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Ding Y, Wang MY, Yang DH, Hao DC, Li WS, Ling P, Xie SQ. Transcriptome analysis of flower colour reveals the correlation between SNP and differential expression genes in Phalaenopsis. Genes Genomics 2023; 45:1611-1621. [PMID: 37414912 DOI: 10.1007/s13258-023-01422-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Phalaenopsis is an important ornamental plant that has great economic value in the world flower market as one of the most popular flower resources. OBJECTIVE To investigate the flower colour formation of Phalaenopsis at the transcription level, the genes involved in flower color formation were identified from RNA-seq in this study. METHODS In this study, white and purple petals of Phalaenopsis were collected and analyzed to obtained (1) differential expression genes (DEGs) between white and purple flower color and (2) the association between single nucleotide polymorphisms (SNP) mutations and DEGs at the transcriptome level. RESULTS The results indicated that a total of 1,175 DEGs were identified, and 718 and 457 of them were up- and down-regulated genes, respectively. Gene Ontology and pathway enrichment showed that the biosynthesis of the secondary metabolites pathway was key to color formation, and the expression of 12 crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase, and E1.11.17) that are involved in the regulation of flower color in Phalaenopsis. CONCLUSION This study reported the association between the SNP mutations and DEGs for color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.
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Affiliation(s)
- Yu Ding
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China
| | - Ma-Yin Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China
| | - Ding-Hai Yang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China
| | - Dai-Cheng Hao
- Hainan Boda Orchid Technology Co. Ltd, Haikou, 570311, China
| | - Wei-Shi Li
- Hainan Boda Orchid Technology Co. Ltd, Haikou, 570311, China
| | - Peng Ling
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China.
| | - Shang-Qian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China.
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Song A, Su J, Wang H, Zhang Z, Zhang X, Van de Peer Y, Chen F, Fang W, Guan Z, Zhang F, Wang Z, Wang L, Ding B, Zhao S, Ding L, Liu Y, Zhou L, He J, Jia D, Zhang J, Chen C, Yu Z, Sun D, Jiang J, Chen S, Chen F. Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum. Nat Commun 2023; 14:2021. [PMID: 37037808 PMCID: PMC10085997 DOI: 10.1038/s41467-023-37730-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/29/2023] [Indexed: 04/12/2023] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.
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Affiliation(s)
- Aiping Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Yves Van de Peer
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Fei Chen
- College of tropical crops, Sanya Nanfan Research Institute, Hainan University & Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhenxing Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Baoqing Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shuang Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Lijie Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jun He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Diwen Jia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiali Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Chuwen Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongyu Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Daojin Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Sumei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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3
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Liu Y, Anderson NO. Phenotypic differences among and within extant populations of Chrysanthemum arcticum L. and C. a. subsp. arcticum. BMC PLANT BIOLOGY 2022; 22:517. [PMID: 36335304 PMCID: PMC9636833 DOI: 10.1186/s12870-022-03902-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Chrysanthemum arcticum, arctic daisy and its two subspecies (Chrysanthemum arcticum subsp. arcticum, Chrysanthemum arcticum subsp. polaré) are the only chrysanthemum species native to North America. A study on species' variation in morphological and diagnostic traits is important to link morphological traits with previously described single nucleotide polymorphism (SNP) markers, particularly when the genomes are sequenced. The purpose of this study was to establish phenotypic differences and soil conditions among wild C. arcticum and C. a. subsp. arcticum populations, when grown in a uniform environment for two years, for potential linkages with our SNP library. Sixteen quantitative morphological traits and five qualitative morphological traits were investigated for 255 individuals from nine C. arcticum populations and 326 individuals from 21 C. a. subsp. arcticum populations. RESULTS In long-day controlled environment, C. arcticum flowering rate was 0% in Year 1, increased to 2.7% in Year 2, while C. a. subsp. arcticum flowering rate was 98.5% in Year 2. Two distinct clusters, distributed by taxonomic classification, were detected by Principal component analysis (PCoA) for 551 individuals from C. arcticum and C. a. subsp. arcticum. Pearson's correlation coefficient analysis indicated a positive and significant correlation between plant height, flower fresh and dry weights. Flower fresh weights were correlated with Δflower weight, while inflorescence length had showed a negative correlation with leaf number. Soil samples had high Na levels along with heavy metals. Thus, the species are salt-tolerant. CONCLUSION A high level of salt tolerance (Na) is tolerated by these maritime species which is a unique trait in Chrysanthemum. A new diagnostic trait of inflorescence length was discovered to distinguish among C. arcticum and C. a. subsp. arcticum. Significant flowering differences occurred among the species C. arcticum and C. a. subsp. arcticum under same photoperiodic environment, including flowering rates and visible bud date. This study on the species' variation in morphological and diagnostic traits is of importance to link morphological traits with single nucleotide polymorphism (SNP) markers.
