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Wang Y, Cheng J, Jiang W, Chen S. Metabolomics study of flavonoids in Coreopsis tinctoria of different origins by UPLC-MS/MS. PeerJ 2022; 10:e14580. [PMID: 36570002 PMCID: PMC9774014 DOI: 10.7717/peerj.14580] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
To analyze the flavonoids in Coreopsis tinctoria and compare the differences in flavonoids among C. tinctoria of different origins, the chemical composition of C. tinctoria capitulum was analyzed by ultra-high-performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and the flavonoid metabolites were analyzed and identified based on their retention time, mass-to-charge ratio and fragment ions in the UPLC-QTOF-MS matrix. Capitulum samples of C. tinctoria were collected from three locations in the Xinjiang region at different altitudes. A total of 204 flavonoid compounds were identified, and 31 different flavonoid metabolites were then identified from flowers of C. tinctoria of different origins. Further analysis of these 31 significantly accumulated metabolites identified seven flavonoid metabolites, namely, homoplantaginin, kaempferol, quercetin, isorhamnetin, avicularin, quercetin 3-O-(6'-galloyl)-β-D-galactopyranoside and isorhamnetin 3-O-glucoside, with high accumulation only in sample collected from Tashkurgan Tajik (TX) and low expression in sample collected from Yutian County (YT) and Shaya County (SY). Moreover, 7,4'-dihydroxyflavone and 4,4'-dimethoxychalcone showed high accumulation only in SY, and afzelin was specifically highly accumulated in YT. In addition, the identified flavonoid metabolites were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and key pathways that might regulate the biosynthesis of these flavonoid compounds were analyzed. These findings provide key information for research on flavonoids and their biosynthesis in C. tinctoria and will provide a theoretical basis for studying the herbal quality and origin of C. tinctoria.
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Cai Y, Gao Y, Zhang Z, Liu H, Wang Y, Ma Y, Li Y, Feng S, Wang H. Development and Application of a Cultivar-Specific Sequence-Characterized Amplified Region (SCAR) Marker for the Detection of Chrysanthemum morifolium Ramat. 'Daboju'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050604. [PMID: 35270074 PMCID: PMC8912837 DOI: 10.3390/plants11050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 05/13/2023]
Abstract
Chrysanthemummorifolium Ramat. 'Daboju' is a C. morifolium cultivar with important ornamental and medicinal values, and is often used in the treatment of colds, blurred vision, dizziness, and itchy skin. As the morphological characteristics of C. morifolium 'Daboju' are very similar to those of other C. morifolium cultivars, they are often confused in practice. However, the medicinal value and practical use of C. morifolium depends on using the correct rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, morphologically similar C. × morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific DNA marker was developed with the aim of the rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, similar C. morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific 385-bp amplicon (named SCoT36-385), amplified only in C. morifolium 'Daboju' (and in all samples of this cultivar), was identified, cloned, and sequenced. Subsequently, a sequence-characterized amplified region (SCAR) marker (named DBJF/DBJR), generating a 360-bp amplicon, was developed from SCoT36-385 and tested for amplification in all 21 C. morifolium cultivars, ten C. morifolium 'Daboju' populations, and different simulated adulterations of 'Daboju' with other cultivars. The primers amplified the specific 360-bp-long DNA fragment in all the tested C. morifolium 'Daboju' samples but failed in the absence of 'Daboju'. The detection limit of the SCAR primer pair (DBJF/DBJR) was 100 pg of DNA extracted from C. morifolium 'Daboju'. Hence, this SCAR marker has a very high detection sensitivity, and can be used for accurate and rapid identification of C. morifolium 'Daboju'. It can play an important role in ensuring the quality of medicinal preparations and protecting C. morifolium 'Daboju' germplasm resources in breeding programs and in identifying lines generated from this cultivar.
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Affiliation(s)
- Yuchen Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Yadi Gao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhenhao Zhang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huijie Liu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yifan Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yuxin Ma
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yixin Li
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
| | - Huizhong Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
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Samarina LS, Malyarovskaya VI, Reim S, Yakushina LG, Koninskaya NG, Klemeshova KV, Shkhalakhova RM, Matskiv AO, Shurkina ES, Gabueva TY, Slepchenko NA, Ryndin AV. Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:1302. [PMID: 34199003 PMCID: PMC8309030 DOI: 10.3390/plants10071302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022]
Abstract
Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20-50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization.
