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Yan S, Li J, Zhang Q, Jia S, Zhang Q, Wang R, Ju M, Gu P. Transcriptional Response of Wolfberry to Infestation with the Endophytic Fusarium nematophilum Strain NQ8GII4. PLANT DISEASE 2024; 108:1514-1525. [PMID: 38050402 DOI: 10.1094/pdis-07-23-1397-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Fusarium nematophilum NQ8GII4 is an endophytic fungus isolated from the root of healthy wolfberry (Lycium barbarum). Previous studies have reported that NQ8GII4 could dwell in wolfberry roots and enhance the defense responses in wolfberry against root rot, which is caused by F. oxysporum. To further elucidate the molecular mechanism of wolfberry disease resistance induced by NQ8GII4, in the present study, we adopted RNA sequencing analysis to profile the transcriptome of wolfberry response to NQ8GII4 infestation over a time course of 3 and 7 days postinoculation. Gene ontology enrichment analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation, response to stimulus, signaling, detoxification, immune system process, transporter activity, electron carrier activity, transcription factor activity, nucleic acid binding transcription factor, and antioxidant activity. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many of these DEGs were enriched in pathways related to plant-pathogen interactions, hormone signal transduction, and the phenylpropanoid biosynthesis pathway in wolfberry. This result suggested that innate immunity, phytohormone signaling, and numerous phenylpropanoid compounds comprise a complex defense network in wolfberry. Chloroplast 50S ribosomal proteins were consistently located at the core position of the response in wolfberry following infestation with NQ8GII4 analyzed by the protein-protein interaction network. This study elucidated the molecular mechanism underlying the interaction between NQ8GII4 and wolfberry, clarified the wolfberry immune response network to endophytic fungi infestation, identified candidate resistance genes in wolfberry, and provided a fundamental date for subsequent work.
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Affiliation(s)
- Siyuan Yan
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
| | - Jin Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Qingchen Zhang
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, FL 32611, U.S.A
| | - Shuxin Jia
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Qiangqiang Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
| | - Ruotong Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Mingxiu Ju
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
| | - Peiwen Gu
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
- School of Agriculture, Ningxia University, Yinchuan 750021, China
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Wu Y, Zheng Y, Xu W, Zhang Z, Li L, Wang Y, Cui J, Wang QM. Chimeric deletion mutation of rpoC2 underlies the leaf-patterning of Clivia miniata var. variegata. PLANT CELL REPORTS 2023; 42:1419-1431. [PMID: 37326841 DOI: 10.1007/s00299-023-03039-0] [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: 03/18/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
KEY MESSAGE The deletion mutated rpoC2 leads to yellow stripes of Clivia miniata var. variegata by down regulating the transcription of 28 chloroplast genes and disturbing chloroplast biogenesis and thylakoid membrane development. Clivia miniata var. variegata (Cmvv) is a common mutant of Clivia miniata but its genetic basis is unclear. Here, we found that a 425 bp deletion mutation of chloroplast rpoC2 underlies the yellow stripes (YSs) of Cmvv. Both RNA polymerase PEP and NEP coexist in seed-plant chloroplasts and the β″ subunit of PEP is encoded by rpoC2. The rpoC2 mutation changed the discontinuous cleft domain required to form the PEP central cleft for DNA binding from 1103 to 59 aa. RNA-Seq revealed that 28 chloroplast genes (cpDEGs) were all down-regulated in YSs, of which, four involved in chloroplast protein translation and 21 of photosynthesis system (PS)I, PSII, cytochrome b6/f complex and ATP synthase are crucial for chloroplast biogenesis/development. The accuracy and reliability of RNA-Seq was verified by qRT-PCR. Moreover, the chlorophyll (Chl) a/b content, ratio of Chla/Chlb and photosynthetic rate (Pn) of YS decreased significantly. Meanwhile, chloroplasts of the YS mesophyll cells were smaller, irregular in shape, contain almost no thylakoid membrane, and even proplastid was found in YS. These findings indicate that the rpoC2 mutation down-regulated expression of the 28 cpDEGs, which disturb chloroplast biogenesis and its thylakoid membrane development. Thus, there are not enough PSI and II components to bind Chl, so that the corresponding areas of the leaf are yellow and show a low Pn. In this study, the molecular mechanism of three phenotypes of F1 (Cmvv ♀ × C. miniata ♂) was revealed, which lays a foundation for the breeding of variegated plants.
