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Grattapaglia D, Alves WBDS, Pacheco CAP. High-density linkage to physical mapping in a unique Tall × Dwarf coconut ( Cocos nucifera L.) outbred F 2 uncovers a major QTL for flowering time colocalized with the FLOWERING LOCUS T (FT). FRONTIERS IN PLANT SCIENCE 2024; 15:1408239. [PMID: 38887458 PMCID: PMC11180721 DOI: 10.3389/fpls.2024.1408239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
Abstract
Introduction The coconut tree crop (Cocos nucifera L.) provides vital resources for millions of people worldwide. Coconut germplasm is largely classified into 'Tall' (Typica) and 'Dwarf' (Nana) types. While Tall coconuts are outcrossing, stress tolerant, and late flowering, Dwarf coconuts are inbred and flower early with a high rate of bunch emission. Precocity determines the earlier production of a plantation and facilitates management and harvest. Methods A unique outbred F2 population was used, generated by intercrossing F1 hybrids between Brazilian Green Dwarf from Jiqui (BGDJ) and West African Tall (WAT) cultivars. Single-nucleotide polymorphism (SNP) markers fixed for alternative alleles in the two varieties, segregating in an F2 configuration, were used to build a high-density linkage map with ~3,000 SNPs, anchored to the existing chromosome-level genome assemblies, and a quantitative trait locus (QTL) mapping analysis was carried out. Results The linkage map established the chromosome numbering correspondence between the two reference genome versions and the relationship between recombination rate, physical distance, and gene density in the coconut genomes. Leveraging the strong segregation for precocity inherited from the Dwarf cultivar in the F2, a major effect QTL with incomplete dominance was mapped for flowering time. FLOWERING LOCUS T (FT) gene homologs of coconut previously described as putatively involved in flowering time by alternative splice variant analysis were colocalized within a ~200-kb window of the major effect QTL [logarithm of the odds (LOD) = 11.86]. Discussion Our work provides strong phenotype-based evidence for the role of the FT locus as the putative underlying functional variant for the flowering time difference between Dwarf and Tall coconuts. Major effect QTLs were also detected for developmental traits of the palm, plausibly suggesting pleiotropism of the FT locus for other precocity traits. Haplotypes of the two SNPs flanking the flowering time QTL inherited from the Dwarf parent BGDJ caused a reduction in the time to flower of approximately 400 days. These SNPs could be used for high-throughput marker-assisted selection of early-flowering and higher-productivity recombinant lines, providing innovative genetic material to the coconut industry.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA - Recursos Genéticos e Biotecnologia, Brazilian Agricultural Research Corporation, Brasília, DF, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Wellington Bruno dos Santos Alves
- EMBRAPA - Recursos Genéticos e Biotecnologia, Brazilian Agricultural Research Corporation, Brasília, DF, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
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Wang Y, Li J, Guo P, Liu Q, Ren S, Juan L, He J, Tan X, Yan J. Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase gene increased plant height and promoted secondary cell walls deposition in Arabidopsis. PLANTA 2023; 258:65. [PMID: 37566145 DOI: 10.1007/s00425-023-04222-z] [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: 12/13/2022] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
MAIN CONCLUSION Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase 1 caused a taller phenotype, promoted secondary cell wall deposition, leaf enlargement, and early flowering, and reduced chlorophyll and anthocyanin accumulation and seed enlargement phenotype in Arabidopsis. Plant height and secondary cell wall (SCW) deposition are important plant traits. Gibberellins (GAs) play important roles in regulating plant height and SCWs deposition. Gibberellin 20-oxidase (GA20ox) is an important enzyme involved in GA biosynthesis. In the present study, we identified a GA synthesis gene in Camellia oleifera. The total length of the CoGA20ox1 gene sequence was 1146 bp, encoding 381 amino acids. Transgenic plants with CoGA20ox1 had a taller phenotype; a seed enlargement phenotype; promoted SCWs deposition, leaf enlargement, and early flowering; and reduced chlorophyll and anthocyanin accumulation. Genetic analysis showed that the mutant ga20ox1-3 Arabidopsis partially rescued the phenotype of CoGA20ox1 overexpression plants. The results showed that CoGA20ox1 participates in the growth and development of C. oleifera. The morphological changes in CoGA20ox1 overexpressed plants provide a theoretical basis for further exploration of GA biosynthesis and analysis of the molecular mechanism in C. oleifera.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Jian'an Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
| | - Purui Guo
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Qian Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Shuangshuang Ren
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Lemei Juan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Jiacheng He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
| | - Jindong Yan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
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Félix JW, Granados-Alegría MI, Gómez-Tah R, Tzec-Simá M, Ruíz-May E, Canto-Canché B, Zamora-Briseño JA, Bojórquez-Velázquez E, Oropeza-Salín C, Islas-Flores I. Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation. Int J Mol Sci 2023; 24:10431. [PMID: 37445609 DOI: 10.3390/ijms241310431] [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: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.