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Affiliation(s)
- Lidia S. Samarina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Valentina I. Malyarovskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Stefanie Reim
- Institute for Breeding Research on Fruit Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, 01326 Dresden, Germany;
| | - Lyudmila G. Yakushina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Natalia G. Koninskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Kristina V. Klemeshova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Ruset M. Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Alexandra O. Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Ekaterina S. Shurkina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Tatiana Y. Gabueva
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Natalia A. Slepchenko
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Alexey V. Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
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Chen H, Guo A, Wang J, Gao J, Zhang S, Zheng J, Huang X, Xi J, Yi K. Evaluation of genetic diversity within asparagus germplasm based on morphological traits and ISSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:305-315. [PMID: 32153325 PMCID: PMC7036371 DOI: 10.1007/s12298-019-00738-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/01/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Asparagus officinalis L. is a dioecious perennial plant globally known for its fine flavor and high nutritional value. An evaluation of genetic diversity in 46 asparagus accessions was carried out based on morphological and inter-simple sequence repeat (ISSR) markers. The result show that the coefficient of variation for 20 morphological characteristics is between 12.45 and 62.22%. Factor analysis revealed that nine factors explained 83.37% of the total variance. At Euclidean distance of 135.7, 46 accessions were divided into two clusters. Genetic similarity coefficient (GSC) based on ISSR data ranged from 0.60 to 0.97, suggesting a relatively abundant genetic base. Furthermore, the 46 asparagus accessions could also be grouped into three major clusters at a GSC of 0.74. And there is no significant relation between the two marker systems using the Mantel test. Clustering based on morphological traits compared with that based on ISSR data was not consistent, however, some common groupings were observed between two dendrograms. Therefore the results elucidated asparagus germplasm genetic background and determined hybrid parents, which will facilitate optimal application of asparagus germplasm resources and provide additional data for genetic improvement.
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Affiliation(s)
- Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), No. 4 Xueyuan Road, Longhua District, Haikou City, 571101 Hainan Province People’s Republic of China
- Institute of Tropical Bioscience and Biotechnology/Hainan Academy of Tropical Agricultural Resource, CATAS/Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101 People’s Republic of China
| | - Anping Guo
- Institute of Tropical Bioscience and Biotechnology/Hainan Academy of Tropical Agricultural Resource, CATAS/Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101 People’s Republic of China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 571101 People’s Republic of China
| | - Jian Wang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 571101 People’s Republic of China
| | - Jianming Gao
- Institute of Tropical Bioscience and Biotechnology/Hainan Academy of Tropical Agricultural Resource, CATAS/Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101 People’s Republic of China
| | - Shiqing Zhang
- Institute of Tropical Bioscience and Biotechnology/Hainan Academy of Tropical Agricultural Resource, CATAS/Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101 People’s Republic of China
| | - Jinlong Zheng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), No. 4 Xueyuan Road, Longhua District, Haikou City, 571101 Hainan Province People’s Republic of China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), No. 4 Xueyuan Road, Longhua District, Haikou City, 571101 Hainan Province People’s Republic of China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), No. 4 Xueyuan Road, Longhua District, Haikou City, 571101 Hainan Province People’s Republic of China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), No. 4 Xueyuan Road, Longhua District, Haikou City, 571101 Hainan Province People’s Republic of China
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Widely Targeted Metabolomics Analysis Reveals the Effect of Flooding Stress on the Synthesis of Flavonoids in Chrysanthemum morifolium. Molecules 2019; 24:molecules24203695. [PMID: 31615126 PMCID: PMC6832227 DOI: 10.3390/molecules24203695] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
Chrysanthemum morifolium. cv "Hangju" is an important medicinal material with many functions in China. Flavonoids as the main secondary metabolites are a major class of medicinal components in "Hangju" and its composition and content can change significantly after flooding. This study mimicked the flooding stress of "Hangju" during flower bud differentiation and detected its metabolites in different growth stages. From widely targeted metabolomics data, 661 metabolites were detected, of which 46 differential metabolites exist simultaneously in the different growth stages of "Hangju". The top three types of the 46 differential metabolites were flavone C-glycosides, flavonol and flavone. Our results demonstrated that the accumulation of flavonoids in different growth stages of "Hangju" was different; however, quercetin, eriodictyol and most of the flavone C-glycosides were significantly enhanced in the two stages after flooding stress. The expression of key enzyme genes in the flavonoid synthesis pathway were determined using RT-qPCR, which verified the consistency of the expression levels of CHI, F3H, DFR and ANS with the content of the corresponding flavonoids. A regulatory network of flavonoid biosynthesis was established to illustrate that flooding stress can change the accumulation of flavonoids by affecting the expression of the corresponding key enzymes in the flavonoid synthesis pathway.
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Han H, Ma Z, Wang W, Xu M, Zhou S, Li L, Jiang H. Deglycosylation and absorption of marein, flavanomarein and taxifolin-7-O-β-D-glucopyranoside from capitula of Coreopsis tinctoria in rats and humans. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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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.