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Affiliation(s)
- Yiming Wu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yi Zheng
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Weiman Xu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Lujia Li
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yucheng Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Jianguo Cui
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Qin-Mei Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
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Wang X, Bai S, Zhang Z, Zheng F, Song L, Wen L, Guo M, Cheng G, Yao W, Gao Y, Li J. Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1179009. [PMID: 37229122 PMCID: PMC10203424 DOI: 10.3389/fpls.2023.1179009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K A/K S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
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Affiliation(s)
- Xiaomin Wang
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Shengyi Bai
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Fushun Zheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lina Song
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lu Wen
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Meng Guo
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Guoxin Cheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Wenkong Yao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Yanming Gao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jianshe Li
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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Postel Z, Mauri T, Lensink MF, Touzet P. What is the potential impact of genetic divergence of plastid ribosomal genes between Silene nutans lineages in hybrids? An in silico approach using the 3D structure of the plastid ribosome. FRONTIERS IN PLANT SCIENCE 2023; 14:1167478. [PMID: 37223795 PMCID: PMC10201985 DOI: 10.3389/fpls.2023.1167478] [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: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
Abstract
Introduction Following the integration of cyanobacteria into the eukaryotic cells, many genes were transferred from the plastid to the nucleus. As a result, plastid complexes are encoded both by plastid and nuclear genes. Tight co-adaptation is required between these genes as plastid and nuclear genomes differ in several characteristics, such as mutation rate and inheritance patterns. Among these are complexes from the plastid ribosome, composed of two main subunits: a large and a small one, both composed of nuclear and plastid gene products. This complex has been identified as a potential candidate for sheltering plastid-nuclear incompatibilities in a Caryophyllaceae species, Silene nutans. This species is composed of four genetically differentiated lineages, which exhibit hybrid breakdown when interlineage crosses are conducted. As this complex is composed of numerous interacting plastid-nuclear gene pairs, in the present study, the goal was to reduce the number of gene pairs that could induce such incompatibilities. Method We used the previously published 3D structure of the spinach ribosome to further elucidate which of the potential gene pairs might disrupt plastid-nuclear interactions within this complex. After modeling the impact of the identified mutations on the 3D structure, we further focused on one strongly mutated plastid-nuclear gene pair: rps11-rps21. We used the centrality measure of the mutated residues to further understand if the modified interactions and associated modified centralities might be correlated with hybrid breakdown. Results and discussion This study highlights that lineage-specific mutations in essential plastid and nuclear genes might disrupt plastid-nuclear protein interactions of the plastid ribosome and that reproductive isolation correlates with changes in residue centrality values. Because of this, the plastid ribosome might be involved in hybrid breakdown in this system.
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Affiliation(s)
- Zoé Postel
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Théo Mauri
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marc F. Lensink
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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Chen H, Wang Q, Fan M, Zhang X, Feng P, Zhu L, Wu J, Cheng X, Wang J. A Single Nucleotide Variation of CRS2 Affected the Establishment of Photosynthetic System in Rice. Int J Mol Sci 2023; 24:ijms24065796. [PMID: 36982870 PMCID: PMC10054620 DOI: 10.3390/ijms24065796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Chloroplasts are essential sites for plant photosynthesis, and the biogenesis of the photosynthetic complexes involves the interaction of nuclear genes and chloroplast genes. In this study, we identified a rice pale green leaf mutant, crs2. The crs2 mutant showed different degrees of low chlorophyll phenotypes at different growth stages, especially at the seedling stage. Fine mapping and DNA sequencing of crs2 revealed a single nucleotide substitution (G4120A) in the eighth exons of CRS2, causing a G-to-R mutation of the 229th amino acid of CRS2 (G229R). The results of complementation experiments confirmed that this single-base mutation in crs2 is responsible for the phenotype of the crs2 mutant. CRS2 encodes a chloroplast RNA splicing 2 protein localized in the chloroplast. Western blot results revealed an abnormality in the abundance of the photosynthesis-related protein in crs2. However, the mutation of CRS2 leads to the enhancement of antioxidant enzyme activity, which could reduce ROS levels. Meanwhile, with the release of Rubisco activity, the photosynthetic performance of crs2 was improved. In summary, the G229R mutation in CRS2 causes chloroplast protein abnormalities and affects photosystem performance in rice; the above findings facilitate the elucidation of the physiological mechanism of chloroplast proteins affecting photosynthesis.
