1
|
Yang F, Guo Y, Li J, Lu C, Wei Y, Gao J, Xie Q, Jin J, Zhu G. Genome-wide association analysis identified molecular markers and candidate genes for flower traits in Chinese orchid ( Cymbidium sinense). HORTICULTURE RESEARCH 2023; 10:uhad206. [PMID: 38046850 PMCID: PMC10689080 DOI: 10.1093/hr/uhad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/07/2023] [Indexed: 12/05/2023]
Abstract
The orchid, the champagne of flowers, brings luxury, elegance, and novelty to nature. Cymbidium sinense is a symbol of gigantic floral variability on account of wavering shapes and sizes of floral organs, although marker-trait association (MTA) has not been studied for its floral traits. We evaluated markers associated with 14 floral traits of C. sinense through a genome-wide association study (GWAS) of 195 accessions. A total of 65 318 522 single-nucleotide polymorphisms (SNPs) and 3 906 176 insertion/deletion (InDel) events were identified through genotyping-by-sequencing. Among these, 4694 potential SNPs and 477 InDels were identified as MTAs at -log10 P > 5. The genes related to these SNPs and InDels were largely associated with floral regulators, hormonal pathways, cell division, and metabolism, playing essential roles in tailoring floral morphology. Moreover, 20 candidate SNPs/InDels linked to 11 genes were verified, 8 of which were situated on exons, one was located in the 5'-UTR and two were positioned in introns. Here, the multitepal trait-related gene RABBIT EARS (RBE) was found to be the most crucial gene. We analyzed the role of CsRBE in the regulation of flower-related genes via efficient transient overexpression in C. sinense protoplasts, and found that the floral homeotic genes CsAP3 and CsPI, as well as organ boundary regulators, including CsCUC and CsTCP genes, were regulated by CsRBE. Thus, we obtained key gene loci for important ornamental traits of orchids using genome-wide association analysis of populations with natural variation. The findings of this study can do a great deal to expedite orchid breeding programs for shape variability.
Collapse
Affiliation(s)
- Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yudi Guo
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qi Xie
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| |
Collapse
|
2
|
Ashfaq M, Rasheed A, Sajjad M, Ali M, Rasool B, Javed MA, Allah SU, Shaheen S, Anwar A, Ahmad MS, Mubashar U. Genome wide association mapping of yield and various desirable agronomic traits in Rice. Mol Biol Rep 2022; 49:11371-11383. [PMID: 35939183 DOI: 10.1007/s11033-022-07687-5] [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: 01/22/2022] [Revised: 04/28/2022] [Accepted: 06/08/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the staple foods worldwide. To feed the growing population, the improvement of rice cultivars is important. To make the improvement in the rice breeding program, it is imperative to understand the similarities and differences of the existing rice accessions to find out the genetic diversity. Previous studies demonstrated the existence of abundant elite genes in rice landraces. A genome-wide association study (GWAS) was performed for yield and yield related traits to find the genetic diversity. DESIGN Experimental study. METHODS AND RESULTS A total of 204 SSRs markers were used among 17 SSRs found to be located on each chromosome in the rice genome. The diversity was analyzed using different genetic characters i.e., the total number of alleles (TNA), polymorphic information content (PIC), and gene diversity by Power markers, and the values for each genetic character per marker ranged from 2 to 9, 0.332 to 0.887 and 0.423 to 0.900 respectively across the whole genome. The results of population structure identified four main groups. MTA identified several markers associated with many agronomically important traits. These results will be very useful for the selection of potential parents, recombinants, and MTAs that govern the improvements and developments of new high yielding rice varieties. CONCLUSIONS Analysis of diversity in germplasm is important for the improvement of cultivars in the breeding program. In the present study, the diversity was analyzed with different methods and found that enormous diversity was present in the studied rice germplasm. The structure analysis found the presence of 4 genetic groups in the existing germplasm. A total of 129 marker-trait associations (MTAs) have been found in this study.