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Affiliation(s)
- Yunjia Liu
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55018, USA
| | - Neil O Anderson
- Department of Plant Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Life Sciences Bldg., University Park, PA, 16802, USA.
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4
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Mekapogu M, Kwon OK, Song HY, Jung JA. Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances. Int J Mol Sci 2022; 23:ijms232012284. [PMID: 36293140 PMCID: PMC9603847 DOI: 10.3390/ijms232012284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
Incessant development and introduction of novel cultivars with improved floral attributes are vital in the dynamic ornamental industry. Chrysanthemum (Chrysanthemum morifolium) is a highly favored ornamental plant, ranking second globally in the cut flower trade, after rose. Development of new chrysanthemum cultivars with improved and innovative modifications in ornamental attributes, including floral color, shape, plant architecture, flowering time, enhanced shelf life, and biotic and abiotic stress tolerance, is a major goal in chrysanthemum breeding. Despite being an economically important ornamental plant, the application of conventional and molecular breeding approaches to various key traits of chrysanthemum is hindered owing to its genomic complexity, heterozygosity, and limited gene pool availability. Although classical breeding of chrysanthemum has resulted in the development of several hundreds of cultivars with various morphological variations, the genetic and transcriptional control of various important ornamental traits remains unclear. The coveted blue colored flowers of chrysanthemums cannot be achieved through conventional breeding and mutation breeding due to technical limitations. However, blue-hued flower has been developed by genetic engineering, and transgenic molecular breeding has been successfully employed, leading to substantial progress in improving various traits. The recent availability of whole-genome sequences of chrysanthemum offers a platform to extensively employ MAS to identify a large number of markers for QTL mapping, and GWAS to dissect the genetic control of complex traits. The combination of NGS, multi-omic platforms, and genome editing technologies has provided a tremendous scope to decipher the molecular and regulatory mechanisms. However, the application and integration of these technologies remain inadequate for chrysanthemum. This review, therefore, details the significance of floral attributes, describes the efforts of recent advancements, and highlights the possibilities for future application towards the improvement of crucial ornamental traits in the globally popular chrysanthemum plant.
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5
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Carrasco B, Arévalo B, Perez-Diaz R, Rodríguez-Alvarez Y, Gebauer M, Maldonado JE, García-Gonzáles R, Chong-Pérez B, Pico-Mendoza J, Meisel LA, Ming R, Silva H. Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools. PLANTS 2022; 11:plants11162151. [PMID: 36015454 PMCID: PMC9414553 DOI: 10.3390/plants11162151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
Abstract
A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.
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Affiliation(s)
- Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Talca 3480094, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados (CEAP), Talca 3480094, Chile
| | | | - Yohaily Rodríguez-Alvarez
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Marlene Gebauer
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Jonathan E Maldonado
- Laboratorio de Genómica Funcional y Bioinformática, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile
- Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9160000, Chile
| | | | - Borys Chong-Pérez
- Sociedad de Investigación y Servicios, BioTECNOS Ltda., San Javier 3660000, Chile
| | - José Pico-Mendoza
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador
| | - Lee A Meisel
- Laboratorio de Genética Molecular Vegetal, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830490, Chile
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Herman Silva
- Laboratorio de Genómica Funcional y Bioinformática, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile
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Bhat JA, Adeboye KA, Ganie SA, Barmukh R, Hu D, Varshney RK, Yu D. Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.). Front Genet 2022; 13:953833. [PMID: 36419833 PMCID: PMC9677453 DOI: 10.3389/fgene.2022.953833] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production and productivity. Here, 211 soybean genotypes were evaluated across six environments for four yield-related traits, including seed yield per plant (SYP), number of pods per plant number of seeds per plant and 100-seed weight (HSW). Genome-wide association study (GWAS) and genomic prediction (GP) analyses were performed using 12,617 single nucleotide polymorphism markers from NJAU 355K SoySNP Array. A total of 57 SNPs were significantly associated with four traits across six environments and a combined environment using five Genome-wide association study models. Out of these, six significant SNPs were consistently identified in more than three environments using multiple GWAS models. The genomic regions (±670 kb) flanking these six consistent SNPs were considered stable QTL regions. Gene annotation and in silico expression analysis revealed 15 putative genes underlying the stable QTLs that might regulate soybean yield. Haplotype analysis using six significant SNPs revealed various allelic combinations regulating diverse phenotypes for the studied traits. Furthermore, the GP analysis revealed that accurate breeding values for the studied soybean traits is attainable at an earlier generation. Our study paved the way for increasing soybean yield performance within a short breeding cycle.
