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Gebretsadik K, Chen W, Duan Y, Sun Y, He Y, Liao Q, Wang C, Bo K. Map-based cloning reveals Cpgp gene encoding an APRR2 protein to regulate the green fruit peel formation in Cucurbita pepo. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:53. [PMID: 39130616 PMCID: PMC11315825 DOI: 10.1007/s11032-024-01492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
Fruit peel color is a major factor that influences fruit quality and customers' demand. However, the molecular mechanisms underlying the green fruit peel color trait of Cucurbita pepo L. remain unknown. Two parental lines, RP16 and RP38, were used to study the fruit peel color trait in C. pepo. The parental line RP16 shows white peel color, whereas RP38 exhibits green peel color. 384 F2 populations were used to identify the inheritance pattern associated with green fruit and white fruit peel in Cucurbita pepo L. 293 F2 individuals were white, and 91 F2 individuals were green, resulting in a ratio of 3:1. Hence, white peel is dominant over the green fruit peel trait, and a single recessive green peel gene (Cpgp) controls the green fruit peel. The fruit chlorophyll (Chll) content decreases as fruit matures in the RP16 line. In contrast, Chll increases during the fruit growing periods on fruit peels of the RP38 line. The BSA-sequence analysis revealed the Cpgp locus on Chr5, within a 2.3 Mb region. Subsequent fine-mapping analysis, using 699 F2 plants, narrowed down this region to 23.90 kb on the same chromosome. Within this region, two annotated genes, namely Cp4.1LG05g02070 and Cp4.1LG05g02060, are present. These genes are predicted to encode a two-component Arabidopsis Pseudo-Response Regulator 2-like protein (APRR2), which may be involved in green pigmentation processes in plants. Consequently, sequence alignment and gene expression analyses at various fruit development stages supported that Cp4.1LG05g02070 may be the primary candidate gene responsible for regulating the green fruit peel color trait in Cucurbita pepo L. This study may provide a basis for further study on the basic mechanisms that control the fruit peel colors in Cucurbita spp. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01492-7.
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Affiliation(s)
- Kiros Gebretsadik
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Department of Plant Sciences, Aksum University Shire Campus, Shire, Ethiopia
| | - Wanlu Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ying Duan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yapei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yadi He
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qinggui Liao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Changlin Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Kailiang Bo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Vasquez-Teuber P, Rouxel T, Mason AS, Soyer JL. Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:192. [PMID: 39052130 PMCID: PMC11272824 DOI: 10.1007/s00122-024-04641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/29/2024] [Indexed: 07/27/2024]
Abstract
Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.
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Affiliation(s)
- Paula Vasquez-Teuber
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
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Wang H, Santuari L, Wijsman T, Wachsman G, Haase H, Nodine M, Scheres B, Heidstra R. Arabidopsis ribosomal RNA processing meerling mutants exhibit suspensor-derived polyembryony due to direct reprogramming of the suspensor. THE PLANT CELL 2024; 36:2550-2569. [PMID: 38513608 PMCID: PMC11218825 DOI: 10.1093/plcell/koae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Embryo development in Arabidopsis (Arabidopsis thaliana) starts off with an asymmetric division of the zygote to generate the precursors of the embryo proper and the supporting extraembryonic suspensor. The suspensor degenerates as the development of the embryo proper proceeds beyond the heart stage. Until the globular stage, the suspensor maintains embryonic potential and can form embryos in the absence of the developing embryo proper. We report a mutant called meerling-1 (mrl-1), which shows a high penetrance of suspensor-derived polyembryony due to delayed development of the embryo proper. Eventually, embryos from both apical and suspensor lineages successfully develop into normal plants and complete their life cycle. We identified the causal mutation as a genomic rearrangement altering the promoter of the Arabidopsis U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 18 (UTP18) homolog that encodes a nucleolar-localized WD40-repeat protein involved in processing 18S preribosomal RNA. Accordingly, root-specific knockout of UTP18 caused growth arrest and accumulation of unprocessed 18S pre-rRNA. We generated the mrl-2 loss-of-function mutant and observed asynchronous megagametophyte development causing embryo sac abortion. Together, our results indicate that promoter rearrangement decreased UTP18 protein abundance during early stage embryo proper development, triggering suspensor-derived embryogenesis. Our data support the existence of noncell autonomous signaling from the embryo proper to prevent direct reprogramming of the suspensor toward embryonic fate.
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Affiliation(s)
- Honglei Wang
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Luca Santuari
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tristan Wijsman
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guy Wachsman
- Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hannah Haase
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael Nodine
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renze Heidstra
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Maruta T, Tanaka Y, Yamamoto K, Ishida T, Hamada A, Ishikawa T. Evolutionary insights into strategy shifts for the safe and effective accumulation of ascorbate in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2664-2681. [PMID: 38452239 DOI: 10.1093/jxb/erae062] [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: 11/09/2023] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
Plants accumulate high concentrations of ascorbate, commonly in their leaves, as a redox buffer. While ascorbate levels have increased during plant evolution, the mechanisms behind this phenomenon are unclear. Moreover, has the increase in ascorbate concentration been achieved without imposing any detrimental effects on the plants? In this review, we focus on potential transitions in two regulatory mechanisms related to ascorbate biosynthesis and the availability of cellular dehydroascorbate (DHA) during plant evolution. The first transition might be that the trigger for the transcriptional induction of VTC2, which encodes the rate-limiting enzyme in ascorbate biosynthesis, has shifted from oxidative stress (in green algae) to light/photosynthesis (in land plants), probably enabling the continuous accumulation of ascorbate under illumination. This could serve as a preventive system against the unpredictable occurrence of oxidative stress. The second transition might be that DHA-degrading enzymes, which protect cells from the highly reactive DHA in green algae and mosses, have been lost in ferns or flowering plants. Instead, flowering plants may have increased glutathione concentrations to reinforce the DHA reduction capacity, possibly allowing ascorbate accumulation and avoiding the toxicity of DHA. These potential transitions may have contributed to strategies for plants' safe and effective accumulation of ascorbate.
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Affiliation(s)
- Takanori Maruta
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Yasuhiro Tanaka
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
| | - Kojiro Yamamoto
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Tetsuya Ishida
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Akane Hamada
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Takahiro Ishikawa
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
- Bioresource and Life Sciences, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
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Smirnoff N, Wheeler GL. The ascorbate biosynthesis pathway in plants is known, but there is a way to go with understanding control and functions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2604-2630. [PMID: 38300237 PMCID: PMC11066809 DOI: 10.1093/jxb/erad505] [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: 11/09/2023] [Accepted: 01/29/2024] [Indexed: 02/02/2024]
Abstract
Ascorbate (vitamin C) is one of the most abundant primary metabolites in plants. Its complex chemistry enables it to function as an antioxidant, as a free radical scavenger, and as a reductant for iron and copper. Ascorbate biosynthesis occurs via the mannose/l-galactose pathway in green plants, and the evidence for this pathway being the major route is reviewed. Ascorbate accumulation is leaves is responsive to light, reflecting various roles in photoprotection. GDP-l-galactose phosphorylase (GGP) is the first dedicated step in the pathway and is important in controlling ascorbate synthesis. Its expression is determined by a combination of transcription and translation. Translation is controlled by an upstream open reading frame (uORF) which blocks translation of the main GGP-coding sequence, possibly in an ascorbate-dependent manner. GGP associates with a PAS-LOV protein, inhibiting its activity, and dissociation is induced by blue light. While low ascorbate mutants are susceptible to oxidative stress, they grow nearly normally. In contrast, mutants lacking ascorbate do not grow unless rescued by supplementation. Further research should investigate possible basal functions of ascorbate in severely deficient plants involving prevention of iron overoxidation in 2-oxoglutarate-dependent dioxygenases and iron mobilization during seed development and germination.
