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Li Y, Xu Y, Han R, Liu L, Pei X, Zhao X. Widely Targeted Metabolomic Profiling Combined with Transcriptome Analysis Provides New Insights into Lipid Biosynthesis in Seed Kernels of Pinus koraiensis. Int J Mol Sci 2023; 24:12887. [PMID: 37629067 PMCID: PMC10454069 DOI: 10.3390/ijms241612887] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/08/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Lipid-rich Pinus koraiensis seed kernels are highly regarded for their nutritional and health benefits. To ascertain the molecular mechanism of lipid synthesis, we conducted widely targeted metabolomic profiling together with a transcriptome analysis of the kernels in P. koraiensis cones at various developmental stages. The findings reveal that 148 different types of lipid metabolites, or 29.6% of total metabolites, are present in kernels. Among those metabolites, the concentrations of linoleic acid, palmitic acid, and α-linolenic acid were higher, and they steadily rose as the kernels developed. An additional 10 hub genes implicated in kernel lipid synthesis were discovered using weighted gene co-expression network analysis (WGCNA), gene interaction network analysis, oil body biosynthesis, and transcriptome analysis. This study used lipid metabolome and transcriptome analyses to investigate the mechanisms of key regulatory genes and lipid synthesis molecules during kernel development, which served as a solid foundation for future research on lipid metabolism and the creation of P. koraiensis kernel food.
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Affiliation(s)
- Yan Li
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (Y.X.); (R.H.); (L.L.)
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yujin Xu
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (Y.X.); (R.H.); (L.L.)
| | - Rui Han
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (Y.X.); (R.H.); (L.L.)
| | - Lin Liu
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (Y.X.); (R.H.); (L.L.)
| | - Xiaona Pei
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (Y.X.); (R.H.); (L.L.)
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Cui J, Qiu T, Li L, Cui S. De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments. BMC Genomics 2023; 24:180. [PMID: 37020272 PMCID: PMC10077656 DOI: 10.1186/s12864-023-09271-y] [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: 10/29/2022] [Accepted: 03/23/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies. RESULTS In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments. CONCLUSIONS Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.
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Affiliation(s)
- Jipeng Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Tianhang Qiu
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Li Li
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Suxia Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China.
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China.
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Liu C, Zhang M, Zhao X. Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae). BMC Plant Biol 2023; 23:87. [PMID: 36759771 PMCID: PMC9912670 DOI: 10.1186/s12870-023-04086-1] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. RESULTS Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. CONCLUSIONS Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.
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Affiliation(s)
- Chaoyu Liu
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Maomao Zhang
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Xueli Zhao
- College of Forestry, Southwest Forestry University, Kunming, 650224, China.
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650224, China.
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
- Correspondence: (X.L.); (R.Q.)
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Yan P, Xie Z, Feng K, Qiu X, Zhang L, Zhang H. Genetic diversity analysis and fingerprint construction of Korean pine ( Pinus koraiensis) clonal seed orchard. Front Plant Sci 2023; 13:1079571. [PMID: 36726668 PMCID: PMC9886227 DOI: 10.3389/fpls.2022.1079571] [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: 10/25/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Korean pine is a native tree species in Northeast China. In order to meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of Korean pine, we collected Korean pine clones from 7 populations in Northeast China, analyzed the genetic diversity and genetic structure by SSR molecular marker technology and clustered them to revealed the inter- and intrapopulation differentiation characteristics of each clone. The fingerprint profiles of 161 Korean pine clones were also constructed. 77 alleles were detected for 11 markers, and 18 genotypes were identified on average for each marker. The PIC of the different markers ranged from 0.155-0.855, and the combination of PI and PIsibs for the 11 markers was 3.1 × 10-8 and 1.14 × 10-3, respectively. MANOVA showed that genetic variation existed mainly within populations, accounting for 98% of the total variation. The level of genetic differentiation among populations was low, with an average Nm between populations of 11.036. Genetic diversity is lower in the Lushuihe population and higher in the Tieli population. The 161 Korean pine clones were divided into 4 or 7 populations, and the 7 populations were not clearly distinguished from each other, with only the Lushuihe population showing partial differentiation. There is no significant correlation between the genetic distance of Korean pine populations and the geographical distance of their superior tree sources. This result can provide recommendations for future Korean pine breeding programs. The combination of 11 markers could completely distinguish 161 clones and establish the fingerprint. Genetic diversity of Korean pine clones from the 7 populations was abundant, and the genetic distances of individuals and populations were evenly dispersed. The fingerprint map can be used for the identification of Korean pine clones.