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Affiliation(s)
- Jean Wildort Félix
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - María Inés Granados-Alegría
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Miguel Tzec-Simá
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Carlos Oropeza-Salín
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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Sheng C, Song S, Zhou W, Dossou SSK, Zhou R, Zhang Y, Li D, You J, Wang L. Integrating transcriptome and phytohormones analysis provided insights into plant height development in sesame. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107695. [PMID: 37058966 DOI: 10.1016/j.plaphy.2023.107695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/12/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023]
Abstract
Plant height is a key agronomic trait influencing crops yield. The height of sesame plants is important for yield performance, lodging resistance and plant architecture. Although plant height is significantly distinct among sesame varieties, the genetic basis of plant height remains largely unknown. In this study, in order to tackle genetic insights into the sesame plant height development, a comprehensive transcriptome analysis was conducted using the stem tips from two sesame varieties with distinct plant height, Zhongzhi13 and ZZM2748, at five time points by BGI MGIseq2000 sequencing platform. A total of 16,952 genes were differentially expressed between Zhongzhi13 and ZZM2748 at five time points. KEGG and MapMan enrichment analyses and quantitative analysis of phytohormones indicated that hormones biosynthesis and signaling pathways were associated with sesame plant height development. Plenty of candidate genes involved in biosynthesis and signaling of brassinosteroid (BR), cytokinin (CK) and gibberellin (GA) which were major differential hormones between two varieties were identified, suggesting their critical roles in plant height regulation. WGCNA revealed a module which was significantly positively associated with the plant height trait and founded SiSCL9 was the hub gene involved in plant height development in our network. Further overexpression in transgenic Arabidopsis validated the function of SiSCL9 in the increase of plant height by 26.86%. Collectively, these results increase our understanding of the regulatory network controlling the development of plant height and provide a valuable genetic resource for improvement of plant architecture in sesame.
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Affiliation(s)
- Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wangyi Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Isolation and characterization of glycoprotein (CNP) isolated from Cocos nucifera L. nutshell and its immunomodulatory role on macrophage activation. J Funct Foods 2023. [DOI: 10.1016/j.jff.2022.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Liu M, Huang L, Zhang Y, Yan Z, Wang N. Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins. TREE PHYSIOLOGY 2022; 42:tpac086. [PMID: 35980326 DOI: 10.1093/treephys/tpac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In previous studies, GA20 oxidase (GA20ox) has been identified to be an important enzyme in the biosynthesis of GA, and SHOOTMERISTEMLESS (STM) can repress the expression of GA20ox. In this study, the GATA transcription factor PdeGATA3 was identified in the poplar line NL895, and its overexpression (OE) transgenic lines showed a dwarf phenotype. RNA sequencing (RNA-Seq) analysis suggested that OE PdeGATA3 could promote the expression of PdeSTM and repress the expression of PdeGA20ox. Therefore, we hypothesized that PdeGATA3 would directly promote the expression of PdeSTM and that PdeSTM would repress the expression of PdeGA20ox. Four experiments, a dual-luciferase reporter assay, GUS transient coexpression assay, yeast one-hybrid assay and electrophoretic mobility shift assay, were conducted and verified that PdeGATA3 could promote the expression of PdeSTM by binding GATA-Boxes in its promoter. OE PdeSTM in poplar resulted in a dwarf phenotype and repressed the expression of PdeGA20ox. GA measurement of the OE PdeSTM and PdeGATA3 lines showed that GA3 and GA4 contents were significantly lower than those in the wild type (WT). Accordingly, we put forward a regulation model involving plant height regulation by PdeGATA3, PdeSTM and PdeGA20ox.
