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Zhuo J, Vasupalli N, Wang Y, Zhou G, Gao H, Zheng Y, Li B, Hou D, Lin X. Molecular identification of Bambusa changningensis is the natural bamboo hybrid of B. rigida × Dendrocalamus farinosus. Front Plant Sci 2023; 14:1231940. [PMID: 37727859 PMCID: PMC10505617 DOI: 10.3389/fpls.2023.1231940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023]
Abstract
Bamboo is one of the fastest-growing plants commonly used in food, fibre, paper, biofuel, ornamental and medicinal industries. Natural hybridization in bamboo is rare due to its long vegetative period followed by gregarious flowering and death of the entire population. In the current study, a new bamboo species, Bambusa changningensis, shows intermediate characteristics of Dendrocalamus farinosus and B. rigida morphologically, but it is unknown whether B. changningensis is a natural hybrid. Moreover, B. changningensis has been identified as a superior variety of Sichuan Province with high pulping yield, fibre length and width. Therefore, we analyzed the morphological characteristics, DNA markers, DNA barcoding and chloroplast genomes to identify the hybrid origin of B. changningensis and possible maternal parent. We have developed the transcriptomic data for B. changningensis and mined the SSR loci. The putative parental lines and hybrid were screened for 64 SSR makers and identified that SSR14, SSR28, SSR31 and SSR34 markers showed both alleles of the parental species in B. changningensis, proving heterozygosity. Sequencing nuclear gene GBSSI partial regions and phylogenetic analysis also confirm the hybrid nature of B. changningensis. Further, we have generated the complete chloroplast genome sequence (139505 bp) of B. changningensis. By analyzing the cp genomes of both parents and B. changningensis, we identified that B. rigida might be the female parent. In conclusion, our study identified that B. changningensis is a natural hybrid, providing evidence for bamboo's natural hybridization. This is the first report on confirming a natural bamboo hybrid and its parents through SSR and chloroplast genome sequence.
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Affiliation(s)
- Juan Zhuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Naresh Vasupalli
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Yong Wang
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Guoqiang Zhou
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Huibin Gao
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Benxiang Li
- Sichuan Changning Century Bamboo Garden, Yibin, Sichuan, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
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Meena RK, Negi N, Shankhwar R, Bhandari MS, Kant R, Pandey S, Kumar N, Sharma R, Ginwal HS. Ecological niche modelling and population genetic analysis of Indian temperate bamboo Drepanostachyum falcatum in the western Himalayas. J Plant Res 2023:10.1007/s10265-023-01465-5. [PMID: 37140755 DOI: 10.1007/s10265-023-01465-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/24/2023] [Indexed: 05/05/2023]
Abstract
The present study was conducted to understand the key ecological and biological questions of conservation importance in Drepanostachyum falcatum which aimed to map potential distribution in the western Himalayas and decipher spatial genetic structure. Eco-distribution maps were generated through ecological niche modelling using the Maximum Entropy (MaxEnt) algorithm implemented with 228 geocoordinates of species presence and 12 bioclimatic variables. Concomitantly, 26 natural populations in the western Himalayas were genetically analysed using ten genomic sequence-tagged microsatellite (STMS) markers. Model-derived distribution was adequately supported with appropriate statistical measures, such as area under the 'receiver operating characteristics (ROC)' curve (AUC; 0.917 ± 0.034)", Kappa (K; 0.418), normalized mutual information (NMI; 0.673) and true skill statistic (TSS; 0.715). Further, Jackknife test and response curves showed that the precipitation (pre- and post-monsoon) and temperature (average throughout the year and pre-monsoon) maximize the probabilistic distribution of D. falcatum. We recorded a wide and abundant (4096.86 km2) distribution of D. falcatum in the western Himalayas with maximum occurrence at 1500 to 2500 m asl. Furthermore, marker analysis exemplified high gene diversity with low genetic differentiation in D. falcatum. Relatively, the populations of Uttarakhand are more genetically diverse than Himachal Pradesh, whereas within the Uttarakhand, the Garhwal region captured a higher allelic diversity than Kumaon. Clustering and structure analysis indicated two major gene pools, where genetic admixing appeared to be controlled by long-distance gene flow, horizontal geographical distance, aspect, and precipitation. Both the species distribution map and population genetic structure derived herein may serve as valuable resources for conservation and management of Himalayan hill bamboos.
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Affiliation(s)
- Rajendra K Meena
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India.
| | - Nitika Negi
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Rajeev Shankhwar
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Maneesh S Bhandari
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Rama Kant
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand, 248 006, India
| | - Narinder Kumar
- Division of Genetics and Tree Improvement, Himalayan Forest Research Institute, Shimla, 171 013, Himachal Pradesh, India
| | - Rajesh Sharma
- Division of Genetics and Tree Improvement, Himalayan Forest Research Institute, Shimla, 171 013, Himachal Pradesh, India
- Division of Biodiversity and Climate Change, Indian Council of Forestry Research and Education, Dehradun, Uttarakhand, 248 006, India
| | - Harish S Ginwal
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
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Meena RK, Kashyap P, Shamoon A, Dhyani P, Sharma H, Bhandari MS, Barthwal S, Ginwal HS. Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus. Funct Integr Genomics 2023; 23:103. [PMID: 36973584 DOI: 10.1007/s10142-023-01033-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (FST = 0.119), severe inbreeding (FIS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.