Collapse
Affiliation(s)
- Muhammad Ashfaq
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
| | - Abdul Rasheed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, 45550, Islamabad, Pakistan
| | - Muhammad Ali
- Department of Entomology Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.,Department of Biosciences, COMSAT University, Islamabad, Pakistan
| | - Bilal Rasool
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sami Ul Allah
- Department of Plant Breeding and Genetics, Bahuddin Zakaria University Bahudar Campus Layyah, Bahudar, Pakistan
| | - Shabnum Shaheen
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Alia Anwar
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shafiq Ahmad
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Urooj Mubashar
- Government Training Education Academy, Gujranwala, Pakistan
| |
Collapse
|
3
|
Gebeyehu A, Hammenhag C, Tesfaye K, Vetukuri RR, Ortiz R, Geleta M. RNA-Seq Provides Novel Genomic Resources for Noug ( Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome. FRONTIERS IN PLANT SCIENCE 2022; 13:882136. [PMID: 35646044 PMCID: PMC9132581 DOI: 10.3389/fpls.2022.882136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/23/2022] [Indexed: 06/02/2023]
Abstract
Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
Collapse
Affiliation(s)
- Adane Gebeyehu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kassahun Tesfaye
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| |
Collapse
|
4
|
High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
Collapse
|
5
|
Zheng K, Cai Y, Chen W, Gao Y, Jin J, Wang H, Feng S, Lu J. Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo. FRONTIERS IN PLANT SCIENCE 2021; 12:669458. [PMID: 34054907 PMCID: PMC8160518 DOI: 10.3389/fpls.2021.669458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.
Collapse
Affiliation(s)
- Kaixin Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yuchen Cai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Weijie Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yadi Gao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiangjie Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| |
Collapse
|
6
|
Molecular Characterization and Positive Impact of Brassinosteroids and Chitosan on Solidago canadensis cv. Tara Characteristics. HORTICULTURAE 2020. [DOI: 10.3390/horticulturae6040100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although goldenrod (Solidago canadensis) is considered an invasive plant in many countries, it is a global cut-flower species. In addition, demand for goldenrod has increased significantly in recent years. Thus, the present study aimed to evaluate the response of Solidago canadensis cv. Tara to brassinosteroids (BRs) at levels of 0.10−3, 10−6, and 10−8 M, and chitosan at 0, 100, 150, and 200 mg/L as a foliar application to increase the quality and quantity of production, and its polyphenolic compounds. Moreover, antibacterial activity and genetic polymorphism for both untreated and the optimally treated goldenrod were investigated. The results showed that the highest mean of growth characteristics was found when plants were treated with BRs at 10−8 M, whereas the longer vase life was obtained using 200 mg/L chitosan. Furthermore, higher pigment values, N, P, K, and total phenolic content, antioxidant capacity, chlorogenic acid, and rutin content were detected on plants treated with 200 mg/L chitosan. In addition, foliar application with 200 mg/L chitosan caused higher antibacterial activity among the control and BRs. The optimal treatment of BR at 10−8 M (89%) showed a low genetic similarity, based on sequence-related amplified polymorphism (SRAP) analysis, comparable with the control and 200 mg/L chitosan. BR at 10−8 M and 200 mg/L chitosan showed a significant enhancement of growth parameters. As a result, it can be concluded that goldenrod, as a herb extract, shows significant promise as a natural preservative in pharmaceutical, food, and cosmetic products.