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Affiliation(s)
- Hongwei Chen
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Qi Wang
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingqian Fan
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Xijuan Zhang
- Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Pulin Feng
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Lin Zhu
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Jiayi Wu
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyi Cheng
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (X.C.); or (J.W.)
| | - Jiayu Wang
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (X.C.); or (J.W.)
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Postel Z, Poux C, Gallina S, Varré JS, Godé C, Schmitt E, Meyer E, Van Rossum F, Touzet P. Reproductive isolation among lineages of Silene nutans (Caryophyllaceae): A potential involvement of plastid-nuclear incompatibilities. Mol Phylogenet Evol 2022; 169:107436. [DOI: 10.1016/j.ympev.2022.107436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/26/2022]
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Tang X, Shi F, Wang Y, Huang S, Zhao Y, Feng H. Proteomic analysis of a plastid gene encoding RPS4 mutant in Chinese cabbage (Brassica campestris L. ssp. pekinensis). Funct Integr Genomics 2021; 22:113-130. [PMID: 34881421 DOI: 10.1007/s10142-021-00808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/20/2021] [Accepted: 09/18/2021] [Indexed: 10/19/2022]
Abstract
Plastids are important plant cell organelles containing a genome and bacterial-type 70S ribosomes-primarily composed of plastid ribosomal proteins and ribosomal RNAs. In this study, a chlorophyll-deficient mutant (cdm) obtained from double-haploid Chinese cabbage 'FT' was identified as a plastome mutant with an A-to-C base substitution in the plastid gene encoding the ribosomal protein RPS4. To further elucidate the function and regulatory mechanisms of RPS4, a comparative proteomic analysis was conducted between cdm and its wild-type 'FT' plants by isobaric tags and a relative and absolute quantitation (iTRAQ)-based strategy. A total of 6,245 proteins were identified, 540 of which were differentially abundant proteins (DAPs) in the leaves of cdm as compared to those of 'FT'-including 233 upregulated and 307 downregulated proteins. Upregulated DAPs were mainly involved in translation, organonitrogen compound biosynthetic process, ribosomes, and spliceosomes. Meanwhile, downregulated DAPs were mainly involved in photosynthesis, photosynthetic reaction centres, photosynthetic light harvesting, carbon fixation, and chlorophyll binding. These results indicated an important role of RPS4 in the regulation of growth and development of Chinese cabbage, possibly by regulating plastid translation activity by affecting the expression of specific photosynthesis- and cold stress-related proteins. Moreover, a multiple reaction monitoring (MRM) test and quantitative real-time polymerase chain reaction analysis confirmed our iTRAQ results. Quantitative proteomic analysis allowed us to confirm diverse changes in the metabolic pathways between cdm and 'FT' plants. This work provides new insights into the regulation of chlorophyll biosynthesis and photosynthesis in Chinese cabbage.
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Affiliation(s)
- Xiaoyan Tang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding College of Horticulture, Anhui Agricultural University, 130 Changjiang West Road, Shushan District, Hefei, China
| | - Fengyan Shi
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yiheng Wang
- Biotechnology Research Institute, Xiqing District, Tianjin Academy of Agricultural Sciences, Jinjing Road 17 km, Tianjin, 300384, China
| | - Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Ying Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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Kemat N, Visser RGF, Krens FA. Hypolignification: A Decisive Factor in the Development of Hyperhydricity. PLANTS (BASEL, SWITZERLAND) 2021; 10:2625. [PMID: 34961095 PMCID: PMC8707489 DOI: 10.3390/plants10122625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 06/12/2023]
Abstract
One of the characteristics of hyperhydric plants is the reduction of cell wall lignification (hypolignification), but how this is related to the observed abnormalities of hyperhydricity (HH), is still unclear. Lignin is hydrophobic, and we speculate that a reduction in lignin levels leads to more capillary action of the cell wall and consequently to more water in the apoplast. p-coumaric acid is the hydroxyl derivative of cinnamic acid and a precursor for lignin and flavonoids in higher plant. In the present study, we examined the role of lignin in the development of HH in Arabidopsis thaliana by checking the wild-types (Ler and Col-0) and mutants affected in phenylpropanoid biosynthesis, in the gene coding for cinnamate 4-hydroxylase, C4H (ref3-1 and ref3-3). Exogenously applied p-coumaric acid decreased the symptoms of HH in both wild-type and less-lignin mutants. Moreover, the results revealed that exogenously applied p-coumaric acid inhibited root growth and increased the total lignin content in both wild-type and less-lignin mutants. These effects appeared to diminish the symptoms of HH and suggest an important role for lignin in HH.