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Affiliation(s)
- Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liyu Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China
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Somyong S, Phetchawang P, Bihi AK, Sonthirod C, Kongkachana W, Sangsrakru D, Jomchai N, Pootakham W, Tangphatsornruang S. A SNP variation in an expansin ( EgExp4) gene affects height in oil palm. PeerJ 2022; 10:e13046. [PMID: 35313525 PMCID: PMC8934041 DOI: 10.7717/peerj.13046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/10/2022] [Indexed: 01/11/2023] Open
Abstract
Oil palm (Elaeis guineensis Jacq.), an Aracaceae family plant, is utilized for both consumable and non-consumable products, including cooking oil, cosmetics and biodiesel production. Oil palm is a perennial tree with 25 years of optimal harvesting time and a height of up to 18 m. However, harvesting of oil palm fruit bunches with heights of more than 2-3 meters is challenging for oil palm farmers. Thus, understanding the genetic control of height would be beneficial for using gene-based markers to speed up oil palm breeding programs to select semi-dwarf oil palm varieties. This study aims to identify Insertion/Deletions (InDels) and single nucleotide polymorphisms (SNPs) of five height-related genes, including EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4, in short and tall oil palm groups by PacBio SMRT sequencing technology. Then, the SNP variation's association with height was validated in the Golden Tenera (GT) population. All targeted genes were successfully amplified by two rounds of PCR amplification with expected sizes that ranged from 2,516 to 3,015 base pair (bp), covering 5' UTR, gene sequences and 3' UTR from 20 short and 20 tall oil palm trees. As a result, 1,166, 909, 1,494, 387 and 5,384 full-length genomic DNA sequences were revealed by PacBio SMRT sequencing technology, from EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4 genes, respectively. Twelve variations, including eight InDels and four SNPs, were identified from EgDELLA1, EgGRF1, EgGA20ox1 and EgExp4. No variation was found for EgAPG1. After SNP through-put genotyping of 4 targeted SNP markers was done by PACE™ SNP genotyping, the association with height was determined in the GT population. Only the mEgExp4_SNP118 marker, designed from EgExp4 gene, was found to associate with height in 2 of 4 height-recordings, with p values of 0.0383 for height (HT)-1 and 0.0263 for HT-4. In conclusion, this marker is a potential gene-based marker that may be used in oil palm breeding programs for selecting semi-dwarf oil palm varieties in the near future.
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Affiliation(s)
- Suthasinee Somyong
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Phakamas Phetchawang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Abdulloh Kafa Bihi
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand,School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
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Wang W, Bai Y, Koilkonda P, Guan L, Zhuge Y, Wang X, Liu Z, Jia H, Wang C, Fang J. Genome-wide identification and characterization of gibberellin metabolic and signal transduction (GA MST) pathway mediating seed and berry development (SBD) in grape (Vitis vinifera L.). BMC PLANT BIOLOGY 2020; 20:384. [PMID: 32825825 PMCID: PMC7441673 DOI: 10.1186/s12870-020-02591-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/12/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine. RESULTS In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed. CONCLUSIONS Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.
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Affiliation(s)
- Wenran Wang
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
- China Agricultural University, College of Horticulture, Beijing, 100193 China
| | - Yunhe Bai
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Padmalatha Koilkonda
- Division of Crop Sciences, ICAR-Central Research Institute for Dryland Agriculture, Santoshnagar, Hyderabad, Telangana 500059 India
| | - Le Guan
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Yaxian Zhuge
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Xicheng Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Zhongjie Liu
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Haifeng Jia
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Chen Wang
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Jinggui Fang
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
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