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Vieites-Álvarez Y, Reigosa MJ, Sánchez-Moreiras AM. A decade of advances in the study of buckwheat for organic farming and agroecology (2013-2023). FRONTIERS IN PLANT SCIENCE 2024; 15:1354672. [PMID: 38510443 PMCID: PMC10950947 DOI: 10.3389/fpls.2024.1354672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
During the last decade, research has shown the environment and human health benefits of growing buckwheat (Fagopyrum spp.). This comprehensive review aims to summarize the major advancements made in the study of buckwheat from 2013 to 2023, focusing on its agronomic characteristics, nutritional value, and potential applications in sustainable agriculture. The review examines the diverse applications of buckwheat in organic and agroecological farming systems, and discusses the ability of buckwheat to control weeds through allelopathy, competition, and other sustainable farming methods, such as crop rotation, intercropping and green manure, while improving soil health and biodiversity. The review also explores the nutritional value of buckwheat. It delves into the composition of buckwheat grains, emphasizing their high protein content, and the presence of essential amino acids and valuable micronutrients, which is linked to health benefits such as lowering cholesterol levels, controlling diabetes and acting against different types of cancer, among others. Finally, the review concludes by highlighting the gaps in current knowledge, and proposing future research directions to further optimize buckwheat production in organic or agroecological farming systems. It emphasizes the need for interdisciplinary collaboration, and the integration of traditional knowledge with modern scientific approaches to unlock the full potential of buckwheat as a sustainable crop.
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Affiliation(s)
- Yedra Vieites-Álvarez
- Universidade de Vigo, Departamento de Bioloxía Vexetal e Ciencias do Solo, Facultade de Bioloxía, Vigo, Spain
- Instituto de Agroecoloxía e Alimentación (IAA), Universidade de Vigo, Ourense, Spain
| | - Manuel J. Reigosa
- Universidade de Vigo, Departamento de Bioloxía Vexetal e Ciencias do Solo, Facultade de Bioloxía, Vigo, Spain
- Instituto de Agroecoloxía e Alimentación (IAA), Universidade de Vigo, Ourense, Spain
| | - Adela M. Sánchez-Moreiras
- Universidade de Vigo, Departamento de Bioloxía Vexetal e Ciencias do Solo, Facultade de Bioloxía, Vigo, Spain
- Instituto de Agroecoloxía e Alimentación (IAA), Universidade de Vigo, Ourense, Spain
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Naik S, Sudan J, Urwat U, Pakhtoon MM, Bhat B, Sharma V, Sofi PA, Shikari AB, Bhat BA, Sofi NR, Prasad PVV, Zargar SM. Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat. THE PLANT GENOME 2024; 17:e20427. [PMID: 38239091 DOI: 10.1002/tpg2.20427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/22/2023] [Indexed: 03/22/2024]
Abstract
Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.
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Affiliation(s)
- Samiullah Naik
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jebi Sudan
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Varun Sharma
- Bioinformatics Division, NMC Genetics India Pvt. Ltd., Gurugram, India
| | - Parvaze A Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Asif B Shikari
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Bilal A Bhat
- Mountain Agriculture Research & Extension Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Najeebul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, Kansas, USA
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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Li J, Wu K, Li L, Ma G, Fang L, Zeng S. Identification of HpMYB1 inducing anthocyanin accumulation in Hippeastrum Hybridum tepals by RNA-seq. BMC PLANT BIOLOGY 2023; 23:594. [PMID: 38012575 PMCID: PMC10683291 DOI: 10.1186/s12870-023-04582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Cultivated Hippeastrum × hybridum is a popular ornamental plant with large and colorful flowers, long flowering duration, and high commercial value. As its main ornamental feature, its flower color is related to the anthocyanin content in the tepals. However, the molecular regulatory mechanisms of anthocyanin biosynthesis in H. × hybridum have not yet been elucidated. RESULTS In the present study, 12 cDNA libraries of four stages of H.× hybridum 'Royal Velvet' tepal development were used for RNA-seq, obtaining 79.83 gigabases (GB) of clean data. The data were assembled into 148,453 unigenes, and 11,262 differentially expressed genes were identified. Forty key enzymes participating in anthocyanin biosynthesis were investigated, and the results showed that most of the anthocyanin structural genes were expressed at low levels in S1 and were markedly upregulated in S2 and S3. The expression profiles of 12 selected genes were verified by qRT-PCR. Furthermore, the R2R3-MYB transcription factor (TF), HpMYB1, involved in the regulation of anthocyanin biosynthesis was identified by sequence, expression pattern, and subcellular localization analyses. Its overexpression in tobacco significantly increased the anthocyanin levels in various tissues and activated anthocyanin-related genes. CONCLUSIONS Using RNA-seq technology, we successfully identified a potential R2R3-MYB gene, HpMYB1, that regulates anthocyanin biosynthesis in H.× hybridum 'Royal Velvet'. Our findings provide basic transcript information and valuable transcriptome data for further identification of key genes involved in anthocyanin biosynthesis and can be applied in the artificial breeding of new H. × hybridum cultivars with enhanced ornamental value.