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Affiliation(s)
- Nurashikin Kemat
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.G.F.V.); (F.A.K.)
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.G.F.V.); (F.A.K.)
| | - Frans A. Krens
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.G.F.V.); (F.A.K.)
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Fu W, Huang S, Gao Y, Zhang M, Qu G, Wang N, Liu Z, Feng H. Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2937-2948. [PMID: 32656681 DOI: 10.1007/s00122-020-03647-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/01/2020] [Indexed: 05/28/2023]
Abstract
Mapping and resequencing of two allelic early bolting mutants ebm5-1 and ebm5-2 revealed that the BrSDG8 gene is related to bolting in Chinese cabbage (Brassica rapa ssp. pekinensis). Bolting influences the leafy head formation and seed yield of Chinese cabbage therefore being an important agronomic trait. Herein, two allelic early bolting mutants, ebm5-1 and ebm5-2, stably inherited in Chinese cabbage were obtained from wild-type 'FT' seeds by ethyl methane sulfonate mutagenesis. Both mutants flowered significantly earlier than 'FT,' and genetic analysis revealed that the early bolting of the two mutants was controlled by one recessive nuclear gene. With BSR-seq, the mutations originating lines ebm5-1 and ebm5-2 were located to the same region in chromosome A07. Using the 1741 F2 individuals with the ebm5-1 phenotype as the mapping population, this region was narrowed to 56.24 kb between markers InDel18 and InDel45. A single-nucleotide polymorphism (SNP) was aligned to the BraA07g040740.3C (BrSDG8) region by whole-genome resequencing of ebm5-1 mutant and 'FT.' BrSDG8 is a homolog of Arabidopsis thaliana SDG8 encoding a histone methyltransferase affecting H3K4 trimethylation in FLOWERING LOCUS C chromatin. Comparative sequencing established that the SNP occurred on BrSDG8 17th exon in ebm5-1. Genotype analysis showed full co-segregation of the early bolting phenotype with this SNP. Cloning of allelic mutant ebm5-2 indicated that it harbors a deletion mutation on the 12th exon of BrSDG8. Quantitative real-time PCR analysis indicated that BrSDG8 expression level was observably lower in mutant ebm5-1 than in 'FT.' Overall, the present results provide strong evidence that BrSDG8 mutation leads to early bolting in Chinese cabbage, thereby providing a basis to understand the molecular mechanisms underlying this phenotype.
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Affiliation(s)
- Wei Fu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China
| | - Shengnan Huang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China
| | - Yue Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China
| | - Meidi Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China
| | - Gaoyang Qu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China
| | - Nan Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China
| | - Zhiyong Liu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China.
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, People's Republic of China.
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In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice. PLANTS 2020; 9:plants9020233. [PMID: 32054112 PMCID: PMC7076550 DOI: 10.3390/plants9020233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 11/16/2022]
Abstract
Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.
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Zhang K, Mu Y, Li W, Shan X, Wang N, Feng H. Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis). BMC PLANT BIOLOGY 2020; 20:68. [PMID: 32041529 PMCID: PMC7011377 DOI: 10.1186/s12870-020-2271-3] [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: 08/31/2019] [Accepted: 01/29/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation. RESULTS In this study, we identified a stably inherited yellow leaf mutant derived from 'Huaguan' pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm. CONCLUSIONS Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.
