comparative genome-based homologue search. Several of the predicted miRNAs were validated using quantitative real time PCR (qRT-PCR). The length of miRNAs varied from 18 to 22 nt with an average of 20 nt. The length of miRNA precursors also varied from 46 to 684 nt with an average of 138 ±120 nt. For a majority of Asiatic cotton miRNAs, there is only one member per family; however, multiple members were identified for miRNA 156, 414, 837, 838, 1044, 1533, 2902, 2868, 5021 and 5142 families. Nucleotides A and U were dominant, accounted for 62.95%, in the Asiatic cotton pre-miRNAs. The Asiatic cotton pre-miRNAs had high negative minimal folding free energy (MFE) and adjusted MFE (AMFE) and high MFE index (MFEI). Many miRNAs identified in Asiatic cotton suggest that miRNAs also play a similar regulatory mechanism in diploid cotton.
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Affiliation(s)
- Min Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qinglian Wang
- Henan Institute of Sciences and Technology, Xingxiang, Henan, China
| | - Baomin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Sun G, Stewart CN, Xiao P, Zhang B. MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress. PLoS One 2012; 7:e32017. [PMID: 22470418 PMCID: PMC3314629 DOI: 10.1371/journal.pone.0032017] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 01/17/2012] [Indexed: 01/22/2023] Open
Abstract
Switchgrass has increasingly been recognized as a dedicated biofuel crop for its broad adaptation to marginal lands and high biomass. However, little is known about the basic biology and the regulatory mechanisms of gene expression in switchgrass, particularly under stress conditions. In this study, we investigated the effect of salt and drought stress on switchgrass germination, growth and the expression of small regulatory RNAs. The results indicate that salt stress had a gradual but significant negative effect on switchgrass growth and development. The germination rate was significantly decreased from 82% for control to 36% under 1% NaCl treatment. However, drought stress had little effect on the germination rate but had a significant effect on the growth of switchgrass under the severest salinity stress. Both salt and drought stresses altered the expression pattern of miRNAs in a dose-dependent manner. However, each miRNA responded to drought stress in a different pattern. Salt and drought stress changed the expression level of miRNAs mainly from 0.9-fold up-regulation to 0.7-fold down-regulation. miRNAs were less sensitive to drought treatment than salinity treatment, as evidenced by the narrow fold change in expression levels. Although the range of change in expression level of miRNAs was similar under salt and drought stress, no miRNAs displayed significant change in expression level under all tested salt conditions. Two miRNAs, miR156 and miR162, showed significantly change in expression level under high drought stress. This suggests that miR156 and miR162 may attribute to the adaption of switchgrass to drought stress and are good candidates for improving switchgrass as a biofuel crop by transgenic technology.
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Affiliation(s)
- Guiling Sun
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
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Pang M, Xing C, Adams N, Rodriguez-Uribe L, Hughs SE, Hanson SF, Zhang J. Comparative expression of miRNA genes and miRNA-based AFLP marker analysis in cultivated tetraploid cottons. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:824-830. [PMID: 21134704 DOI: 10.1016/j.jplph.2010.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 10/19/2010] [Accepted: 10/30/2010] [Indexed: 05/30/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that down-regulate gene expression in a sequence specific manner to control plant growth and development. The identification and characterization of miRNAs are critical steps in finding their target genes and elucidating their functions. The objective of the present study was to assess the genetic variation of miRNA genes through expression comparisons and miRNA-based AFLP marker analysis. Seven miRNAs were first selected for RT-PCR and four for quantitative RT-PCR analysis that showed considerably high or differential expression levels in early stages of boll development. Except for miR160a, differential gene expression of miR171, 390a, and 396a was detected in early developing bolls at one or more timepoints between two cultivated cotton cultivars, Pima Phy 76 (Gossypium barbadense) and Acala 1517-99 (Gossypium hirsutum). Our further work demonstrated that genetic diversity of miRNA genes can be assessed by miRNA-AFLP analysis using primers designed from 22 conserved miRNA genes in combination with AFLP primers. Homologous miRNA genes can be also identified and isolated for sequencing and confirmation using this homology-based genotyping approach. This strategy offers an alternative to isolating a full length of miRNA genes and their up-stream and down-stream sequences. The significance of the expression and sequence differences of miRNAs between cotton species or genotypes needs further studies.
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Affiliation(s)
- Mingxiong Pang
- Department of Plant and Environmental Sciences, New Mexico State University, MSC 3Q, Las Cruces, NM 88003, USA
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Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ. Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC PLANT BIOLOGY 2010; 10:3. [PMID: 20047695 PMCID: PMC2826338 DOI: 10.1186/1471-2229-10-3] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 01/05/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy. RESULTS In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts. CONCLUSIONS This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.
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Affiliation(s)
- Chuan-Zhi Zhao
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | - Han Xia
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | | | - Ying-Yin Yao
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, PR China
- Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, PR China
| | - Yu-Ping Bi
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | - Ai-Qin Li
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | - Meng-Jun Li
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | - Chang-Sheng Li
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | - Bao-Hong Zhang
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
| | - Xing-Jun Wang
- High-Tech Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture; Jinan 250100, PR China
- Key Laboratory for Genetic Improvement of Crop, Animal and Poultry of Shandong Province, Ji'nan 250100, PR China
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