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Affiliation(s)
- Ji Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kunlin Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Lin Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Guohua Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Lin Fang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
| | - Songjun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, 510650, Guangzhou, China.
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Pinski A, Betekhtin A. Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum. FRONTIERS IN PLANT SCIENCE 2023; 14:1270150. [PMID: 37746024 PMCID: PMC10515086 DOI: 10.3389/fpls.2023.1270150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
Fagopyrum tataricum (L.) Gaertn. is an exceptional crop known for its remarkable health benefits, high levels of beneficial polyphenols and gluten-free properties, making it highly sought-after as a functional food. Its self-fertilisation capability and adaptability to challenging environments further contribute to its potential as a sustainable agricultural option. To harness its unique traits, genetic transformation in F. tataricum is crucial. In this study, we optimised the Agrobacterium-mediated transformation protocol for F. tataricum callus, resulting in a transformation rate of regenerated plants of approximately 20%. The protocol's effectiveness was confirmed through successful GUS staining, GFP expression, and the generation of albino plants via FtPDS gene inactivation. These results validate the feasibility of genetic manipulation and highlight the potential for trait enhancement in F. tataricum.
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Affiliation(s)
- Artur Pinski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Du Y, Lin Y, Zhang K, Rothenberg DO, Zhang H, Zhou H, Su H, Zhang L. The Chemical Composition and Transcriptome Analysis Reveal the Mechanism of Color Formation in Tea ( Camellia sinensis) Pericarp. Int J Mol Sci 2023; 24:13198. [PMID: 37686006 PMCID: PMC10487661 DOI: 10.3390/ijms241713198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. Jinxuan), and Baitangziya (Camellia sinensis L. var. Baitang). Results of biochemical analysis revealed that low chlorophyll content and low chlorophyll/carotene ratio may be the biochemical basis for albino characteristics in the 'Zhongbaiyihao' pericarp. The differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, including DFR, F3'5'H, CCoAOMT, and 4-coumaroyl-CoA, were highly expressed in the purple 'Baitangziya' pericarp. In the chlorophyll synthesis of white pericarp, GUN5 (Genome Uncoupled 5) and 8-vinyl-reductase both showed high expression levels compared to the green one, which indicated that albino 'Zhongbaiyihao' pericarp had a higher chlorophyll synthesis capacity than 'Jinxuan'. Meanwhile, chlorophyllase (CLH, CSS0004684) was lower in 'Baitang' than in 'Jinxuan' and 'Zhongbaiyihao' pericarp. Among the differentially expressed transcription factors, MYB59, WRKY41-like2 (CS ng17509), bHLH62 like1 (CS ng6804), and bHLH62-like3 (CSS0039948) were downregulated in Jinxuan pericarp, suggesting that transcription factors played a role in regulating tea pericarp coloration. These findings provide a better understanding of the molecular mechanisms and theoretical basis for utilizing functional components of tea pericarp.
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Affiliation(s)
| | | | | | | | | | | | | | - Lingyun Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510640, China; (Y.D.); (Y.L.); (K.Z.); (D.O.R.); (H.Z.); (H.Z.); (H.S.)