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Affiliation(s)
- Nicholas Smirnoff
- Biosciences, Faculty of Health and Life Sciences, Exeter EX4 4QD, UK
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Xin Z. Mutagenesis in the Age of Next-Generation-Sequencing and Genome Editing. PLANTS (BASEL, SWITZERLAND) 2023; 12:3403. [PMID: 37836142 PMCID: PMC10574159 DOI: 10.3390/plants12193403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Mutagenesis is a proven, classical technique for inducing a broad spectrum of DNA variations and has led to the creation of thousands of improved varieties in many crop species [...].
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Affiliation(s)
- Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, 3810 4th Street, Lubbock, TX 79415, USA
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7
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Li Y, Luo X, Peng X, Jin Y, Tan H, Wu L, Li J, Pei Y, Xu X, Zhang W. Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.). BMC Genomics 2023; 24:445. [PMID: 37553577 PMCID: PMC10408230 DOI: 10.1186/s12864-023-09528-6] [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: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.). RESULTS In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. CONCLUSIONS The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.
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Affiliation(s)
- Yadong Li
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Xiaobo Luo
- Guizhou Province Academy of Agricultural Sciences, Guizhou Institute of Biotechnology, Guiyang, 550003 China
| | - Xiao Peng
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Yueyue Jin
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Huping Tan
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Linjun Wu
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Jingwei Li
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Yun Pei
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Xiuhong Xu
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Wanping Zhang
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
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Castro JC, Castro CG, Cobos M. Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1099829. [PMID: 37021310 PMCID: PMC10069634 DOI: 10.3389/fpls.2023.1099829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Vitamin C (L-ascorbic acid, AsA) is an essential compound with pleiotropic functions in many organisms. Since its isolation in the last century, AsA has attracted the attention of the scientific community, allowing the discovery of the L-galactose pathway, which is the main pathway for AsA biosynthesis in plants. Thus, the aim of this review is to analyze the genetic and biochemical strategies employed by plant cells for regulating AsA biosynthesis through the L-galactose pathway. In this pathway, participates eight enzymes encoded by the genes PMI, PMM, GMP, GME, GGP, GPP, GDH, and GLDH. All these genes and their encoded enzymes have been well characterized, demonstrating their participation in AsA biosynthesis. Also, have described some genetic and biochemical strategies that allow its regulation. The genetic strategy includes regulation at transcriptional and post-transcriptional levels. In the first one, it was demonstrated that the expression levels of the genes correlate directly with AsA content in the tissues/organs of the plants. Also, it was proved that these genes are light-induced because they have light-responsive promoter motifs (e.g., ATC, I-box, GT1 motif, etc.). In addition, were identified some transcription factors that function as activators (e.g., SlICE1, AtERF98, SlHZ24, etc.) or inactivators (e.g., SlL1L4, ABI4, SlNYYA10) regulate the transcription of these genes. In the second one, it was proved that some genes have alternative splicing events and could be a mechanism to control AsA biosynthesis. Also, it was demonstrated that a conserved cis-acting upstream open reading frame (5'-uORF) located in the 5'-untranslated region of the GGP gene induces its post-transcriptional repression. Among the biochemical strategies discovered is the control of the enzyme levels (usually by decreasing their quantities), control of the enzyme catalytic activity (by increasing or decreasing its activity), feedback inhibition of some enzymes (GME and GGP), subcellular compartmentation of AsA, the metabolon assembly of the enzymes, and control of AsA biosynthesis by electron flow. Together, the construction of this basic knowledge has been establishing the foundations for generating genetically improved varieties of fruits and vegetables enriched with AsA, commonly used in animal and human feed.
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Affiliation(s)
- Juan C. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Carlos G. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Marianela Cobos
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
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Yue X, Ke X, Shi Y, Li Y, Zhang C, Wang Y, Hou X. Chloroplast inner envelope protein FtsH11 is involved in the adjustment of assembly of chloroplast ATP synthase under heat stress. PLANT, CELL & ENVIRONMENT 2023; 46:850-864. [PMID: 36573466 DOI: 10.1111/pce.14525] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The maintenance of a proton gradient across the thylakoid membrane is an integral aspect of photosynthesis that is mainly established by the splitting of water molecules in photosystem II and plastoquinol oxidation at the cytochrome complex, and it is necessary for the generation of ATP in the last step of photophosphorylation. Although environmental stresses, such as high temperatures, are known to disrupt this fundamental process, only a few studies have explored the molecular mechanisms underlying proton gradient regulation during stress. The present study identified a heat-sensitive mutant that displays aberrant photosynthesis at high temperatures. This mutation was mapped to AtFtsH11, which encodes an ATP-dependent AAA-family metalloprotease. We showed that AtFtsH11 localizes to the chloroplast inner envelope membrane and is capable of degrading the ATP synthase assembly factor BFA3 under heat stress. We posit that this function limits the amount of ATP synthase integrated into the thylakoid membrane to regulate proton efflux from the lumen to the stroma. Our data also suggest that AtFtsH11 is critical in stabilizing photosystem II and cytochrome complexes at high temperatures, and additional studies can further elucidate the specific molecular functions of this critical regulator of photosynthetic thermotolerance.
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Affiliation(s)
- Xiaohong Yue
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiangsheng Ke
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafei Shi
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yetao Wang
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xin Hou
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
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Skinner DJ, Dang T, Gasser CS. The Arabidopsis INNER NO OUTER ( INO) gene acts exclusively and quantitatively in regulation of ovule outer integument development. PLANT DIRECT 2023; 7:e485. [PMID: 36845169 PMCID: PMC9947456 DOI: 10.1002/pld3.485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/09/2023] [Accepted: 02/06/2023] [Indexed: 05/25/2023]
Abstract
The INNER NO OUTER (INO) gene is essential for formation of the outer integument of ovules in Arabidopsis thaliana. Initially described lesions in INO were missense mutations resulting in aberrant mRNA splicing. To determine the null mutant phenotype, we generated frameshift mutations and found, in confirmation of results on another recently identified frameshift mutation, that such mutants have a phenotype identical to the most severe splicing mutant (ino-1), with effects specific to outer integument development. We show that the altered protein of an ino mRNA splicing mutant with a less severe phenotype (ino-4) does not have INO activity, and the mutant is partial because it produces a small amount of correctly spliced INO mRNA. Screening for suppressors of ino-4 in a fast neutron-mutagenized population identified a translocated duplication of the ino-4 gene, leading to an increase in the amount of this mRNA. The increased expression led to a decrease in the severity of the mutant effects, indicating that the amount of INO activity quantitatively regulates outer integument growth. The results further confirm that the role of INO in Arabidopsis development is specific to the outer integument of ovules where it quantitatively affects the growth of this structure.
