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Devi A, Seth R, Masand M, Singh G, Holkar A, Sharma S, Singh A, Sharma RK. Spatial Genomic Resource Reveals Molecular Insights into Key Bioactive-Metabolite Biosynthesis in Endangered Angelica glauca Edgew. Int J Mol Sci 2022; 23:ijms231911064. [PMID: 36232367 PMCID: PMC9569870 DOI: 10.3390/ijms231911064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Angelica glauca Edgew, which is an endangered medicinal and aromatic herb, is a rich source of numerous industrially important bioactive metabolites, including terpenoids, phenolics, and phthalides. Nevertheless, genomic interventions for the sustainable utilization and restoration of its genetic resources are greatly offset due to the scarcity of the genomic resources and key regulators of the underlying specialized metabolism. To unravel the global atlas of the specialized metabolism, the first spatial transcriptome sequencing of the leaf, stem, and root generated 109 million high-quality paired-end reads, assembled de novo into 81,162 unigenes, which exhibit a 61.53% significant homology with the six public protein databases. The organ-specific clustering grouped 1136 differentially expressed unigenes into four subclusters differentially enriched in the leaf, stem, and root tissues. The prediction of the transcriptional-interactome network by integrating enriched gene ontology (GO) and the KEGG metabolic pathways identified the key regulatory unigenes that correspond to terpenoid, flavonoid, and carotenoid biosynthesis in the leaf tissue, followed by the stem and root tissues. Furthermore, the stem and root-specific significant enrichments of phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and caffeic acid 3-O-methyltransferase (COMT) indicate that phenylalanine mediated the ferulic acid biosynthesis in the stem and root. However, the root-specific expressions of NADPH-dependent alkenal/one oxidoreductase (NADPH-AOR), S-adenosyl-L-methionine-dependent methyltransferases (SDMs), polyketide cyclase (PKC), and CYP72A15 suggest the “root” as the primary site of phthalide biosynthesis. Additionally, the GC-MS and UPLC analyses corresponded to the organ-specific gene expressions, with higher contents of limonene and phthalide compounds in the roots, while there was a higher accumulation of ferulic acid in the stem, followed by in the root and leaf tissues. The first comprehensive genomic resource with an array of candidate genes of the key metabolic pathways can be potentially utilized for the targeted upscaling of aromatic and pharmaceutically important bioactive metabolites. This will also expedite genomic-assisted conservation and breeding strategies for the revival of the endangered A. glauca.
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Affiliation(s)
- Amna Devi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Mamta Masand
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashlesha Holkar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Shikha Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashok Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Environmental Technology, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Correspondence: or
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Hsiao C, Lin HH, Kang SR, Hung CY, Sun PY, Yu CC, Toh KL, Yu PJ, Ju YT. Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer. PLoS One 2022; 17:e0265311. [PMID: 35363791 PMCID: PMC8975116 DOI: 10.1371/journal.pone.0265311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.
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Affiliation(s)
- Chen Hsiao
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Hsin-Hung Lin
- Kaohsiung Animal Propagation Station, Pingdong, Taiwan
| | | | - Chien-Yi Hung
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Sun
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chieh-Cheng Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Kok-Lin Toh
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Ju Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ten Ju
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
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Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
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Zhang J, Yan J, Huang S, Pan G, Chang L, Li J, Zhang C, Tang H, Chen A, Peng D, Biswas A, Zhang C, Zhao L, Li D. Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers. Front Genet 2020; 11:958. [PMID: 33061939 PMCID: PMC7518120 DOI: 10.3389/fgene.2020.00958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei’s genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabis.
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Affiliation(s)
- Jiangjiang Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jiangtao Yan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siqi Huang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Gen Pan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Li Chang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Jianjun Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Chao Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Huijuan Tang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Anguo Chen
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ashok Biswas
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Cuiping Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Lining Zhao
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Defang Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
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Li X, Liu X, Wei J, Li Y, Tigabu M, Zhao X. Development and Transferability of EST-SSR Markers for Pinus koraiensis from Cold-Stressed Transcriptome through Illumina Sequencing. Genes (Basel) 2020; 11:genes11050500. [PMID: 32370137 PMCID: PMC7291311 DOI: 10.3390/genes11050500] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
Pinus koraiensis has significant economic and ecological value in Northeast China. However, due to the lack of suitable molecular markers, only a few available microsatellite markers were developed for further population genetics studies. In this study, for the first time we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers from the cold-stressed transcriptome of P. koraiensis using Illumina Sequencing. We identified a total of 7,235 EST-SSRs from 97,376 sequences, and we tested their transferability among seven related Pinus species. The results showed that trinucleotides were the most abundant type of repeat (1287, 18.74%) excluding mononucleotides, followed by dinucleotides (1284, 18.7%) and tetranucleotides (72, 1.05%). The most dominant dinucleotides and trinucleotide repeat motifs were AT/AT (535, 7.79%) and AAT/ATT (103, 1.5%). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.002 to 0.986 and 0.017 to 0.743, respectively, and the polymorphism information content (PIC) values and number of alleles (Na) varied from 0.029 to 0.794 and 2 to 23, respectively. A total of 8 natural P. koraiensis populations were divided into two main genetic clusters. Furthermore, nine of twenty polymorphic primer pairs were successfully amplified in seven Pinus species, and at least 80% of the successful P. koraiensis EST-SSR primers could be amplified in more than four species (16, 80%). Combined results for the development of EST-SSR markers in P. koraiensis and transferability among related species would contribute to improved studies on the genetic diversity and population structure in P. koraiensis and phylogenetic relationships among Pinus species. They would also provide a significant source for quantitative trait locus analysis.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Xiaoting Liu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Jiatong Wei
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
| | - Mulualem Tigabu
- Southern Swedish Forest Research Center, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden;
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (X.L.); (J.W.); (Y.L.)
- Correspondence: ; Tel.: +86-451-8219-2225
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Liu M, Hu X, Wang X, Zhang J, Peng X, Hu Z, Liu Y. Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data. FRONTIERS IN PLANT SCIENCE 2020; 11:600249. [PMID: 33424898 PMCID: PMC7785966 DOI: 10.3389/fpls.2020.600249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/02/2020] [Indexed: 05/16/2023]
Abstract
Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon's information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.
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Affiliation(s)
- Man Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xin Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xu Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xubing Peng
- Hubei Kangnong Seed Co., Ltd., Yichang, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- *Correspondence: Zhigang Hu,
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Yifei Liu,
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Fu L, Ding Z, Kumpeangkeaw A, Tan D, Han B, Sun X, Zhang J. De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:133-142. [PMID: 32158126 PMCID: PMC7036385 DOI: 10.1007/s12298-019-00726-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/11/2019] [Accepted: 10/18/2019] [Indexed: 05/12/2023]
Abstract
Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, ~ 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) > 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri- (14.9%), tetra- (4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM ≤ 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.
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Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Anuwat Kumpeangkeaw
- International College, Huazhong Agricultural University, Wuhan, 430070 China
- Department of Agriculture, Song Khla Agricultural Research and Development Center, Ministry of Agriculture and Cooperatives, Had Yai, Song Khla 90110 Thailand
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
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