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Chen C, Zhang Y, Liu Y, Cui J, He X, Wu Y, Yue L, Zhang J, Ding M, Yi Z, Fang X. Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Seed-Shattering-Related Genes in Common Buckwheat. Int J Mol Sci 2023; 24:10013. [PMID: 37373161 DOI: 10.3390/ijms241210013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the F2 population of Gr (green-flower mutant and shattering resistance) and UD (white flower and susceptible to shattering), which included eight linkage groups with 174 loci, and detected seven QTLs of pedicel strength. RNA-seq analysis of pedicel in two parents revealed 214 differentially expressed genes DEGs that play roles in phenylpropanoid biosynthesis, vitamin B6 metabolism, and flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) was performed and screened out 19 core hub genes. Untargeted GC-MS analysis detected 138 different metabolites and conjoint analysis screened out 11 DEGs, which were significantly associated with differential metabolites. Furthermore, we identified 43 genes in the QTLs, of which six genes had high expression levels in the pedicel of common buckwheat. Finally, 21 candidate genes were screened out based on the above analysis and gene function. Our results provided additional knowledge for the identification and functions of causal candidate genes responsible for the variation in seed-shattering and would be an invaluable resource for the genetic dissection of common buckwheat resistance-shattering molecular breeding.
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Affiliation(s)
- Chuyi Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yuke Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Institute of Advanced Agricultural Sciences, Peking University, Weifang 261000, China
| | - Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jingbin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xingxing He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yichao Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Linqing Yue
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Mengqi Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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7
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Ma Y, Devi MJ, Feng X, Li Y, Song L, Gao H, Cao B. Transcriptome analysis reveals the fruit color variation in Ailanthus altissima. PHYSIOLOGIA PLANTARUM 2023; 175:e13867. [PMID: 36708240 DOI: 10.1111/ppl.13867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Anthocyanins are responsible for the intensity of color in plants; however, the systematic mechanisms underlying the color differences in the fruit of Ailanthus altissima remain unknown. Therefore, this study aims to analyze the transcriptomes of the white and red fruit of A. altissima by screening and validating the key genes involved in flavonoid and anthocyanin biosynthesis. Samples of A. altissima fruit were collected 30, 45, and 60 days after flowering, and their pigment and sugar content were determined. The anthocyanin content was significantly higher in red than in white fruits. Transcriptome analysis was also performed on the fruit samples, 73,807 unigenes were assembled and annotated to seven databases. Twenty-one co-expressed modules were identified via weighted gene co-expression network analysis, of which two were associated with flavonoids and anthocyanins. Furthermore, in three growth stages, 126, 30, and 124 differentially expressed genes were screened between white and red fruit. Genes involved in flavonoid and anthocyanin metabolism were identified. AaDFR (A. altissima bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase) and AaANS (A. altissima anthocyanidin synthase) were associated with flavonoid and anthocyanin metabolism. Members of the AaDFR and AaANS families were also identified, and their basic physicochemical characteristics, conserved domains, motif compositions, phylogenetics, and expression levels were analyzed. The overexpression of AaDFR and AaANS in transgenic Arabidopsis significantly increased the content of seed and foliar flavonoids and anthocyanins. The study elucidated the different mechanisms underlying fruit color development and provided insight into A. altissima plants breeding with commercially desirable properties.