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Affiliation(s)
- Debra J. Skinner
- Dept. of Molecular and Cellular BiologyUniversity of California—DavisDavisCaliforniaUSA
- Present address:
Dept. of Plant BiologyUniversity of California—DavisDavisCaliforniaUSA
| | - Trang Dang
- Dept. of Molecular and Cellular BiologyUniversity of California—DavisDavisCaliforniaUSA
- Present address:
Lark Seeds InternationalDavisCaliforniaUSA
| | - Charles S. Gasser
- Dept. of Molecular and Cellular BiologyUniversity of California—DavisDavisCaliforniaUSA
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Zhang J, Toremurat Z, Liang Y, Cheng J, Sun Z, Huang Y, Liu J, Chaogetu BUREN, Ren G, Chen H. Study on the Association between LRRC8B Gene InDel and Sheep Body Conformation Traits. Genes (Basel) 2023; 14:genes14020356. [PMID: 36833283 PMCID: PMC9956668 DOI: 10.3390/genes14020356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/23/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Marker-assisted selection is an important method for livestock breeding. In recent years, this technology has been gradually applied to livestock breeding to improve the body conformation traits. In this study, the LRRC8B (Leucine Rich Repeat Containing 8 VRAC Subunit B) gene was selected to evaluate the association between its genetic variations and the body conformation traits in two native sheep breeds in China. Four body conformation traits, including withers height, body length, chest circumference, and body weight, were collected from 269 Chaka sheep. We also collected the body length, chest width, withers height, chest depth, chest circumference, cannon bone circumference, and height at hip cross of 149 Small-Tailed Han sheep. Two different genotypes, ID and DD, were detected in all sheep. Our data showed that the polymorphism of the LRRC8B gene was significantly associated with chest depth (p < 0.05) in Small-Tailed Han sheep, and it is greater in sheep with DD than those with ID. In conclusion, our data suggested that the LRRC8B gene could serve as a candidate gene for marker-assisted selection in Small-Tailed Han sheep.
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Affiliation(s)
- Jiaqiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Zhansaya Toremurat
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yilin Liang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Zhenzhen Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yangming Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Junxia Liu
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China
| | - BUREN Chaogetu
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture, Delingha 817000, China
| | - Gang Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
- Correspondence: (G.R.); (H.C.); Tel.: +86-029-87092102 (H.C.); Fax: +86-029-87092164 (H.C.)
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
- Correspondence: (G.R.); (H.C.); Tel.: +86-029-87092102 (H.C.); Fax: +86-029-87092164 (H.C.)
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12
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In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae. Genes (Basel) 2023; 14:genes14020332. [PMID: 36833259 PMCID: PMC9956114 DOI: 10.3390/genes14020332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.
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Balimponya EG, Dwiyanti MS, Ito T, Sakaguchi S, Yamamori K, Kanaoka Y, Koide Y, Nagayoshi Y, Kishima Y. Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds. BREEDING SCIENCE 2022; 72:362-371. [PMID: 36776441 PMCID: PMC9895803 DOI: 10.1270/jsbbs.22058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 06/18/2023]
Abstract
Spontaneous mutations are stochastic phenomena that occur in every population. However, deleterious mutated allele present in seeds distributed to farmers must be detected and removed. Here, we eliminated undesirable mutations from the parent population in one generation through a strategy based on next-generation sequencing (NGS). This study dealt with a spontaneous albino mutant in the 'Hinohikari' rice variety grown at the Miyazaki Comprehensive Agricultural Experiment Station, Japan. The incidence of albinism in the population was 1.36%. NGS analysis revealed the genomic basis for differences between green and albino phenotypes. Every albino plant had a C insertion in the Snow-White Leaf1 (SWL1) gene on chromosome 4 causing a frameshift mutation. Selfing plants heterozygous for the mutant allele, swl1-R332P, resulted in a 3:1 green/albino ratio, confirming that a single recessive gene controls albinism. Ultrastructural leaf features in the swl1-R332P mutants displayed deformed chlorophyll-associated organelles in albino plants that were similar to those of previously described swl1 mutants. Detection of the causative gene and its confirmation using heterozygous progenies were completed within a year. The NGS technique outlined here facilitates rapid identification of spontaneous mutations that can occur in breeder seeds.
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Affiliation(s)
- Elias G. Balimponya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Maria S. Dwiyanti
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Toshiaki Ito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Shuntaro Sakaguchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Koichi Yamamori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yoshitaka Kanaoka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yoshifumi Nagayoshi
- Miyazaki Comprehensive Agricultural Experiment Station, Miyazaki 880-0212, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
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14
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Matos IF, Morales LMM, Santana DB, Silva GMC, Gomes MMDA, Ayub RA, Costa JH, de Oliveira JG. Ascorbate synthesis as an alternative electron source for mitochondrial respiration: Possible implications for the plant performance. FRONTIERS IN PLANT SCIENCE 2022; 13:987077. [PMID: 36507441 PMCID: PMC9727407 DOI: 10.3389/fpls.2022.987077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/31/2022] [Indexed: 06/01/2023]
Abstract
The molecule vitamin C, in the chemical form of ascorbic acid (AsA), is known to be essential for the metabolism of humans and animals. Humans do not produce AsA, so they depend on plants as a source of vitamin C for their food. The AsA synthesis pathway occurs partially in the cytosol, but the last oxidation step is physically linked to the respiratory chain of plant mitochondria. This oxidation step is catalyzed by l-galactono-1,4-lactone dehydrogenase (l-GalLDH). This enzyme is not considered a limiting step for AsA production; however, it presents a distinguishing characteristic: the l-GalLDH can introduce electrons directly into the respiratory chain through cytochrome c (Cytc) and therefore can be considered an extramitochondrial electron source that bypasses the phosphorylating Complex III. The use of Cytc as electron acceptor has been debated in terms of its need for AsA synthesis, but little has been said in relation to its impact on the functioning of the respiratory chain. This work seeks to offer a new view about the possible changes that result of the link between AsA synthesis and the mitochondrial respiration. We hypothesized that some physiological alterations related to low AsA may be not only explained by the deficiency of this molecule but also by the changes in the respiratory function. We discussed some findings showing that respiratory mutants contained changes in AsA synthesis. Besides, recent works that also indicate that the excessive electron transport via l-GalLDH enzyme may affect other respiratory pathways. We proposed that Cytc reduction by l-GalLDH may be part of an alternative respiratory pathway that is active during AsA synthesis. Also, it is proposed that possible links of this pathway with other pathways of alternative electron transport in plant mitochondria may exist. The review suggests potential implications of this relationship, particularly for situations of stress. We hypothesized that this pathway of alternative electron input would serve as a strategy for adaptation of plant respiration to changing conditions.