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Affiliation(s)
- Rajendra K Meena
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India.
| | - Priyanka Kashyap
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Payal Dhyani
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Hansraj Sharma
- ICFRE - Bamboo & Rattan Centre, Aizawl, 796007, Mizoram, India
- ICFRE-Rain Forest Research Institute, Jorhat, 785001, Assam, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
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Meena RK, Negi N, Uniyal N, Bhandari MS, Sharma R, Ginwal HS. Genome skimming-based STMS marker discovery and its validation in temperate hill bamboo Drepanostachyum falcatum. J Genet 2021. [DOI: 10.1007/s12041-021-01273-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Meena RK, Negi N, Uniyal N, Shamoon A, Bhandari MS, Pandey S, Negi RK, Sharma R, Ginwal HS. Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos. 3 Biotech 2020; 10:534. [PMID: 33214981 DOI: 10.1007/s13205-020-02508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/24/2020] [Indexed: 10/23/2022] Open
Abstract
The study was conducted to evaluate the discriminatory potential of selected chloroplast-based DNA barcode regions for identifying and resolving phylogeny of the Indian bamboos. Among 11 chloroplast markers screened, only four, namely matK, rbcL, psbK-I and rps16-trnQ showed successful amplification in 88 genotypes of 30 Indian bamboo taxa under Bambuseae and Arundinarieae tribes. A total of 244 sequences were generated for the four chloroplast regions. Tree-based analysis demonstrated that none of the tested regions successfully discriminated the taxa under Bambuseae tribe. Importantly, our highly concerned Himalayan temperate bamboo species under Arundinarieae tribe, were successfully discriminated by matK locus with high bootstrap support (>60%). Sequence comparisons revealed that the discriminatory power demonstrated by matK region actually lies in the few unique fixed nucleotides (UFNs) despite the overall DNA polymorphism. Although, rps16-trnQ region was found to be the most polymorphic and revealed high genetic divergence among different taxonomic levels, it could not successfully discriminated the taxa with strong statistical support. In a taxonomically difficult plant group like bamboos, whose genome is relatively more complex and has a slow rate of molecular evolution, it is difficult to get a universal marker. Further, highly variable barcode regions utilized in other species may not be informative, and thus, the development of DNA barcodes for different taxonomic levels, such as lineages or tribes could be a viable approach.
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Oumer OA, Dagne K, Feyissa T, Tesfaye K, Durai J, Hyder MZ. Genetic diversity, population structure, and gene flow analysis of lowland bamboo [ Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia. Ecol Evol 2020; 10:11217-11236. [PMID: 33144960 PMCID: PMC7593185 DOI: 10.1002/ece3.6762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Bamboo, a member of subfamily Bambusoideae in the grass family (Poaceae), is one of the most important nontimber forest resources and a potential alternative to wood and wood products. Ethiopian lowland bamboo (Oxytenanthera abyssinica) is an economically and ecologically important species which accounts about 85% of total bamboo coverage in the country. This species is experiencing population decline due to a number of anthropogenic factors. As a foundation step, genetic diversity, population structure, and gene flow analysis of various O. abyssinica populations found in Ethiopia are studied using inter-simple sequence repeat markers. One hundred and thirty isolates of bamboo belonging to 13 geographically diverse populations were collected for DNA extraction and analysis. Heterozygosity, level of polymorphism, marker efficiency, Nei's gene diversity (H), and Shannon's information index (I) analysis, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA), and admixture analyses were performed based on the markers banding pattern. The results indicated high genetic variation (84.48%) at species level. The H, I, observed and effective number of alleles at the species level were 0.2702, 0.4061, 1.8448, and 1.4744, respectively, suggesting a relatively high level of genetic diversity. However, genetic differentiation at the population level was relatively low. Using grouped populations, AMOVA revealed that most (61.05%) of the diversity was distributed within the populations with F ST = 0.38949, F SC = 0.10486, and F CT = 0.31797. Cluster analysis grouped the populations into markedly distinct clusters, suggesting confined propagation in distinct geographic regions. STRUCTURE analyses showed K = 2 for all populations and K = 11 excluding Gambella population. Using these markers, we found strong evidence that the genetic diversity of the lowland bamboo is associated with distinct geographic regions and that isolates of Gambella Region, with their unique genetic origin, are quite different from other bamboos found in the country.
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Affiliation(s)
- Oumer Abdie Oumer
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa University (AAU)Addis AbabaEthiopia
- Department of BiologyAssosa University (ASU)AssosaEthiopia
| | - Kifle Dagne
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa University (AAU)Addis AbabaEthiopia
| | - Tileye Feyissa
- Institute of Biotechnology (IoB)Addis Ababa University (AAU)Addis AbabaEthiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology (IoB)Addis Ababa University (AAU)Addis AbabaEthiopia
- Ethiopian Biotechnology Institute (EBTi)Ministry of Science and Technology (MoST)Addis AbabaEthiopia
| | - Jayaraman Durai
- International Network for Bamboo and Rattan (INBAR) East Africa Regional Office (EARO)Addis AbabaEthiopia
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