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Liu J, Miao P, Qin W, Hu W, Wei Z, Ding W, Zhang H, Wang Z. A novel single nucleotide mutation of TFL1 alters the plant architecture of Gossypium arboreum through changing the pre-mRNA splicing. PLANT CELL REPORTS 2023; 43:26. [PMID: 38155318 PMCID: PMC10754752 DOI: 10.1007/s00299-023-03086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/10/2023] [Indexed: 12/30/2023]
Abstract
KEY MESSAGE A single nucleotide mutation from G to A at the 201st position changed the 5' splice site and deleted 31 amino acids in the first exon of GaTFL1. Growth habit is an important agronomic trait that plays a decisive role in the plant architecture and crop yield. Cotton (Gossypium) tends to indeterminate growth, which is unsuitable for the once-over mechanical harvest system. Here, we identified a determinate growth mutant (dt1) in Gossypium arboreum by EMS mutagenesis, in which the main axis was terminated with the shoot apical meristem (SAM) converted into flowers. The map-based cloning of the dt1 locus showed a single nucleotide mutation from G to A at the 201st positions in TERMINAL FLOWER 1 (GaTFL1), which changed the alternative RNA 5' splice site and resulted in 31 amino acids deletion and loss of function of GaTFL1. Comparative transcriptomic RNA-Seq analysis identified many transporters responsible for the phytohormones, auxin, sugar, and flavonoids, which may function downstream of GaTFL1 to involve the plant architecture regulation. These findings indicate a novel alternative splicing mechanism involved in the post-transcriptional modification and TFL1 may function upstream of the auxin and sugar pathways through mediating their transport to determine the SAM fate and coordinate the vegetative and reproductive development from the SAM of the plant, which provides clues for the TFL1 mechanism in plant development regulation and provide research strategies for plant architecture improvement.
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Affiliation(s)
- Ji Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Pengfei Miao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhenzhen Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wusi Ding
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Huan Zhang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads. Gene 2023; 852:147065. [PMID: 36435508 DOI: 10.1016/j.gene.2022.147065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.
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Egan LM, Stiller WN. The Past, Present, and Future of Host Plant Resistance in Cotton: An Australian Perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:895877. [PMID: 35873986 PMCID: PMC9297922 DOI: 10.3389/fpls.2022.895877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/06/2022] [Indexed: 05/24/2023]
Abstract
Cotton is a key global fiber crop. However, yield potential is limited by the presence of endemic and introduced pests and diseases. The introduction of host plant resistance (HPR), defined as the purposeful use of resistant crop cultivars to reduce the impact of pests and diseases, has been a key breeding target for the Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program. The program has seen success in releasing cultivars resistant to Bacterial blight, Verticillium wilt, Fusarium wilt, and Cotton bunchy top. However, emerging biotic threats such as Black root rot and secondary pests, are becoming more frequent in Australian cotton production systems. The uptake of tools and breeding methods, such as genomic selection, high throughput phenomics, gene editing, and landscape genomics, paired with the continued utilization of sources of resistance from Gossypium germplasm, will be critical for the future of cotton breeding. This review celebrates the success of HPR breeding activities in the CSIRO cotton breeding program and maps a pathway for the future in developing resistant cultivars.
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Li Y, Mo T, Ran L, Zeng J, Wang C, Liang A, Dai Y, Wu Y, Zhong Z, Xiao Y. Genome resequencing-based high-density genetic map and QTL detection for yield and fiber quality traits in diploid Asiatic cotton (Gossypium arboreum). Mol Genet Genomics 2022; 297:199-212. [PMID: 35048185 DOI: 10.1007/s00438-021-01848-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Cotton is the most important fiber crop in the world. Asiatic cotton (Gossypium arboreum, genome A2) is a diploid cotton species producing spinnable fibers and important germplasm for cotton breeding and a significant model for fiber biology. However, the genetic map of Asiatic cotton has been lagging behind tetraploid cottons, as well as other stable crops. This study aimed to construct a high-density SNP genetic map and to map QTLs for important yield and fiber quality traits. Using a recombinant inbred line (RIL) population and genome resequencing technology, we constructed a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. QTL analysis revealed a total of 297 QTLs for 13 yield and fiber quality traits in three environments, explaining 5.0-37.4% of the phenotypic variance, among which 75 were stably detected in two or three environments. Besides, 47 QTL clusters, comprising 131 QTLs for representative traits, were identified. Our works laid solid foundation for fine mapping and cloning of QTL for yield and fiber quality traits in Asiatic cotton.
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Affiliation(s)
- Yaohua Li
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Tong Mo
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Lingfang Ran
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Jianyan Zeng
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Chuannan Wang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Aimin Liang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Yonglu Dai
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Yiping Wu
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Ziman Zhong
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Yuehua Xiao
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China.