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Affiliation(s)
- Isabelle Faria Matos
- Plant Genetic Breeding Laboratory, Center for Agricultural Sciences and Technologies, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | - Diederson Bortolini Santana
- Plant Genetic Breeding Laboratory, Center for Agricultural Sciences and Technologies, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Gláucia Michelle Cosme Silva
- Plant Genetic Breeding Laboratory, Center for Agricultural Sciences and Technologies, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Mara Menezes de Assis Gomes
- Plant Genetic Breeding Laboratory, Center for Agricultural Sciences and Technologies, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Ricardo Antônio Ayub
- Laboratory of Biotechnology Applied to Fruit Growing, Department of Phytotechny and Phytosanitary, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - José Hélio Costa
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Universidade Federal do Ceará, Fortaleza, CE, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Jurandi Gonçalves de Oliveira
- Plant Genetic Breeding Laboratory, Center for Agricultural Sciences and Technologies, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
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15
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Lan H, Heng Y, Li J, Zhang M, Bian Y, Chu L, Jiang Y, Wang X, Xu D, Deng XW. COP1 SUPPRESSOR 6 represses the PIF4 and PIF5 action to promote light-inhibited hypocotyl growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2097-2110. [PMID: 36029156 DOI: 10.1111/jipb.13350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Light signaling precisely controls photomorphogenic development in plants. PHYTOCHROME INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) play critical roles in the regulation of this developmental process. In this study, we report CONSTITUTIVELY PHOTOMORPHOGENIC 1 SUPPRESSOR 6 (CSU6) functions as a key regulator of light signaling. Loss of CSU6 function largely rescues the cop1-6 constitutively photomorphogenic phenotype. CSU6 promotes hypocotyl growth in the dark, but inhibits hypocotyl elongation in the light. CSU6 not only associates with the promoter regions of PIF4 and PIF5 to inhibit their expression in the morning, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activation activity. CSU6 negatively controls a group of PIF4- and PIF5-regulated gene expressions. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes light-inhibited hypocotyl elongation by negatively regulating PIF4 and PIF5 transcription and biochemical activity.
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Affiliation(s)
- Hongxia Lan
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yueqin Heng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mengdi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
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16
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Liebsch D, Juvany M, Li Z, Wang HL, Ziolkowska A, Chrobok D, Boussardon C, Wen X, Law SR, Janečková H, Brouwer B, Lindén P, Delhomme N, Stenlund H, Moritz T, Gardeström P, Guo H, Keech O. Metabolic control of arginine and ornithine levels paces the progression of leaf senescence. PLANT PHYSIOLOGY 2022; 189:1943-1960. [PMID: 35604104 PMCID: PMC9342962 DOI: 10.1093/plphys/kiac244] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/11/2022] [Indexed: 06/12/2023]
Abstract
Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts-likely due to the lack of induction of amino acids (AAs) transport-can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.
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Affiliation(s)
| | | | | | - Hou-Ling Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Agnieszka Ziolkowska
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
| | - Daria Chrobok
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
| | - Clément Boussardon
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
| | - Xing Wen
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Simon R Law
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
| | - Helena Janečková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | | | - Pernilla Lindén
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden
| | - Hans Stenlund
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden
- Novo Nordisk Centre for Basic Metabolic Research, University of Copenhagen, D-2200 Copenhagen N, Denmark
| | - Per Gardeström
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-90187 Umeå, Sweden
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Yang Y, La TC, Gillman JD, Lyu Z, Joshi T, Usovsky M, Song Q, Scaboo A. Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession. FRONTIERS IN PLANT SCIENCE 2022; 13:938100. [PMID: 35968122 PMCID: PMC9372550 DOI: 10.3389/fpls.2022.938100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Modern soybean [Glycine max (L.) Merr] cultivars have low overall genetic variation due to repeated bottleneck events that arose during domestication and from selection strategies typical of many soybean breeding programs. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) alleles is a viable option to increase genetic diversity and identify new sources for traits of value. The objectives of our study were to examine the genetic architecture responsible for seed protein and oil using a recombinant inbred line (RIL) population derived from hybridizing a G. max line ('Osage') with a G. soja accession (PI 593983). Linkage mapping identified a total of seven significant quantitative trait loci on chromosomes 14 and 20 for seed protein and on chromosome 8 for seed oil with LOD scores ranging from 5.3 to 31.7 for seed protein content and from 9.8 to 25.9 for seed oil content. We analyzed 3,015 single F4:9 soybean plants to develop two residual heterozygotes derived near isogenic lines (RHD-NIL) populations by targeting nine SNP markers from genotype-by-sequencing, which corresponded to two novel quantitative trait loci (QTL) derived from G. soja: one for a novel seed oil QTL on chromosome 8 and another for a novel protein QTL on chromosome 14. Single marker analysis and linkage analysis using 50 RHD-NILs validated the chromosome 14 protein QTL, and whole genome sequencing of RHD-NILs allowed us to reduce the QTL interval from ∼16.5 to ∼4.6 Mbp. We identified two genomic regions based on recombination events which had significant increases of 0.65 and 0.72% in seed protein content without a significant decrease in seed oil content. A new Kompetitive allele-specific polymerase chain reaction (KASP) assay, which will be useful for introgression of this trait into modern elite G. max cultivars, was developed in one region. Within the significantly associated genomic regions, a total of eight genes are considered as candidate genes, based on the presence of gene annotations associated with the protein or amino acid metabolism/movement. Our results provide better insights into utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement utilizing native traits.
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Affiliation(s)
- Yia Yang
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Thang C. La
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Jason D. Gillman
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Columbia, MO, United States
| | - Zhen Lyu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
| | - Trupti Joshi
- Department of Health Management and Informatics, MU Institute of Data Science and Informatics and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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Zhou H, Zhu W, Wang X, Bian Y, Jiang Y, Li J, Wang L, Yin P, Deng XW, Xu D. A missense mutation in WRKY32 converts its function from a positive regulator to a repressor of photomorphogenesis. THE NEW PHYTOLOGIST 2022; 235:111-125. [PMID: 34935148 DOI: 10.1111/nph.17932] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mediates various cellular and physiological processes in plants by targeting a large number of substrates for ubiquitination and degradation. In this study, we reveal that a substitution of Pro for Leu at amino acid position 409 in WRKY32 largely suppresses the short hypocotyls and expanded cotyledon phenotypes of cop1-6. WRKY32P409L promotes hypocotyl growth and inhibits the opening of cotyledons in Arabidopsis. Loss of WRKY32 function mutant seedlings display elongated hypocotyls, whereas overexpression of WRKY32 leads to shortened hypocotyls. WRKY32 directly associates with the promoter regions of HY5 to activate its transcription. COP1 interacts with and targets WRKY32 for ubiquitination and degradation in darkness. WRKY32P409L exhibits enhanced DNA binding ability and affects the expression of more genes compared with WRKY32 in Arabidopsis. Our results not only reveal the basic role for WRKY32 in promoting photomorphogenesis, but also provide insights into manipulating plant growth by engineering key components of light signaling.