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Affiliation(s)
- Pingyu Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zixiong Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kele Feng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Qiu
- Heilongjiang Academy of Forestry, Harbin, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Chen J, Cui H, Huang H, Wei S, Liu Y, Yu H, Ma Y, Li X, Ma X. EST-SSR Markers' Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of Eleusine indica in China. Curr Issues Mol Biol 2022; 45:141-150. [PMID: 36661497 PMCID: PMC9856800 DOI: 10.3390/cimb45010011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Goosegrass (Eleusine indica) is one of the worst agricultural weeds in China. Molecular markers were developed for genetic diversity and population structure analyses. In this study, we identified 8391 expressed sequence tag-simple sequence repeat (EST-SSR) markers from the de novo assembled unigenes of E. indica. Mononucleotides were the most abundant type of repeats (3591, 42.79%), followed by trinucleotides (3162, 37.68%). The most dominant mononucleotide and trinucleotide repeat motifs were A/T (3406, 40.59%) and AAT/ATT (103, 1.5%), respectively. Fourteen pairs of EST-SSR primers were verified and used to analyze the genetic diversity and population structure of 59 goosegrass populations. A total of 49 alleles were amplified, with the number of alleles (Na) ranging from two to eleven per locus, and the effective number of alleles (Ne) ranged from 1.07 to 4.53. The average polymorphic information content (PIC) was 0.36. Genetic structure analysis (K = 2) and principal coordinate analysis divided 59 E. indica populations into two groups in a manner similar to the unweighted pair-group method (Dice genetic similarity coefficient = 0.700). This study developed a set of EST-SSR markers in E. indica and successfully analyzed the diversity and population genetic structures of 59 E. indica populations in China.
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Affiliation(s)
- Jingchao Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hailan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongjuan Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shouhui Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yan Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haiyan Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yan Ma
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiangju Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (X.L.); (X.M.); Tel.: +86-010-62813309 (X.L.); +86-372-2562294 (X.M.)
| | - Xiaoyan Ma
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Correspondence: (X.L.); (X.M.); Tel.: +86-010-62813309 (X.L.); +86-372-2562294 (X.M.)
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Zhang R, Wang J, Xia R, Li D, Wang F. Antioxidant processes involving epicatechin decreased symptoms of pine wilt disease. Front Plant Sci 2022; 13:1015970. [PMID: 36570913 PMCID: PMC9780601 DOI: 10.3389/fpls.2022.1015970] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Since the pine wood nematode (PWN, Bursaphelenchus xylophilus) invasion of Northeast China, both symptomatic and asymptomatic PWN carriers have been found. Asymptomatic PWN carriers, which are more dangerous than symptomatic carriers, constitute a source of infection in the following spring. The simultaneous presence of symptomatic and asymptomatic PWN carriers indicates that Pinus koraiensis has different tolerance levels to PWN. In this study, validity of susceptibility testing discovered differential types of P. koraiensis including Latent Reservoirs, Low Susceptibles, High Susceptibles and Bell Ringers. Among those types, the Low Susceptibles and Latent Reservoirs were asymptomatic PWN carriers, and Latent Reservoirs were the most dangerous. Transcriptome and metabolomic data showed that 5 genes (3 ans and 2 anr gene) involved in the epicatechin (EC) synthesis pathway were significantly upregulated, which increased the content of EC antioxidants in Latent Reservoirs. Hydrogen peroxide (H2O2) staining and content determination showed that the hypersensitive response (HR) and H2O2, which functions as a signaling molecule in systemic acquired resistance, decreased in Latent Reservoirs. However, low contents of EC and high contents of H2O2 were found in the High Susceptibles of P. koraiensis. RT-PCR results showed that the expression of ans and anr was upregulated together only in Latent Reservoirs. These results show that the susceptibility of P. koraiensis to PWN differed among different individuals, although no resistant individuals were found. Latent Reservoirs, in which more PWNs resided without visible symptoms via prolonged incubation period, inhibited the symptoms caused by H2O2 because of increased contents of the EC antioxidants.