Collapse
|
7
|
Huang L, Yan X. Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades. PLoS One 2019; 14:e0209128. [PMID: 30849086 PMCID: PMC6407771 DOI: 10.1371/journal.pone.0209128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/20/2019] [Indexed: 11/18/2022] Open
Abstract
Pyropia yezoensis is an economically important seaweed but its molecular genetics is poorly understood. In the present study, we used a doubled haploid (DH) population that was established in our previous work to construct a genetic linkage map of P. yezoensis and analyze the quantitative trait loci (QTLs) of blades. The DH population was genotyped with fluorescent sequence-related amplified polymorphism (SRAP) markers. A chi-square test identified 301 loci with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed segregation (0.001 ≤ P < 0.01). The genetic map was constructed after a total of 92 loci were assembled into three linkage groups (LGs). The map spanned 557.36 cM covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM. Kolmogorov-Smirnov test (α = 5%) showed a uniform distribution of the markers along each LG. On the genetic map, 10 QTLs associated with five economic traits of blades were detected. One QTL was for length, one for width, two for fresh weight, two for specific growth rate of length and four for specific growth rate of fresh weight. These QTLs could explain 2.29–7.87% of the trait variations, indicating that their effects were all minor. The results may serve as a framework for future marker-assisted breeding in P. yezoensis.
Collapse
Affiliation(s)
- Linbin Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, P. R. China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, P. R. China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, P. R. China
| | - Xinghong Yan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, P. R. China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, P. R. China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, P. R. China
- * E-mail:
| |
Collapse
|
8
|
Zheng SG, Hu YD, Zhao RX, Yan S, Zhang XQ, Zhao TM, Chun Z. Genome-wide researches and applications on Dendrobium. PLANTA 2018; 248:769-784. [PMID: 30066218 DOI: 10.1007/s00425-018-2960-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/21/2018] [Indexed: 05/10/2023]
Abstract
This review summarizes current knowledge of chromosome characterization, genetic mapping, genomic sequencing, quality formation, floral transition, propagation, and identification in Dendrobium. The widely distributed Dendrobium has been studied for a long history, due to its important economic values in both medicine and ornamental. In recent years, some species of Dendrobium and other orchids had been reported on genomic sequences, using the next-generation sequencing technology. And the chloroplast genomes of many Dendrobium species were also revealed. The chromosomes of most Dendrobium species belong to mini-chromosomes, and showed 2n = 38. Only a few of genetic studies were reported in Dendrobium. After revealing of genomic sequences, the techniques of transcriptomics, proteomics and metabolomics could be employed on Dendrobium easily. Some other molecular biological techniques, such as gene cloning, gene editing, genetic transformation and molecular marker developing, had also been applied on the basic research of Dendrobium, successively. As medicinal plants, insights into the biosynthesis of some medicinal components were the most important. As ornamental plants, regulation of flower related characteristics was the most important. More, knowledge of growth and development, environmental interaction, evolutionary analysis, breeding of new cultivars, propagation, and identification of species and herbs were also required for commercial usage. All of these studies were improved using genomic sequences and related technologies. To answer some key scientific issues in Dendrobium, quality formation, flowering, self-incompatibility and seed germination would be the focus of future research. And genome related technologies and studies would be helpful.