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Affiliation(s)
- Hua Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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19
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Huang X, Liu Y, Huang J, Fernando WGD, Li X, Xia S. Activation of NLR-Mediated Autoimmunity in Arabidopsis Early in Short Days 4 Mutant. FRONTIERS IN PLANT SCIENCE 2022; 13:881212. [PMID: 35693184 PMCID: PMC9174647 DOI: 10.3389/fpls.2022.881212] [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: 02/22/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
From a reverse genetic screen using CRISPR/Cas9 gene editing tool, we unintentionally identified an autoimmune mutant. Map-based cloning and whole-genome sequencing revealed that it contains a deletion in SMALL UBIQUITIN-RELATED MODIFIER (SUMO) protease encoding gene EARLY IN SHORT DAYS 4 (ESD4). Previous studies reported that esd4 mutants accumulate elevated levels of plant defense hormone salicylic acid (SA). However, upregulated PATHOGENESIS-RELATED GENE 1 (PR1) expression in esd4 only partly relies on SA level. In this study, we show that plant metabolite N-hydroxypipecolic acid (NHP) biosynthetic genes are upregulated in esd4, and NHP biosynthesis mutant flavin-dependent-monooxygenase 1 (fmo1) partially suppresses the autoimmune phenotypes of esd4, suggestive of a requirement of NHP signaling for the autoimmunity in esd4. As activation of nucleotide-binding leucine-rich repeat immune receptors (NLRs) are associates with the biosynthesis of SA and NHP and lipase-like protein ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) is a key component downstream of many NLRs, we examined the relationship between EDS1 and ESD4 by analyzing the eds1 esd4 double mutant. We found that eds1 largely suppresses esd4 autoimmunity and blocks the elevated expressions of SA and NHP biosynthesis-related genes in esd4. Overall, our study provides evidence supporting the hypothesis that SUMO protease ESD4 likely targets a yet to be identified guardee of NLR by removing its SUMO modification to avoid recognition by the cognate NLR. Loss of ESD4 results in activation of NLR-mediated autoimmunity.
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Affiliation(s)
- Xingchuan Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Yanan Liu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jianhua Huang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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Lee YY, Cal-Kayitmazbatir S, Francey LJ, Bahiru MS, Hayer KE, Wu G, Zeller MJ, Roberts R, Speers J, Koshalek J, Berres ME, Bittman EL, Hogenesch JB. duper is a null mutation of Cryptochrome 1 in Syrian hamsters. Proc Natl Acad Sci U S A 2022; 119:e2123560119. [PMID: 35471909 PMCID: PMC9170138 DOI: 10.1073/pnas.2123560119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
The duper mutation is a recessive mutation that shortens the period length of the circadian rhythm in Syrian hamsters. These animals show a large phase shift when responding to light pulses. Limited genetic resources for the Syrian hamster (Mesocricetus auratus) presented a major obstacle to cloning duper. This caused the duper mutation to remain unknown for over a decade. In this study, we did a de novo genome assembly of Syrian hamsters with long-read sequencing data from two different platforms, Pacific Biosciences and Oxford Nanopore Technologies. Using two distinct ecotypes and a fast homozygosity mapping strategy, we identified duper as an early nonsense allele of Cryptochrome 1 (Cry1) leading to a short, unstable protein. CRY1 is known as a highly conserved component of the repressive limb of the core circadian clock. The genome assembly and other genomic datasets generated in this study will facilitate the use of the Syrian hamster in biomedical research.
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Affiliation(s)
- Yin Yeng Lee
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Sibel Cal-Kayitmazbatir
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Lauren J. Francey
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Michael Seifu Bahiru
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
- Program in Neuroscience & Behavior, University of Massachusetts Amherst, Amherst, MA 01003
| | - Katharina E. Hayer
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | - Gang Wu
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Molly J. Zeller
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Robyn Roberts
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - James Speers
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Justin Koshalek
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Mark E. Berres
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Eric L. Bittman
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
- Program in Neuroscience & Behavior, University of Massachusetts Amherst, Amherst, MA 01003
| | - John B. Hogenesch
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
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Launay A, Jolivet S, Clément G, Zarattini M, Dellero Y, Le Hir R, Jossier M, Hodges M, Expert D, Fagard M. DspA/E-Triggered Non-Host Resistance against E. amylovora Depends on the Arabidopsis GLYCOLATE OXIDASE 2 Gene. Int J Mol Sci 2022; 23:ijms23084224. [PMID: 35457046 PMCID: PMC9029980 DOI: 10.3390/ijms23084224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 12/04/2022] Open
Abstract
DspA/E is a type three effector injected by the pathogenic bacterium Erwinia amylovora inside plant cells. In non-host Arabidopsis thaliana, DspA/E inhibits seed germination, root growth, de novo protein synthesis and triggers localized cell death. To better understand the mechanisms involved, we performed EMS mutagenesis on a transgenic line, 13-1-2, containing an inducible dspA/E gene. We identified three suppressor mutants, two of which belonged to the same complementation group. Both were resistant to the toxic effects of DspA/E. Metabolome analysis showed that the 13-1-2 line was depleted in metabolites of the TCA cycle and accumulated metabolites associated with cell death and defense. TCA cycle and cell-death associated metabolite levels were respectively increased and reduced in both suppressor mutants compared to the 13-1-2 line. Whole genome sequencing indicated that both suppressor mutants displayed missense mutations in conserved residues of Glycolate oxidase 2 (GOX2), a photorespiratory enzyme that we confirmed to be localized in the peroxisome. Leaf GOX activity increased in leaves infected with E. amylovora in a DspA/E-dependent manner. Moreover, the gox2-2 KO mutant was more sensitive to E. amylovora infection and displayed reduced JA-signaling. Our results point to a role for glycolate oxidase in type II non-host resistance and to the importance of central metabolic functions in controlling growth/defense balance.
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Affiliation(s)
- Alban Launay
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
| | - Sylvie Jolivet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
| | - Marco Zarattini
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
| | - Younes Dellero
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (Y.D.); (M.J.); (M.H.)
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Rozenn Le Hir
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
| | - Mathieu Jossier
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (Y.D.); (M.J.); (M.H.)
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Michael Hodges
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (Y.D.); (M.J.); (M.H.)
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Dominique Expert
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
| | - Mathilde Fagard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France; (A.L.); (S.J.); (G.C.); (M.Z.); (R.L.H.); (D.E.)