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Affiliation(s)
- Ruizhi Zhang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Jianan Wang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Rui Xia
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Danlei Li
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
| | - Feng Wang
- Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University, Harbin, China
- Liaoning Provincial Key Laboratory of Dangerous Forest Pest Management and Control, Liaoning forestry and grassland Bureau, Fushun, China
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Yang W, Bai Z, Wang F, Zou M, Wang X, Xie J, Zhang F. Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers. BMC Genomics 2022; 23:597. [PMID: 35974306 PMCID: PMC9382759 DOI: 10.1186/s12864-022-08832-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied. Results We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R2 = 0.3304, p < 0.05), and structure and principal coordinate analyses supported classification of populations into three clusters, which was consistent with the findings of cluster analysis. Conclusions As a rare medicinal plants, the protection of M. savatieri does not look optimistic, and accordingly, protective efforts should be beefed up on the natural wild populations. This study provided novel tools and insights for designing effective collection and conservation strategies for M. savatieri. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08832-x.
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Affiliation(s)
- Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhiyi Bai
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fuqiang Wang
- Yichun Academy of Sciences, Yichun, 336000, China
| | - Mingzhu Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xinru Wang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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Zhou Z, Zhang L, Shu J, Wang M, Li H, Shu H, Wang X, Sun Q, Zhang S. Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple. Plants (Basel) 2022; 11:1408. [PMID: 35684181 PMCID: PMC9182997 DOI: 10.3390/plants11111408] [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: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.
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Affiliation(s)
- Zhou Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Lei Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Mengyu Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Han Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Huairui Shu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Xiaoyun Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
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Liu H, Zhang Y, Wang Z, Su Y, Wang T. Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences. Front Genet 2021; 12:759557. [PMID: 34868238 PMCID: PMC8635753 DOI: 10.3389/fgene.2021.759557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
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Affiliation(s)
- Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuli Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Li Y, Li X, Zhao M, Pang Z, Wei J, Tigabu M, Chiang VL, Sederoff H, Sederoff R, Zhao X. An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use. Horticulturae 2021; 7:252. [DOI: 10.3390/horticulturae7080252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Flowering, the beginning of the reproductive growth, is a significant stage in the growth and development of plants. Conifers are economically and ecologically important, characterized by straight trunks and a good wood quality and, thus, conifer plantations are widely distributed around the world. In addition, conifer species have a good tolerance to biotic and abiotic stress, and a stronger survival ability. Seeds of some conifer species, such as Pinus koraiensis, are rich in vitamins, amino acids, mineral elements and other nutrients, which are used for food and medicine. Although conifers are the largest (giant sequoia) and oldest living plants (bristlecone pine), their growth cycle is relatively long, and the seed yield is unstable. In the present work, we reviewed selected literature and provide a comprehensive overview on the most influential factors and on the methods and techniques that can be adopted in order to improve flowering and seed production in conifers species. The review revealed that flowering and seed yields in conifers are affected by a variety of factors, such as pollen, temperature, light, water availability, nutrients, etc., and a number of management techniques, including topping off, pruning, fertilization, hormone treatment, supplementary pollination, etc. has been developed for improving cone yields. Furthermore, several flowering-related genes (FT, Flowering locus T and MADS-box, MCMI, AGAMOUS, DEFICIENCES and SRF) that play a crucial role in flowering in coniferous trees were identified. The results of this study can be useful for forest managers and for enhancing seed yields in conifer plantations for commercial use.