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Affiliation(s)
- Yaping Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- College of Forestry, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mura Jyostna Devi
- USDA-ARS, Vegetable Crops Research Unit, Madison, Wisconsin, USA
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xuerui Feng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yunmao Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Lihua Song
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Handong Gao
- College of Forestry, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Southern Tree Seed Inspection Center, Nanjing, China
| | - Bing Cao
- School of Agriculture, Ningxia University, Yinchuan, China
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8
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Wang Y, Yin H, Long Z, Zhu W, Yin J, Song X, Li C. DhMYB2 and DhbHLH1 regulates anthocyanin accumulation via activation of late biosynthesis genes in Phalaenopsis-type Dendrobium. FRONTIERS IN PLANT SCIENCE 2022; 13:1046134. [PMID: 36457536 PMCID: PMC9705975 DOI: 10.3389/fpls.2022.1046134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Phalaenopsis-type Dendrobium is a popular orchid with good ornamental and market value. Despite their popularity, molecular regulation of anthocyanin biosynthesis during flower development remains poorly understood. In this study, we systematically investigated the regulatory roles of the transcription factors DhMYB2 and DhbHLH1 in anthocyanins biosynthesis. Gene expression analyses indicated that both DhMYB2 and DhbHLH1 are specifically expressed in flowers and have similar expression patterns, showing high expression in purple floral tissues with anthocyanin accumulation. Transcriptomic analyses showed 29 differentially expressed genes corresponding to eight enzymes in anthocyanin biosynthesis pathway have similar expression patterns to DhMYB2 and DhbHLH1, with higher expression in the purple lips than the yellow petals and sepals of Dendrobium 'Suriya Gold'. Further gene expression analyses and Pearson correlation matrix analyses of Dendrobium hybrid progenies revealed expression profiles of DhMYB2 and DhbHLH1 were positively correlated with the structural genes DhF3'H1, DhF3'5'H2, DhDFR, DhANS, and DhGT4. Yeast one-hybrid and dual-luciferase reporter assays revealed DhMYB2 and DhbHLH1 can bind to promoter regions of DhF3'H1, DhF3'5'H2, DhDFR, DhANS and DhGT4, suggesting a role as transcriptional activators. These results provide new evidence of the molecular mechanisms of DhMYB2 and DhbHLH1 in anthocyanin biosynthesis in Phalaenopsis-type Dendrobium.
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Affiliation(s)
- Yachen Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, School of Life Sciences, Hainan University, Haikou, China
| | - Hantai Yin
- Haikou Experimental Station, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou, China
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou, China
| | - Zongxing Long
- Haikou Experimental Station, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou, China
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou, China
| | - Wenjuan Zhu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, School of Life Sciences, Hainan University, Haikou, China
| | - Junmei Yin
- Haikou Experimental Station, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou, China
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou, China
| | - Xiqiang Song
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, School of Life Sciences, Hainan University, Haikou, China
| | - Chonghui Li
- Haikou Experimental Station, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou, China
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou, China
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9
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Comparative transcriptome profiling and molecular marker development for oil palm fruit color. Sci Rep 2022; 12:15507. [PMID: 36109663 PMCID: PMC9478095 DOI: 10.1038/s41598-022-19890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
Oil palm harvesting is normally determined by fruit exocarp color. To detect expressed sequence tag (EST)-simple sequence repeat (SSR) markers in oil palm hybrid populations, de novo transcriptomic profiling of Nigeria black and Suratthani 1 (Deli × Calabar) plants was performed. More than 46 million high-quality clean reads with a mean length of 1117 bp were generated. Functional annotation and gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) revealed that the genes were involved in fruit color development and pigment synthesis. Comparison of immature/mature DEGs indicated that nigrescent fruit color was driven by the anthocyanin biosynthesis pathway (ABP); however, the carotenoid biosynthesis pathway (CBP) was involved in the color development of both fruit types. The transcripts of both unique and different genes involved in the ABP and CBP in higher plants were highlighted for further study, especially 3GT, downstream genes in the ABP, and DEARF27 in the CBP. Additionally, SSR primer motifs, namely, 9949, discovered from the DEGs upregulated in the virescent type that encode vacuolar iron transporter (VIT), could separate the nigrescence and virescence traits of Nigeria hybrids. This novel primer has potential to be used as a molecular for further selection in breeding programs especially involving the specific genetic backgrounds described in this study.