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Affiliation(s)
- Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- International Genome Center, Jiangsu University, Zhenjiang, China
- *Correspondence: Javaid Akhter Bhat, ; Rajeev K. Varshney, ; Deyue Yu,
| | | | - Showkat Ahmad Ganie
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Surrey, United Kingdom
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dezhou Hu
- Soybean Research Institution, National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch’s Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA, Australia
- *Correspondence: Javaid Akhter Bhat, ; Rajeev K. Varshney, ; Deyue Yu,
| | - Deyue Yu
- Soybean Research Institution, National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Javaid Akhter Bhat, ; Rajeev K. Varshney, ; Deyue Yu,
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7
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Hao DC, Song Y, Xiao P, Zhong Y, Wu P, Xu L. The genus Chrysanthemum: Phylogeny, biodiversity, phytometabolites, and chemodiversity. FRONTIERS IN PLANT SCIENCE 2022; 13:973197. [PMID: 36035721 PMCID: PMC9403765 DOI: 10.3389/fpls.2022.973197] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/18/2022] [Indexed: 05/31/2023]
Abstract
The ecologically and economically important genus Chrysanthemum contains around 40 species and many hybrids and cultivars. The dried capitulum of Chrysanthemum morifolium (CM) Ramat. Tzvel, i.e., Flos Chrysanthemi, is frequently used in traditional Chinese medicine (TCM) and folk medicine for at least 2,200 years. It has also been a popular tea beverage for about 2,000 years since Han Dynasty in China. However, the origin of different cultivars of CM and the phylogenetic relationship between Chrysanthemum and related Asteraceae genera are still elusive, and there is a lack of comprehensive review about the association between biodiversity and chemodiversity of Chrysanthemum. This article aims to provide a synthetic summary of the phylogeny, biodiversity, phytometabolites and chemodiversity of Chrysanthemum and related taxonomic groups, focusing on CM and its wild relatives. Based on extensive literature review and in light of the medicinal value of chrysanthemum, we give some suggestions for its relationship with some genera/species and future applications. Mining chemodiversity from biodiversity of Chrysanthemum containing subtribe Artemisiinae, as well as mining therapeutic efficacy and other utilities from chemodiversity/biodiversity, is closely related with sustainable conservation and utilization of Artemisiinae resources. There were eight main cultivars of Flos Chrysanthemi, i.e., Hangju, Boju, Gongju, Chuju, Huaiju, Jiju, Chuanju and Qiju, which differ in geographical origins and processing methods. Different CM cultivars originated from various hybridizations between multiple wild species. They mainly contained volatile oils, triterpenes, flavonoids, phenolic acids, polysaccharides, amino acids and other phytometabolites, which have the activities of antimicrobial, anti-viral, antioxidant, anti-aging, anticancer, anti-inflammatory, and closely related taxonomic groups could also be useful as food, medicine and tea. Despite some progresses, the genetic/chemical relationships among varieties, species and relevant genera have yet to be clarified; therefore, the roles of pharmacophylogeny and omics technology are highlighted.