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Qiu J, Guo R, Li Y, Zhang Y, Jia K, Lei Y, Zan L, Li A. De Novo Transcriptome Assembly, Functional Annotation and SSR Marker Discovery of Qinling Takin ( Budorcas taxicolor bedfordi). Animals (Basel) 2021; 11:2366. [PMID: 34438823 PMCID: PMC8388659 DOI: 10.3390/ani11082366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
The takin (Budorcas taxicolor) is an endemic ruminant species belonging to the bovine family. The International Union for Conservation of Nature (IUCN) has listed it as an endangered and vulnerable species. However, little is known about its molecular characterization since it lacks a reference genome. This study used RNA sequencing followed by de novo assembly, annotation and simple sequence repeats (SSRs) prediction to assess the transcriptome of Qinling takin (Budorcas taxicolor bedfordi) muscles. In total, 21,648 unigenes with an N50 and mean length of 1388 bp and 817 bp, respectively, were successfully detected and annotated against the public databases (NR, GO, KEGG, and EggNOG). Furthermore, 6222 SSRs were identified using the MIcroSAtellite (MISA) identification tool software. Taken together, these findings will provide valuable information for genetic, genomic, and evolutionary studies on takin.
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Affiliation(s)
- Ju Qiu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Rui Guo
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Yidan Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Yuyao Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry, Xi'an 710402, China; (K.J.); (Y.L.)
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry, Xi'an 710402, China; (K.J.); (Y.L.)
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry, Xi'an 710402, China; (K.J.); (Y.L.)
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Q.); (R.G.); (Y.L.); (Y.Z.); (L.Z.)
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Li X, Zhao M, Xu Y, Li Y, Tigabu M, Zhao X. Genetic Diversity and Population Differentiation of Pinus koraiensis in China. Horticulturae 2021; 7:104. [DOI: 10.3390/horticulturae7050104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pinus koraiensis is a well-known precious tree species in East Asia with high economic, ornamental and ecological value. More than fifty percent of the P. koraiensis forests in the world are distributed in northeast China, a region with abundant germplasm resources. However, these natural P. koraiensis sources are in danger of genetic erosion caused by continuous climate changes, natural disturbances such as wildfire and frequent human activity. Little work has been conducted on the population genetic structure and genetic differentiation of P. koraiensis in China because of the lack of genetic information. In this study, 480 P. koraiensis individuals from 16 natural populations were sampled and genotyped. Fifteen polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to evaluate genetic diversity, population structure and differentiation in P. koraiensis. Analysis of molecular variance (AMOVA) of the EST-SSR marker data showed that 33% of the total genetic variation was among populations and 67% was within populations. A high level of genetic diversity was found across the P. koraiensis populations, and the highest levels of genetic diversity were found in HH, ZH, LS and TL populations. Moreover, pairwise Fst values revealed significant genetic differentiation among populations (mean Fst = 0.177). According to the results of the STRUCTURE and Neighbor-joining (NJ) tree analyses and principal component analysis (PCA), the studied geographical populations cluster into two genetic clusters: cluster 1 from Xiaoxinganling Mountains and cluster 2 from Changbaishan Mountains. These results are consistent with the geographical distributions of the populations. The results provide new genetic information for future genome-wide association studies (GWAS), marker-assisted selection (MAS) and genomic selection (GS) in natural P. koraiensis breeding programs and can aid the development of conservation and management strategies for this valuable conifer species.
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Xu R, Wang Z, Su Y, Wang T. Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing. Front Genet 2020; 11:574304. [PMID: 33193679 PMCID: PMC7593448 DOI: 10.3389/fgene.2020.574304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.
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Affiliation(s)
- Ruixiang Xu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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