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10
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Germano TA, de Oliveira MFR, Aziz S, Oliveira AER, da Cruz Saraiva KD, Dos Santos CP, Moura CFH, Costa JH. Transcriptome profiling of cashew apples (Anacardium occidentale) genotypes reveals specific genes linked to firmness and color during pseudofruit development. PLANT MOLECULAR BIOLOGY 2022; 109:83-100. [PMID: 35332428 DOI: 10.1007/s11103-022-01257-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
We found 34 and 71 key genes potentially involved in flavonoid biosynthesis and cell wall disassembly, respectively, which could be associated with specific peel coloration and softening of each genotype. Cashew apple (Anacardium occidentale) has a great economic importance worldwide due to its high nutritional value, peculiar flavor and aroma. During ripening, the peduncle develops different peel color and becomes quickly fragile due to its oversoftening, impacting its consumers' acceptance. In view of this, the understanding about its transcriptional dynamics throughout ripening is imperative. In this study, we performed a transcriptome sequencing of two cashew apple genotypes (CCP 76 and BRS 265), presenting different firmness and color peel, in the immature and ripe stages. Comparative transcriptome analysis between immature and ripe cashew apple revealed 4374 and 3266 differentially expressed genes (DEGs) to CCP 76 and BRS 265 genotypes, respectively. These genes included 71 and 34 GDEs involved in the cell wall disassembly and flavonoid biosynthesis, respectively, which could be associated with firmness loss and anthocyanin accumulation during cashew apple development. Then, softer peduncle of CCP 76 could be justified by down-regulated EXP and up-regulation of genes involved in pectin degradation (PG, PL and PAE) and in cell wall biosynthesis. Moreover, genes related to flavonoid biosynthesis (PAL, C4H and CHS) could be associated with early high accumulation of anthocyanin in red-peel peduncle of BRS 265. Finally, expression patterns of the selected genes were tested by real-time quantitative PCR (qRT-PCR), and the qRT-PCR results were consistent with transcriptome data. The information generated in this work will provide insights into transcriptome responses to cashew apple ripening and hence, it will be helpful for cashew breeding programs aimed at developing genotypes with improved quality traits.
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Affiliation(s)
- Thais Andrade Germano
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Matheus Finger Ramos de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Shahid Aziz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil
| | - Antonio Edson Rocha Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, CEP 05508-900, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Ciência e Tecnologia da Paraíba, Instituto Federal de Educação, Campus Princesa Isabel, Princesa Isabel, PB, CEP 58755-000, Brazil
| | - Clesivan Pereira Dos Santos
- Departamento de Química, Universidade Estadual de Ponta Grossa, Campus Uvaranas, Ponta Grossa, PR, CEP 84030-900, Brazil
| | | | - José Hélio Costa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, CEP 60440-554, Brazil.
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11
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Liu Y, Fang X, Tang T, Wang Y, Wu Y, Luo J, Wu H, Wang Y, Zhang J, Ruan R, Zhou M, Zhang K, Yi Z. Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat ( Fagopyrum esculentum). PLANTS (BASEL, SWITZERLAND) 2022; 11:742. [PMID: 35336623 PMCID: PMC8950064 DOI: 10.3390/plants11060742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.