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Affiliation(s)
- Da-Cheng Hao
- School of Environment and Chemical Engineering, Biotechnology Institute, Dalian Jiaotong University, Dalian, China
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Yanjun Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
| | - Yi Zhong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peiling Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lijia Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
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8
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Genetic Diversity and Genome-Wide Association Study of Architectural Traits of Spray Cut Chrysanthemum Varieties. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The architecture of spray cut chrysanthemum is crucial for the quality and quantity of cut flower production. However, the mechanism underlying plant architecture still needs to be clarified. In this study, we measured nine architecture-related traits of 195 spray cut chrysanthemum varieties during a two-year period. The results showed that the number of upper primary branches, number of lateral flower buds and primary branch length widely varied. Additionally, plant height had a significant positive correlation with number of leaf nodes and total number of lateral buds. Number of upper primary branches had a significant negative correlation with primary branch diameter, primary branch angle and primary branch length. Plant height, total number of lateral buds, number of upper primary branches, stem diameter, primary branch diameter and primary branch length were vulnerable to environmental impacts. All varieties could be divided into five categories according to cluster analysis, and the typical plant architecture of the varieties was summarized. Finally, a genome-wide association study (GWAS) was performed to find potential functional genes.
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9
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Ji Q, Zhu H, Huang X, Zhou K, Liu Z, Sun Y, Wang Z, Ke W. Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers. PLoS One 2021; 16:e0249825. [PMID: 34228738 PMCID: PMC8259969 DOI: 10.1371/journal.pone.0249825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/25/2021] [Indexed: 12/02/2022] Open
Abstract
The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.
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Affiliation(s)
- Qun Ji
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Honglian Zhu
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xinfang Huang
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Kai Zhou
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhengwei Liu
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yalin Sun
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhixin Wang
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weidong Ke
- Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
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10
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Mekapogu M, Vasamsetti BMK, Kwon OK, Ahn MS, Lim SH, Jung JA. Anthocyanins in Floral Colors: Biosynthesis and Regulation in Chrysanthemum Flowers. Int J Mol Sci 2020; 21:ijms21186537. [PMID: 32906764 PMCID: PMC7554973 DOI: 10.3390/ijms21186537] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium) is an economically important ornamental crop across the globe. As floral color is the major factor determining customer selection, manipulation of floral color has been a major objective for breeders. Anthocyanins are one of the main pigments contributing to a broad variety of colors in the ray florets of chrysanthemum. Manipulating petal pigments has resulted in the development of a vast range of floral colors. Although the candidate genes involved in anthocyanin biosynthesis have been well studied, the genetic and transcriptional control of floral color remains unclear. Despite advances in multi-omics technology, these methods remain in their infancy in chrysanthemum, owing to its large complex genome and hexaploidy. Hence, there is a need to further elucidate and better understand the genetic and molecular regulatory mechanisms in chrysanthemum, which can provide a basis for future advances in breeding for novel and diverse floral colors in this commercially beneficial crop. Therefore, this review describes the significance of anthocyanins in chrysanthemum flowers, and the mechanism of anthocyanin biosynthesis under genetic and environmental factors, providing insight into the development of novel colored ray florets. Genetic and molecular regulatory mechanisms that control anthocyanin biosynthesis and the various breeding efforts to modify floral color in chrysanthemum are detailed.
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Affiliation(s)
- Manjulatha Mekapogu
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
| | - Bala Murali Krishna Vasamsetti
- Chemical Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea;
| | - Oh-Keun Kwon
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
| | - Myung-Suk Ahn
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyoung National University, Anseong 17579, Korea;
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
- Correspondence:
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11
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Li T, Qu J, Tian X, Lao Y, Wei N, Wang Y, Hao Y, Zhang X, Xue J, Xu S. Identification of Ear Morphology Genes in Maize ( Zea mays L.) Using Selective Sweeps and Association Mapping. Front Genet 2020; 11:747. [PMID: 32793283 PMCID: PMC7384441 DOI: 10.3389/fgene.2020.00747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/23/2020] [Indexed: 12/19/2022] Open
Abstract
The performance of maize hybrids largely depend on two parental inbred lines. Improving inbred lines using artificial selection is a key task in breeding programs. However, it is important to elucidate the effects of this selection on inbred lines. Altogether, 208 inbred lines from two maize heterosis groups, named Shaan A and Shaan B, were sequenced by the genotype-by-sequencing to detect genomic changes under selection pressures. In addition, we completed genome-wide association analysis in 121 inbred lines to identify candidate genes for ear morphology related traits. In a genome-wide selection scan, the inbred lines from Shaan A and Shaan B groups showed obvious population divergences and different selective signals distributed in 337 regions harboring 772 genes. Meanwhile, functional enrichment analysis showed those selected genes are mainly involved in regulating cell development. Interestingly, some ear morphology related traits showed significant differentiation between the inbred lines from the two heterosis groups. The genome-wide association analysis of ear morphology related traits showed that four associated genes were co-localized in the selected regions with high linkage disequilibrium. Our spatiotemporal pattern and gene interaction network results for the four genes further contribute to our understanding of the mechanisms behind ear and fruit length development. This study provides a novel insight into digging a candidate gene for complex traits using breeding materials. Our findings in relation to ear morphology will help accelerate future maize improvement.