- Correspondence:
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22
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Development of InDel markers and establishment of a specific molecular marker of the new strain (SW-81) in Pyropia haitanensis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Ishida H, Okashita Y, Ishida H, Hayashi M, Izumi M, Makino A, Bhuiyan NH, van Wijk KJ. GFS9 Affects Piecemeal Autophagy of Plastids in Young Seedlings of Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2021; 62:1372-1386. [PMID: 34086965 DOI: 10.1093/pcp/pcab084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
Chloroplasts, and plastids in general, contain abundant protein pools that can be major sources of carbon and nitrogen for recycling. We have previously shown that chloroplasts are partially and sequentially degraded by piecemeal autophagy via the Rubisco-containing body. This degradation occurs during plant development and in response to the environment; however, little is known about the fundamental underlying mechanisms. To discover the mechanisms of piecemeal autophagy of chloroplasts/plastids, we conducted a forward-genetics screen following ethyl-methanesulfonate mutagenesis of an Arabidopsis (Arabidopsis thaliana) transgenic line expressing chloroplast-targeted green fluorescent protein (CT-GFP). This screen allowed us to isolate a mutant, gfs9-5, which hyperaccumulated cytoplasmic bodies labeled with CT-GFP of up to 1.0 μm in diameter in the young seedlings. We termed these structures plastid bodies (PBs). The mutant was defective in a membrane-trafficking factor, green fluorescent seed 9 (GFS9), and PB accumulation in gfs9-5 was promoted by darkness and nutrient deficiency. Transmission electron microscopy indicated that gfs9-5 hyperaccumulated structures corresponding to autophagosomes and PBs. gfs9-5 hyperaccumulated membrane-bound endogenous ATG8 proteins, transgenic yellow fluorescent protein (YFP)-ATG8e proteins and autophagosome-like structures labeled with YFP-ATG8e. The YFP-ATG8e signal was associated with the surface of plastids and their protrusions in gfs9-5. Double mutants of gfs9 and autophagy-defective 5 did not accumulate PBs. In gfs9-5, the YFP-ATG8e proteins and PBs could be delivered to the vacuole and autophagic flux was increased. We discuss a possible connection between GFS9 and autophagy and propose a potential use of gfs9-5 as a new tool to study piecemeal plastid autophagy.
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Affiliation(s)
- Hiroyuki Ishida
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Sendai 980-8572, Japan
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yu Okashita
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Sendai 980-8572, Japan
| | - Hiromi Ishida
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Sendai 980-8572, Japan
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Amane Makino
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Sendai 980-8572, Japan
| | - Nazmul H Bhuiyan
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
- Eurofins Lancaster Lab PSS, Richmond, VA, USA
| | - Klaas J van Wijk
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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24
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Xin Z, Wang M, Cuevas HE, Chen J, Harrison M, Pugh NA, Morris G. Sorghum genetic, genomic, and breeding resources. PLANTA 2021; 254:114. [PMID: 34739592 PMCID: PMC8571242 DOI: 10.1007/s00425-021-03742-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/28/2021] [Indexed: 05/24/2023]
Abstract
Sorghum research has entered an exciting and fruitful era due to the genetic, genomic, and breeding resources that are now available to researchers and plant breeders. As the world faces the challenges of a rising population and a changing global climate, new agricultural solutions will need to be developed to address the food and fiber needs of the future. To that end, sorghum will be an invaluable crop species as it is a stress-resistant C4 plant that is well adapted for semi-arid and arid regions. Sorghum has already remained as a staple food crop in many parts of Africa and Asia and is critically important for animal feed and niche culinary applications in other regions, such as the United States. In addition, sorghum has begun to be developed into a promising feedstock for forage and bioenergy production. Due to this increasing demand for sorghum and its potential to address these needs, the continuous development of powerful community resources is required. These resources include vast collections of sorghum germplasm, high-quality reference genome sequences, sorghum association panels for genome-wide association studies of traits involved in food and bioenergy production, mutant populations for rapid discovery of causative genes for phenotypes relevant to sorghum improvement, gene expression atlas, and online databases that integrate all resources and provide the sorghum community with tools that can be used in breeding and genomic studies. Used in tandem, these valuable resources will ensure that the rate, quality, and collaborative potential of ongoing sorghum improvement efforts is able to rival that of other major crops.
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Affiliation(s)
- Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA.
| | - Mingli Wang
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA, 30223, USA
| | - Hugo E Cuevas
- Tropical Agriculture Research Station, USDA-ARS, Mayagüez, 00680, Puerto Rico
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA
| | - Melanie Harrison
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA, 30223, USA
| | - N Ace Pugh
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA
| | - Geoffrey Morris
- Crop Quantitative Genomics, Soil and Crop Sciences, Colorado State University, Plant Sciences Building, Fort Collins, CO, 80523, USA
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25
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Chen JB, Bao SW, Fang YL, Wei LY, Zhu WS, Peng YL, Fan J. An LRR-only protein promotes NLP-triggered cell death and disease susceptibility by facilitating oligomerization of NLP in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:1808-1822. [PMID: 34403491 DOI: 10.1111/nph.17680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) constitute a superfamily of proteins toxic to dicot plants, but the molecular basis of this toxicity remains obscure. Using quantitative trait locus (QTL) analysis we investigated the genetic variation underlying ion leakage in Arabidopsis plants elicited with MoNLP1 derived from Magnaporthe oryzae. The QTL conditioning MoNLP1 toxicity was positionally cloned and further characterized to elucidate its mode of action. MoNLP1-triggered cell death varied significantly across > 250 Arabidopsis accessions and three QTLs were identified conferring the observed variation. The QTL on chromosome 4 was uncovered to encode a leucine-rich repeat (LRR)-only protein designated as NTCD4, which shares high sequence identity with a set of nucleotide-binding LRR proteins. NTCD4 was secreted into the apoplast and physically interacted with multiple NLPs. Apoplastic NTCD4 facilitated the oligomerization of NLP, which was closely associated with toxicity in planta. The natural genetic variation causing D3N change in NTCD4 reduced the secretion efficiency of NTCD4 and the infection of Botrytis cinerea on Arabidopsis plants. These observations demonstrate that the plant-derived NTCD4 is recruited by NLPs to promote toxicity via facilitating their oligomerization, which extends our understanding of a key step in the toxic mode of action of NLPs.