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Iqbal MS, Tang S, Sarfraz Z, Iqbal MS, Li H, He S, Jia Y, Sun G, Pan Z, Xiaoli G, Mahmood A, Ahmad S, Nazir MF, Chen B, Wang L, Pang B, Wei S, Du X. Genetic Factors Underlying Single Fiber Quality in A-Genome Donor Asian Cotton ( Gossypium arboreum). Front Genet 2021; 12:758665. [PMID: 34950189 PMCID: PMC8689003 DOI: 10.3389/fgene.2021.758665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/17/2021] [Indexed: 11/22/2022] Open
Abstract
The study of A-genome Asian cotton as a potential fiber donor in Gossypium species may offer an enhanced understanding of complex genetics and novel players related to fiber quality traits. Assessment of individual fibers providing classified fiber quality information to the textile industry is Advanced Fiber Information System (AFIS) in the recent technological era. Keeping the scenario, a diverse collection of 215 Asiatic cotton accessions were evaluated across three agro-ecological zones of China. Genome-Wide Association Studies (GWAS) was performed to detect association signals related to 17 AFIS fiber quality traits grouped into four categories viz: NEPs, fiber length, maturity, and fineness. Significant correlations were found within as well as among different categories of various traits related to fiber quality. Fiber fineness has shown a strong correlation to all other categories, whereas these categories are shown interrelationships via fiber-fineness. A total of 7,429 SNPs were found in association with 17 investigated traits, of which 177 were selected as lead SNPs. In the vicinity of these lead SNPs, 56 differentially expressed genes in various tissues/development stages were identified as candidate genes. This compendium connecting trait-SNP-genes may allow further prioritization of genes in GWAS loci to enable mechanistic studies. These identified quantitative trait nucleotides (QTNs) may prove helpful in fiber quality improvement in Asian cotton through marker-assisted breeding as well as in reviving eroded genetic factors of G. hirsutum via introgression breeding.
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Affiliation(s)
- Muhammad Shahid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China.,Ayub Agricultural Research Institute Faisalabad, Cotton Research Institute, Multan, Pakistan
| | - Shurong Tang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Zareen Sarfraz
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Sajid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China.,Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hongge Li
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Geng Xiaoli
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Abid Mahmood
- Ayub Agricultural Research Institute Faisalabad, Cotton Research Institute, Multan, Pakistan
| | - Saghir Ahmad
- Ayub Agricultural Research Institute Faisalabad, Cotton Research Institute, Multan, Pakistan
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Baoyin Pang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Shoujun Wei
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
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Khushboo S, Priyanka S, Surender KV. Simple sequence repeats (SSR) and interspersed sequence repeats (ISSR) markers for genetic diversity analysis among selected genotypes of Gossypium arboreum race bengalense. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2015.14878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Sethi K, Siwach P, Verma SK. Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:531-9. [PMID: 26600679 PMCID: PMC4646864 DOI: 10.1007/s12298-015-0326-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/20/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it has not been explored fully. During the present study, 100 polymorphic SSR loci were used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.
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Affiliation(s)
- Khushboo Sethi
- />Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - Priyanka Siwach
- />Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
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Chen Y, Wang Y, Zhao T, Yang J, Feng S, Nazeer W, Zhang T, Zhou B. A New Synthetic Amphiploid (AADDAA) between Gossypium hirsutum and G. arboreum Lays the Foundation for Transferring Resistances to Verticillium and Drought. PLoS One 2015; 10:e0128981. [PMID: 26061996 PMCID: PMC4465178 DOI: 10.1371/journal.pone.0128981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/04/2015] [Indexed: 11/18/2022] Open
Abstract
Gossypium arboreum, a cultivated cotton species (2n = 26, AA) native to Asia, possesses invaluable characteristics unavailable in the tetraploid cultivated cotton gene pool, such as resistance to pests and diseases and tolerance to abiotic stresses. However, it is quite difficult to transfer favorable traits into Upland cotton through conventional methods due to the cross-incompatibility of G. hirsutum (2n = 52, AADD) and G. arboreum. Here, we improved an embryo rescue technique to overcome the cross-incompatibility between these two parents for transferring favorable genes from G. arboreum into G. hirsutum. Our results indicate that MSB2K supplemented with 0.5 mgl-1 kinetin and 250 mg-1 casein hydrolysate is an efficient initial medium for rescuing early (3 d after pollination) hybrid embryos. Eight putative hybrids were successfully obtained, which were further verified and characterized by cytology, molecular markers and morphological analysis. The putative hybrids were subsequently treated with different concentrations of colchicine solution to double their chromosomes. The results demonstrate that four putative hybrid plants were successfully chromosome-doubled by treatment with 0.1% colchicine for 24 h and become amphiploid, which were confirmed by cytological observation, self-fertilization and backcrossing. Preliminary assessments of resistance at seedling stage indicate that the synthetic amphiploid showed highly resistant to Verticillium and drought. The synthetic amphiploid between G. hirsutum × G. arboreum would lay the foundation for developing G. arboreum-introgressed lines with the uniform genetic background of G. hirsutum acc TM-1, which would greatly enhance and simplify the mining, isolation, characterization, cloning and use of G. arboreum-specific desirable genes in future cotton breeding programs.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yingying Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Ting Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Jianwei Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Shouli Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Wajad Nazeer
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, People’s Republic of China
- * E-mail:
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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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