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Affiliation(s)
- Ting Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Jianzhou Qu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Xiaokang Tian
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Yonghui Lao
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Ningning Wei
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Yahui Wang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Yinchuan Hao
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Xinghua Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.,The Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, China
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12
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Su J, Jiang J, Zhang F, Liu Y, Ding L, Chen S, Chen F. Current achievements and future prospects in the genetic breeding of chrysanthemum: a review. HORTICULTURE RESEARCH 2019; 6:109. [PMID: 31666962 PMCID: PMC6804895 DOI: 10.1038/s41438-019-0193-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/11/2019] [Accepted: 08/14/2019] [Indexed: 05/05/2023]
Abstract
Chrysanthemum (Chrysanthemum morifolium Ramat.) is a leading flower with applied value worldwide. Developing new chrysanthemum cultivars with novel characteristics such as new flower colors and shapes, plant architectures, flowering times, postharvest quality, and biotic and abiotic stress tolerance in a time- and cost-efficient manner is the ultimate goal for breeders. Various breeding strategies have been employed to improve the aforementioned traits, ranging from conventional techniques, including crossbreeding and mutation breeding, to a series of molecular breeding methods, including transgenic technology, genome editing, and marker-assisted selection (MAS). In addition, the recent extensive advances in high-throughput technologies, especially genomics, transcriptomics, proteomics, metabolomics, and microbiomics, which are collectively referred to as omics platforms, have led to the collection of substantial amounts of data. Integration of these omics data with phenotypic information will enable the identification of genes/pathways responsible for important traits. Several attempts have been made to use emerging molecular and omics methods with the aim of accelerating the breeding of chrysanthemum. However, applying the findings of such studies to practical chrysanthemum breeding remains a considerable challenge, primarily due to the high heterozygosity and polyploidy of the species. This review summarizes the recent achievements in conventional and modern molecular breeding methods and emerging omics technologies and discusses their future applications for improving the agronomic and horticultural characteristics of chrysanthemum.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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13
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Chong X, Su J, Wang F, Wang H, Song A, Guan Z, Fang W, Jiang J, Chen S, Chen F, Zhang F. Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum. PLANT MOLECULAR BIOLOGY 2019; 99:407-420. [PMID: 30701353 DOI: 10.1007/s11103-019-00826-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 01/19/2019] [Indexed: 05/21/2023]
Abstract
81 SNPs were identified for three inflorescence-related traits, in which 15 were highly favorable. Two dCAPS markers were developed for future MAS breeding, and six candidate genes were predicted. Chrysanthemum is a leading ornamental species worldwide and demonstrates a wealth of morphological variation. Knowledge about the genetic basis of its phenotypic variation for key horticultural traits can contribute to its effective management and genetic improvement. In this study, we conducted a genome-wide association study (GWAS) based on two years of phenotype data and a set of 92,617 single nucleotide polymorphisms (SNPs) using a panel of 107 diverse cut chrysanthemums to dissect the genetic control of three inflorescence-related traits. A total of 81 SNPs were significantly associated with the three inflorescence-related traits (capitulum diameter, number of ray florets and flowering time) in at least one environment, with an individual allele explaining 22.72-38.67% of the phenotypic variation. Fifteen highly favorable alleles were identified for the three target traits by computing the phenotypic effect values for the stable associations detected in 2 year-long trials at each locus. Dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between highly favorable allele numbers and corresponding phenotypic performance were observed. Two highly favorable SNP alleles correlating to flowering time and capitulum diameter were converted to derived cleaved amplified polymorphic sequence (dCAPS) markers to facilitate future breeding. Finally, six putative candidate genes were identified that contribute to flowering time and capitulum diameter. These results serve as a foundation for analyzing the genetic mechanisms underlying important horticultural traits and provide valuable insights into molecular marker-assisted selection (MAS) in chrysanthemum breeding programs.