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Affiliation(s)
- Jun-Bin Chen
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Shu-Wen Bao
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Ya-Li Fang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Lu-Yang Wei
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Wang-Sheng Zhu
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - You-Liang Peng
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, 100193, Beijing, China
| | - Jun Fan
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, 100193, Beijing, China
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26
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Nishigaki N, Yoshimi Y, Kuki H, Kunieda T, Hara-Nishimura I, Tsumuraya Y, Takahashi D, Dupree P, Kotake T. Galactoglucomannan structure of Arabidopsis seed-coat mucilage in GDP-mannose synthesis impaired mutants. PHYSIOLOGIA PLANTARUM 2021; 173:1244-1252. [PMID: 34380178 DOI: 10.1111/ppl.13519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Cell-wall polysaccharides are synthesized from nucleotide sugars by glycosyltransferases. However, in what way the level of nucleotide sugars affects the structure of the polysaccharides is not entirely clear. guanosine diphosphate (GDP)-mannose (GDP-Man) is one of the major nucleotide sugars in plants and serves as a substrate in the synthesis of mannan polysaccharides. GDP-Man is synthesized from mannose 1-phosphate and GTP by a GDP-Man pyrophosphorylase, VITAMIN C DEFECTIVE1 (VTC1), which is positively regulated by the interacting protein KONJAC1 (KJC1) in Arabidopsis. Since seed-coat mucilage can serve as a model of the plant cell wall, we examined the influence of vtc1 and kjc1 mutations on the synthesis of mucilage galactoglucomannan. Sugar composition analysis showed that mannose content in adherent mucilage of kjc1 and vtc1 mutants was only 42% and 11% of the wild-type, respectively, indicating a drastic decrease of galactoglucomannan. On the other hand, structural analysis based on specific oligosaccharides released by endo-β-1,4-mannanase indicated that galactoglucomannan had a patterned glucomannan backbone consisting of alternating residues of glucose and mannose and the frequency of α-galactosyl branches was also similar to the wild type structure. These results suggest that the structure of mucilage galactoglucomannan is mainly determined by properties of glycosyltransferases rather than the availability of nucleotide sugars.
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Affiliation(s)
- Naho Nishigaki
- Graduate School of Science and Engineering, Saitama, Japan
| | | | - Hiroaki Kuki
- Graduate School of Science and Engineering, Saitama, Japan
| | - Tadashi Kunieda
- Faculty of Science and Engineering, Konan University, Kobe, Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | | | | | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Toshihisa Kotake
- Graduate School of Science and Engineering, Saitama, Japan
- Green Biology Research Center, Saitama University, Saitama, Japan
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27
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Schleicher S, Binder S. In Arabidopsis thaliana mitochondria 5' end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8. PLANT MOLECULAR BIOLOGY 2021; 106:335-348. [PMID: 33909186 PMCID: PMC8270843 DOI: 10.1007/s11103-021-01153-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
RNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria. In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5' termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5' extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5' end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5' terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5' end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5' end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5' end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5' terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.
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Affiliation(s)
- Sarah Schleicher
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany.
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28
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Itoh RD, Nakajima KP, Sasaki S, Ishikawa H, Kazama Y, Abe T, Fujiwara MT. TGD5 is required for normal morphogenesis of non-mesophyll plastids, but not mesophyll chloroplasts, in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:237-255. [PMID: 33884686 DOI: 10.1111/tpj.15287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Stromules are dynamic membrane-bound tubular structures that emanate from plastids. Stromule formation is triggered in response to various stresses and during plant development, suggesting that stromules may have physiological and developmental roles in these processes. Despite the possible biological importance of stromules and their prevalence in green plants, their exact roles and formation mechanisms remain unclear. To explore these issues, we obtained Arabidopsis thaliana mutants with excess stromule formation in the leaf epidermis by microscopy-based screening. Here, we characterized one of these mutants, stromule biogenesis altered 1 (suba1). suba1 forms plastids with severely altered morphology in a variety of non-mesophyll tissues, such as leaf epidermis, hypocotyl epidermis, floral tissues, and pollen grains, but apparently normal leaf mesophyll chloroplasts. The suba1 mutation causes impaired chloroplast pigmentation and altered chloroplast ultrastructure in stomatal guard cells, as well as the aberrant accumulation of lipid droplets and their autophagic engulfment by the vacuole. The causal defective gene in suba1 is TRIGALACTOSYLDIACYLGLYCEROL5 (TGD5), which encodes a protein putatively involved in the endoplasmic reticulum (ER)-to-plastid lipid trafficking required for the ER pathway of thylakoid lipid assembly. These findings suggest that a non-mesophyll-specific mechanism maintains plastid morphology. The distinct mechanisms maintaining plastid morphology in mesophyll versus non-mesophyll plastids might be attributable, at least in part, to the differential contributions of the plastidial and ER pathways of lipid metabolism between mesophyll and non-mesophyll plastids.
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Affiliation(s)
- Ryuuichi D Itoh
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Kohdai P Nakajima
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Shun Sasaki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo, 102-8554, Japan
| | - Hiroki Ishikawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo, 102-8554, Japan
| | - Yusuke Kazama
- Nishina Center, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Tomoko Abe
- Nishina Center, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Makoto T Fujiwara
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo, 102-8554, Japan
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Yu L, Nie Y, Jiao J, Jian L, Zhao J. The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes. Int J Mol Sci 2021; 22:ijms22126224. [PMID: 34207582 PMCID: PMC8226582 DOI: 10.3390/ijms22126224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods and developed a sequencing-based mapping method (SBM) for identifying the location of plant variants effectively with a small population and low cost, which is very user-friendly for most popular laboratories. This method used the whole-genome sequencing data of two pooled populations to screen out enough markers. These markers were used to identify and narrow the candidate region by analyzing the marker-indexes and recombinants. Finally, the possible mutational sites were identified using the whole-genome sequencing data and verified in individual mutants. To elaborate the new method, we displayed the cloned processes in one Arabidopsis heterozygous mutant and two rice homozygous mutants. Thus, the sequencing-based mapping method could clone effectively different types of plant mutations and was a powerful tool for studying the functions of plant genes in the species with known genomic sequences.
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30
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Gaillochet C, Develtere W, Jacobs TB. CRISPR screens in plants: approaches, guidelines, and future prospects. THE PLANT CELL 2021; 33:794-813. [PMID: 33823021 PMCID: PMC8226290 DOI: 10.1093/plcell/koab099] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-associated systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in the development of powerful new screens to test gene functions at the genomic scale. While there is tremendous potential to map and interrogate gene regulatory networks at unprecedented speed and scale using CRISPR screens, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools, and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports describing the use of this strategy to generate mutant knockout collections or to diversify DNA sequences. In addition, we provide insight into how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene functions in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the numerous genomic profiles that have been generated over the past two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will lead to great advances in functional and synthetic biology.
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Affiliation(s)
- Christophe Gaillochet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
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31
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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Yi F, Gu W, Li J, Chen J, Hu L, Cui Y, Zhao H, Guo Y, Lai J, Song W. Miniature Seed6, encoding an endoplasmic reticulum signal peptidase, is critical in seed development. PLANT PHYSIOLOGY 2021; 185:985-1001. [PMID: 33793873 PMCID: PMC8133640 DOI: 10.1093/plphys/kiaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/15/2020] [Indexed: 05/15/2023]
Abstract
Endoplasmic reticulum (ER) type I signal peptidases (ER SPases I) are vital proteases that cleave signal peptides from secreted proteins. However, the specific function of ER SPase I in plants has not been genetically characterized, and the substrate is largely unknown. Here, we report the identification of a maize (Zea mays) miniature seed6 (mn6) mutant. The loss-of-function mn6 mutant exhibited severely reduced endosperm size. Map-based cloning and molecular characterization indicated that Mn6 is an S26-family ER SPase I, with Gly102 (box E) in Mn6 critical for protein function during processing. Mass spectrometric and immunoprecipitation analyses revealed that Mn6 is predominantly involved in processing carbohydrate synthesis-related proteins, including the cell wall invertase miniature seed1 (Mn1), which is specifically expressed in the basal endosperm transfer layer. RNA and protein expression levels of Mn1 were both significantly downregulated in the mn6 mutant. Due to the significant reduction in cell wall invertase activity in the transfer cell layer, mutation of Mn6 caused dramatic defects in endosperm development. These results suggest that proper maturation of Mn1 by Mn6 may be a crucial step for proper seed filling and maize development.