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Affiliation(s)
- Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Tian Tang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yudong Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yinhuan Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jinyu Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Haotian Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yingqian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Renwu Ruan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
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12
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Cheng C, Wang J, Hou W, Malik K, Zhao C, Niu X, Liu Y, Huang R, Li C, Nan Z. Elucidating the Molecular Mechanisms by which Seed-Borne Endophytic Fungi, Epichloë gansuensis, Increases the Tolerance of Achnatherum inebrians to NaCl Stress. Int J Mol Sci 2021; 22:ijms222413191. [PMID: 34947985 PMCID: PMC8706252 DOI: 10.3390/ijms222413191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 12/29/2022] Open
Abstract
Seed-borne endophyte Epichloë gansuensis enhance NaCl tolerance in Achnatherum inebrians and increase its biomass. However, the molecular mechanism by which E. gansuensis increases the tolerance of host grasses to NaCl stress is unclear. Hence, we firstly explored the full-length transcriptome information of A. inebrians by PacBio RS II. In this work, we obtained 738,588 full-length non-chimeric reads, 36,105 transcript sequences and 27,202 complete CDSs from A. inebrians. We identified 3558 transcription factors (TFs), 15,945 simple sequence repeats and 963 long non-coding RNAs of A. inebrians. The present results show that 2464 and 1817 genes were differentially expressed by E. gansuensis in the leaves of E+ and E− plants at 0 mM and 200 mM NaCl concentrations, respectively. In addition, NaCl stress significantly regulated 4919 DEGs and 502 DEGs in the leaves of E+ and E− plants, respectively. Transcripts associated with photosynthesis, plant hormone signal transduction, amino acids metabolism, flavonoid biosynthetic process and WRKY TFs were differentially expressed by E. gansuensis; importantly, E. gansuensis up-regulated biology processes (brassinosteroid biosynthesis, oxidation–reduction, cellular calcium ion homeostasis, carotene biosynthesis, positive regulation of proteasomal ubiquitin-dependent protein catabolism and proanthocyanidin biosynthesis) of host grass under NaCl stress, which indicated an increase in the ability of host grasses’ adaptation to NaCl stress. In conclusion, our study demonstrates the molecular mechanism for E. gansuensis to increase the tolerance to salt stress in the host, which provides a theoretical basis for the molecular breed to create salt-tolerant forage with endophytes.
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Affiliation(s)
- Chen Cheng
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Jianfeng Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
- Correspondence:
| | - Wenpeng Hou
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
| | - Kamran Malik
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Chengzhou Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Tibetan Medicine Research Center, College of Tibetan Medicine, Qinghai University, Xining 810016, China
| | - Xueli Niu
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China;
| | - Yinglong Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Rong Huang
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Chunjie Li
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (C.C.); (W.H.); (Y.L.); (R.H.); (C.L.); (Z.N.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
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13
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Ge X, Jing L, Su C, Zhang B, Zhang Q, Li W. The profile, content and antioxidant activity of anthocyanin in germinated naked barley grains with infrared and hot air drying. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.14999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiangzhen Ge
- College of Food Science and Engineering Northwest A&F University Yangling712100China
| | - Luzhen Jing
- College of Food Science and Engineering Northwest A&F University Yangling712100China
| | - Chunyan Su
- College of Food Science and Engineering Northwest A&F University Yangling712100China
| | - Bo Zhang
- College of Food Science and Engineering Northwest A&F University Yangling712100China
| | - Qian Zhang
- College of Food Science and Engineering Northwest A&F University Yangling712100China
| | - Wenhao Li
- College of Food Science and Engineering Northwest A&F University Yangling712100China
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14
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Muñoz-Gómez S, Suárez-Baron H, Alzate JF, González F, Pabón-Mora N. Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales. FRONTIERS IN PLANT SCIENCE 2021; 12:633227. [PMID: 33897722 PMCID: PMC8063865 DOI: 10.3389/fpls.2021.633227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 05/27/2023]
Abstract
Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.
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Affiliation(s)
- Sarita Muñoz-Gómez
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Harold Suárez-Baron
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica – CNSG, Sede de Investigación Universitaria, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, Bogotá, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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15
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Qiao Y, Cheng Q, Zhang Y, Yan W, Yi F, Shi F. Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers. BMC PLANT BIOLOGY 2021; 21:61. [PMID: 33482728 PMCID: PMC7825240 DOI: 10.1186/s12870-021-02827-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/05/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. RESULTS Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the "flavonoid biosynthesis"and "phenylpropanoid biosynthesis" pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. CONCLUSIONS This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.
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Affiliation(s)
- Yu Qiao
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Qiming Cheng
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Yutong Zhang
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Wei Yan
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Fengling Shi
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China.
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16
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Penin AA, Kasianov AS, Klepikova AV, Kirov IV, Gerasimov ES, Fesenko AN, Logacheva MD. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. FRONTIERS IN PLANT SCIENCE 2021; 12:612382. [PMID: 33815435 PMCID: PMC8010679 DOI: 10.3389/fpls.2021.612382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/03/2021] [Indexed: 05/06/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5-1 Mya) multiplied TEs ("transposon burst") and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.
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Affiliation(s)
- Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Maria D. Logacheva,
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