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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
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Strigolactone pathway genes and plant architecture: association analysis and QTL detection for horticultural traits in chrysanthemum. Mol Genet Genomics 2016; 291:957-69. [PMID: 26780913 DOI: 10.1007/s00438-015-1155-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022]
Abstract
Chrysanthemums are important ornamental plants with abundant phenotypic diversity. Especially in cut-flower breeding, shoot branching is important for the success of new varieties. To assess the genetic regulation of shoot branching and other horticultural important traits, we phenotyped and genotyped two types of chrysanthemum populations: a genotype collection of 86 varieties and a biparental F1-population (MK11/3) of 160 individuals. Using two different statistical approaches, a genome-wide association analysis and a single marker ANOVA, with AFLP marker data and candidate gene markers for shoot branching, we tried to identify markers correlated to the traits of interest. As expected for the outcrossing hexasomic chrysanthemums most of the phenotypic traits showed a continuous variation in both populations. With the candidate gene approach we identified 11 significantly associated marker alleles for all 4 strigolactone pathway genes BRC1, CCD7, CCD8 and MAX2 regulating shoot branching in the genotype collection. In the MK11/3 we detected seven markers for all candidate genes except MAX2 explaining a large proportion of the variation. Using anonymous AFLP markers in the GWA with the 86 genotypes and the single locus analysis with the F1-population we could detect 15 and 17 additional marker-trait associations, respectively. Our analyses indicate a polygenic inheritance of the shoot branching in the chrysanthemum, with a fundamental role of the strigolactone pathway genes BRC1, CCD7, CCD8 and MAX2 and we identified 50 associated markers to all traits under study. These markers could be used in the selection of the parental plants for breeding chrysanthemums to enrich them for positive alleles influencing plant architecture traits.
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Li P, Zhang F, Chen S, Jiang J, Wang H, Su J, Fang W, Guan Z, Chen F. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.). Mol Genet Genomics 2016; 291:1117-25. [PMID: 26780102 DOI: 10.1007/s00438-016-1166-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 01/06/2016] [Indexed: 02/04/2023]
Abstract
Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.
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Affiliation(s)
- Pirui Li
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
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Karimi A, Hadian J, Farzaneh M, Khadivi-Khub A. Evaluation of genetic variability, rust resistance and marker-detection in cultivated Artemisia dracunculus from Iran. Gene 2015; 554:224-32. [DOI: 10.1016/j.gene.2014.10.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 11/29/2022]
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11
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Liu F, Guo QS, Shi HZ, Lv F, Yu YB, Lv LL, Huang JT, Wang AM, Liang HX. Genetic diversity analysis of Perinereis aibuhitensis based on ISSR and SRAP markers of Chinese coast populations. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang Y, Dai S, Hong Y, Song X. Application of genomic SSR locus polymorphisms on the identification and classification of chrysanthemum cultivars in China. PLoS One 2014; 9:e104856. [PMID: 25148046 PMCID: PMC4141723 DOI: 10.1371/journal.pone.0104856] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/16/2014] [Indexed: 11/18/2022] Open
Abstract
The Chinese traditional chrysanthemum is a notable group of chrysanthemums (Chrysanthemum×morifolium Ramat.) in which the phenotypic characteristics richly vary. At present, there is a serious controversy regarding homonyms and synonyms within this group. Moreover, the current international chrysanthemum classification systems are not comprehensive enough to be used on Chinese traditional chrysanthemums. Thus, we first identified a broad collection of 480 Chinese traditional chrysanthemum cultivars using the unique DNA fingerprints and molecular identities that were established by 20 simple sequence repeat markers. Five loci, which distinguished all of the selected cultivars, were identified as the core loci to establish unique fingerprints and molecular identities with 19 denary digits for each cultivar. A cluster analysis based on Nei's genetic distance indicated that the selected cultivars were clustered according to their horticultural classification. Population structure analysis was subsequently performed with K values ranging from 2 to 14, and the most likely estimate for the population structure was ten subpopulations, which was nearly consistent with the clustering result. Principal component analysis was further performed to verify the classification results. On the basis of the Q-matrices of K = 10, a total of 19 traits were found to be associated with 42 markers. Taken together, these results can serve as starting points for the identification and classification of chrysanthemums based on the polymorphism of microsatellite markers, which is beneficial to promote the marker-assisted breeding and international communication of this marvelous crop.
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Affiliation(s)
- Yuan Zhang
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Silan Dai
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
- * E-mail:
| | - Yan Hong
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xuebin Song
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
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Flavonoid accumulation during florescence in three Chrysanthemum morifolium Ramat cv. ‘Hangju’ genotypes. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Zhao W, Zhao J, He L, Sun Y, Cai H. Molecular structure and the second introns variation of gene F3'H of two medicinal Chrysanthemum morifolium populations. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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15
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Liu F, Guo QS, Shi HZ, Wang T, Zhu ZB. Genetic diversity and phylogenetic relationships among and within populations of Whitmania pigra and Hirudo nipponica based on ISSR and SRAP markers. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Genetic diversity in Vicia amoena (Fabaceae) germplasm resource in China using SRAP and ISSR markers. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Wang T, Zhu Z, Guo Q, Mao P. Variation in major flavonoids glycosides and caffeoylquinic acids during florescence of three Chrysanthemum morifolium Ramat cv. ‘Hangju’ genotypes. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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18
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