Collapse
Affiliation(s)
- Shi-Gang Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Ya-Dong Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Ruo-Xi Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Shou Yan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100041, China
| | - Xue-Qin Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100041, China
| | - Ting-Mei Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100041, China
| | - Ze Chun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| |
Collapse
|
9
|
Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
Collapse
Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| |
Collapse
|
10
|
Moghaieb REA, Abdelhadi AA, El-Sadawy HA, Allam NAT, Baiome BA, Soliman MH. Molecular identification and genetic diversity among Photorhabdus and Xenorhabdus isolates. 3 Biotech 2017; 7:6. [PMID: 28391470 PMCID: PMC5385175 DOI: 10.1007/s13205-016-0594-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/23/2016] [Indexed: 11/30/2022] Open
Abstract
Five bacterial strains were isolated from the hemocoel of the greater wax moth larvae (Galleria mellonella) infected with the entomopathogenic nematodes: Heterorhabditis bacteriophora HP88, Heterorhabditis indicus RM1 and Heterorhabditis sp (S1), Steinernema abbasi and Steinernema sp. (S II). Strains were identified as Photorhabdus luminescens HRM1, P. luminescens HS1, P. luminescens HP88, Xenorhabdus indica and X. nematophila ATTC19061 using 16S rDNA sequence analysis. To reveal the genetic diversity among these strains, three molecular markers (RAPD, ISSR and SRAP) were employed. RAPD analysis showed 73.8 and 54.5 polymorphism percentages for the Photorhabdus and Xenorhabdus strains, respectively. ISSR analysis resulted in 70.1 and 75.2 polymorphism percentages among the Photorhabdus and Xenorhabdus strains, respectively. The SRAP analysis indicated that 75.6 and 61.2% genetic polymorphism was detected among Photorhabdus and Xenorhabdus strains, respectively. The cluster analysis grouped the three Photorhabdus strains together in one cluster and the two Xenorhabdus strains together in another cluster indicating the phylogenetic relationships among them. The genotype-specific markers detected from the three molecular markers (RAPD, ISSR and SRAP) were sufficient to distinguish between the different bacterial strains tested and can be used in the future IBM program that could be built on the use of these strains.
Collapse
Affiliation(s)
- Reda E A Moghaieb
- Department of Genetics and Genetic Engineering Research Center (GERC), Faculty of Agriculture Cairo University, Giza, 12613, Egypt
- College of Biotechnology, University of Modern Science, UAE, 232816, Dubai, United Arab Emirates
| | - Abdelhadi A Abdelhadi
- Department of Genetics and Genetic Engineering Research Center (GERC), Faculty of Agriculture Cairo University, Giza, 12613, Egypt
| | - Hanan A El-Sadawy
- Parasitology and Animal Diseases Department, National Research Centre, Elbuhoth St., Dokki, Giza, 12311, Egypt
| | - Nesreen A T Allam
- Parasitology and Animal Diseases Department, National Research Centre, Elbuhoth St., Dokki, Giza, 12311, Egypt
| | - Baiome Abdelmaguid Baiome
- Parasitology and Animal Diseases Department, National Research Centre, Elbuhoth St., Dokki, Giza, 12311, Egypt
| | - Mohamed H Soliman
- Department of Genetics and Genetic Engineering Research Center (GERC), Faculty of Agriculture Cairo University, Giza, 12613, Egypt.
| |
Collapse
|
11
|
Feng S, He R, Lu J, Jiang M, Shen X, Jiang Y, Wang Z, Wang H. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars. Front Genet 2016; 7:113. [PMID: 27379163 PMCID: PMC4908101 DOI: 10.3389/fgene.2016.00113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/01/2016] [Indexed: 01/14/2023] Open
Abstract
Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938–0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars.
Collapse
Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Renfeng He
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Xiaoxia Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Hangzhou, China
| | - Yan Jiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Hangzhou, China
| | - Zhi'an Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Hangzhou, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| |
Collapse
|
12
|
Teixeira da Silva JA, Jin X, Dobránszki J, Lu J, Wang H, Zotz G, Cardoso JC, Zeng S. Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding. Mol Phylogenet Evol 2016; 95:196-216. [DOI: 10.1016/j.ympev.2015.10.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
|
13
|
Chen JJ, Wang Y. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
14
|
Zhi Y, Li H, Zhang H, Gang G. Identification and utility of sequence related amplified polymorphism (SRAP) markers linked to bacterial wilt resistance genes in potato. ACTA ACUST UNITED AC 2014. [DOI: 10.5897/ajb2013.13021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
15
|
Feng SG, Lu JJ, Gao L, Liu JJ, Wang HZ. Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China. Biochem Genet 2013; 52:127-36. [PMID: 24213846 DOI: 10.1007/s10528-013-9633-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.
Collapse
Affiliation(s)
- Shang-Guo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310018, China,
| | | | | | | | | |
Collapse
|