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Affiliation(s)
- Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Fan Wang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China.
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14
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Su J, Zhang F, Chong X, Song A, Guan Z, Fang W, Chen F. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. HORTICULTURE RESEARCH 2019; 6:21. [PMID: 30729011 PMCID: PMC6355785 DOI: 10.1038/s41438-018-0101-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/06/2018] [Accepted: 10/09/2018] [Indexed: 05/05/2023]
Abstract
Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r 2 = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.
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Affiliation(s)
- Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
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15
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Su J, Zhang F, Chong X, Song A, Guan Z, Fang W, Chen F. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. HORTICULTURE RESEARCH 2019. [PMID: 30729011 DOI: 10.1038/s41438-018-0101-107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r 2 = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.
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Affiliation(s)
- Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
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16
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Su J, Yang X, Zhang F, Wu S, Xiong S, Shi L, Guan Z, Fang W, Chen F. Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum. PLANTA 2018; 247:899-924. [PMID: 29273861 DOI: 10.1007/s00425-017-2833-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding. Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F1 lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW). The h B2 for the WAT traits ranged from 0.49 to 0.64, and transgressive segregation was observed in both directions. A total of 37 unconditional consensus QTLs with 5.81-18.21% phenotypic variation explanation (PVE) and 51 conditional consensus QTLs with 5.90-24.56% PVE were detected. Interestingly, three unconditional consensus QTLs were consistently identified across different stages, whereas no conditional consensus QTLs were consistently expressed. In addition, considerable epistatic QTLs, all with PVE values ranging from 0.01 to 8.87%, were detected by a joint analysis of WAT phenotypes. These results illustrated that the QTLs (genes) controlling WAT were environmentally dependent and selectively expressed at different times and indicated that both additive and epistatic effects underlie the inheritance of WAT in chrysanthemum. The findings of the current study provide insights into the complex genetic architecture of WAT, and the identification of favourable alleles represents an important step towards the application of molecular marker-assisted selection (MAS) and QTL pyramiding in chrysanthemum WAT breeding programmes.
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Affiliation(s)
- Jiangshuo Su
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xincheng Yang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shaofang Wu
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Siyi Xiong
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liming Shi
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiyong Guan
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Weimin Fang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China.
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Wang F, Zhong X, Wang H, Song A, Chen F, Fang W, Jiang J, Teng N. Investigation of Differences in Fertility among Progenies from Self-Pollinated Chrysanthemum. Int J Mol Sci 2018. [PMID: 29533976 PMCID: PMC5877693 DOI: 10.3390/ijms19030832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Most chrysanthemum cultivars are self-incompatible, so it is very difficult to create pure lines that are important in chrysanthemum breeding and theoretical studies. In our previous study, we obtained a self-compatible chrysanthemum cultivar and its self-pollinated seed set was 56.50%. It was interesting that the seed set of its ten progenies ranged from 0% to 37.23%. Examination of the factors causing the differences in the seed set will lead to an improved understanding of chrysanthemum self-incompatibility, and provide valuable information for creating pure lines. Pollen morphology, pollen germination percentage, pistil receptivity and embryo development were investigated using the in vitro culture method, the paraffin section technique, scanning electron microscopy and transmission electron microscopy. Moreover, RNA sequencing and bioinformatics were applied to analyzing the transcriptomic profiles of mature stigmas and anthers. It was found that the self-pollinated seed set of "Q10-33-1①","Q10-33-1③","Q10-33-1④" and "Q10-33-1⑩" were 37.23%, 26.77%, 7.97% and 0%, respectively. The differences in fertility among four progenies were mainly attributable to differences in pollen germination percentage and pistil receptivity. Failure of the seed set in "Q10-33-1⑩" was possibly due to self-incompatibility. In the transcriptomic files, 22 potential stigma S genes and 8 potential pollen S genes were found out.
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Affiliation(s)
- Fan Wang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Xinghua Zhong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing 210095, China.
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