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Affiliation(s)
- Kun Zhang
- College of Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Yu Mu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Weijia Li
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Xiaofei Shan
- College of Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Nan Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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Martínez-Alberola F, Barreno E, Casano LM, Gasulla F, Molins A, Moya P, González-Hourcade M, Del Campo EM. The chloroplast genome of the lichen-symbiont microalga Trebouxia sp. Tr9 (Trebouxiophyceae, Chlorophyta) shows short inverted repeats with a single gene and loss of the rps4 gene, which is encoded by the nucleus. JOURNAL OF PHYCOLOGY 2020; 56:170-184. [PMID: 31578712 DOI: 10.1111/jpy.12928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
The Trebouxiophyceae is the class of Chlorophyta algae from which the highest number of chloroplast genome (cpDNA) sequences has been obtained. Several species in this class participate in symbioses with fungi to form lichens. However, no cpDNA has been obtained from any Trebouxia lichen-symbiont microalgae, which are present in approximately half of all lichens. Here, we report the sequence of the completely assembled cpDNA from Trebouxia sp. TR9 and a comparative study with other Trebouxio-phyceae. The organization of the chloroplast genome of Trebouxia sp. TR9 has certain features that are unusual in the Trebouxiophyceae and other green algae. The most remarkable characteristics are the presence of long intergenic spacers, a quadripartite structure with short inverted repeated sequences (IRs), and the loss of the rps4 gene. The presence of long intergenic spacers accounts for a larger cpDNA size in comparison to other closely related Trebouxiophyceae. The IRs, which were thought to be lost in the Trebouxiales, are distinct from most of cpDNAs since they lack the rRNA operon and uniquely includes the rbcL gene. The functional transfer of the rps4 gene to the nuclear genome has been confirmed by sequencing and examination of the gene architecture, which includes three spliceosomal introns as well as the verification of the presence of the corresponding transcript. This is the first documented transfer of the rps4 gene from the chloroplast to the nucleus among Viridiplantae. Additionally, a fairly well-resolved phylogenetic reconstruction, including Trebouxia sp. TR9 along with other Trebouxiophyceae, was obtained based on a set of conserved chloroplast genes.
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Affiliation(s)
- Fernando Martínez-Alberola
- ICBIBE, Botánica, Facultad de Ciencias Biológicas, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, 46100, Spain
| | - Eva Barreno
- ICBIBE, Botánica, Facultad de Ciencias Biológicas, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, 46100, Spain
| | - Leonardo M Casano
- Department of Life Sciences, University of Alcalá, Alcalá de Henares, Madrid, 28805, Spain
| | - Francisco Gasulla
- Department of Life Sciences, University of Alcalá, Alcalá de Henares, Madrid, 28805, Spain
| | - Arantzazu Molins
- ICBIBE, Botánica, Facultad de Ciencias Biológicas, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, 46100, Spain
| | - Patricia Moya
- ICBIBE, Botánica, Facultad de Ciencias Biológicas, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, 46100, Spain
| | | | - Eva M Del Campo
- Department of Life Sciences, University of Alcalá, Alcalá de Henares, Madrid, 28805, Spain
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Li X, Huang S, Liu Z, Hou L, Feng H. Mutation in EMB1923 gene promoter is associated with chlorophyll deficiency in Chinese cabbage (Brassica campestris ssp. pekinensis). PHYSIOLOGIA PLANTARUM 2019; 166:909-920. [PMID: 31058333 DOI: 10.1111/ppl.12979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/07/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
Leaf color mutants are widespread in higher plants and can be used as markers in crop breeding or as important material in understanding the regulatory mechanisms of chlorophyll biosynthesis and chloroplast development. A stably inherited plant etiolated mutation (pem) was obtained from its wild-type 'FT' (a doubled haploid line of the Chinese cabbage variety 'Fukuda 50') by combining 60 Co-γ radiation and isolated microspore culture in Chinese cabbage. Compared to the wild-type 'FT', the chlorophyll content in the pem mutant was decreased, the photosynthetic capacity was reduced and the chloroplast development was retarded. These physiological changes may lead to a reduction in growth and yield in the pem mutant line. Genetic analysis showed that the mutant phenotype was controlled by the single recessive nuclear pem gene. The pem gene was mapped to a 25.88 kb region on the A03 chromosome. Cloning and sequencing results showed that there was only one DNA sequence variation in this region, which was a 30 bp deletion on the promoter of Bra024218. Its homologous gene encodes EMBRYO DEFECTIVE 1923 (EMB1923) in Arabidopsis thaliana. We therefore predicted that Bra024218 was the mutated gene associated with etiolated leaves in Chinese cabbage. The pem mutant is a useful line for researching chloroplast development and the mechanism of leaf color mutation in Chinese cabbage.
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Affiliation(s)
- Xiang Li
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Li Hou
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
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