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China
| | - Wei Gu
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Jianfang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Jian Chen
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Li Hu
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Yang Cui
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Author for communication:
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Babu P, Baranwal DK, Harikrishna, Pal D, Bharti H, Joshi P, Thiyagarajan B, Gaikwad KB, Bhardwaj SC, Singh GP, Singh A. Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:567147. [PMID: 33013989 PMCID: PMC7516254 DOI: 10.3389/fpls.2020.567147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2023]
Abstract
Wheat is an important source of dietary protein and calories for the majority of the world's population. It is one of the largest grown cereal in the world occupying over 215 M ha. Wheat production globally is challenged by biotic stresses such as pests and diseases. Of the 50 diseases of wheat that are of economic importance, the three rust diseases are the most ubiquitous causing significant yield losses in the majority of wheat production environments. Under severe epidemics they can lead to food insecurity threats amid the continuous evolution of new races of the pathogens, shifts in population dynamics and their virulence patterns, thereby rendering several effective resistance genes deployed in wheat breeding programs vulnerable. This emphasizes the need to identify, characterize, and deploy effective rust-resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance has been marked as eco-friendly and to curb the further evolution of rust pathogens. Deployment of multiple rust resistance genes including major and minor genes in wheat lines could enhance the durability of resistance thereby reducing pathogen evolution. Advances in next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The sequence alignment of the wheat genome is the most important landmark which will enable genomics to identify marker-trait associations, candidate genes and enhanced breeding values in genomic selection (GS) studies. High throughput genotyping platforms have demonstrated their role in the estimation of genetic diversity, construction of the high-density genetic maps, dissecting polygenic traits, and better understanding their interactions through GWAS (genome-wide association studies) and QTL mapping, and isolation of R genes. Application of breeder's friendly KASP assays in the wheat breeding program has expedited the identification and pyramiding of rust resistance alleles/genes in elite lines. The present review covers the evolutionary trends of the rust pathogen and contemporary wheat varieties, and how these research strategies galvanized to control the wheat killer genus Puccinia. It will also highlight the outcome and research impact of cost-effective NGS technologies and cloning of rust resistance genes amid the public availability of common and tetraploid wheat reference genomes.
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Affiliation(s)
- Prashanth Babu
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Harikrishna
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Dharam Pal
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Hemlata Bharti
- Directorate of Medicinal and Aromatic Plants Research (ICAR), Anand, India
| | - Priyanka Joshi
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | | | | | | | - Anupam Singh
- DCM SHRIRAM-Bioseed Research India, ICRISAT, Hyderabad, India
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Mao C, Ju X, Cheng H, Huang X, Jiang F, Yao Y, Lan X, Song E. Determination of genetic variation within the DYRK2 gene and its associations with milk traits in cattle. Arch Anim Breed 2020; 63:315-323. [PMID: 32964102 PMCID: PMC7500071 DOI: 10.5194/aab-63-315-2020] [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: 02/05/2020] [Accepted: 07/25/2020] [Indexed: 11/11/2022] Open
Abstract
To speed up the progress of marker-assisted selection (MAS) in cattle
breeding, the dual-specificity tyrosine phosphorylation-regulated kinase 2
(DYRK2), cadherin 2 (CDH2), and kinesin family member 1A (KIF1A) genes were chosen based
on our pervious genome-wide association study (GWAS) analysis results.
DYRK2 is a kinase that may participate in cell growth and/or development; it
shows phosphorylation activity toward serine, threonine, and tyrosine
fragments of proteins, and it is different from other protein kinases. The CDH2 gene
encodes a classic cadherin, which is a member of the cadherin superfamily. The
protein encoded by KIF1A is a member of the kinesin family and plays a role in
the transportation of membrane organelles along axon microtubules. We
detected insertion/deletion (InDel) variation in these three candidate genes
in 438 individual cattle (Xinjiang Brown cattle and Wagyu × Luxi
crossbreed cattle). Only DYRK2-P3-11 bp was polymorphic and genotyped. The
polymorphism information content of DYRK2-P3-11 bp was 0.336. Correlation analyses
showed that InDel polymorphism was significantly associated with six
different milk traits. These findings may aid future analyses of InDel
genotypes in cattle breeds, and speed up the progress of MAS in cattle
breeding.
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Affiliation(s)
- Cui Mao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Xing Ju
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, 830000, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haijian Cheng
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Xixia Huang
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, 830000, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Yuni Yao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Enliang Song
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China.,College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250000, China
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Wang W, Ryu KH, Bruex A, Barron C, Schiefelbein J. Molecular Basis for a Cell Fate Switch in Response to Impaired Ribosome Biogenesis in the Arabidopsis Root Epidermis. THE PLANT CELL 2020; 32:2402-2423. [PMID: 32371546 PMCID: PMC7346552 DOI: 10.1105/tpc.19.00773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/30/2020] [Accepted: 04/29/2020] [Indexed: 05/12/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) root epidermis consists of a position-dependent pattern of root hair cells and non-hair cells. Underlying this cell type patterning is a network of transcription factors including a central MYB-basic helix-loop-helix-WD40 complex containing WEREWOLF (WER), GLABRA3 (GL3)/ENHANCER OF GLABRA3, and TRANSPARENT TESTA GLABRA1. In this study, we used a genetic enhancer screen to identify apum23-4, a mutant allele of the ribosome biogenesis factor (RBF) gene ARABIDOPSIS PUMILIO23 (APUM23), which caused prospective root hair cells to instead adopt the non-hair cell fate. We discovered that this cell fate switch relied on MYB23, a MYB protein encoded by a WER target gene and acting redundantly with WER. In the apum23-4 mutant, MYB23 exhibited ectopic expression that was WER independent and instead required ANAC082, a recently identified ribosomal stress response mediator. We examined additional RBF mutants that produced ectopic non-hair cells and determined that this cell fate switch is generally linked to defects in ribosome biogenesis. Furthermore, the flagellin peptide flg22 triggers the ANAC082-MYB23-GL2 pathway. Taken together, our study provides a molecular explanation for root epidermal cell fate switch in response to ribosomal defects and, more generally, it demonstrates a novel regulatory connection between stress conditions and cell fate control in plants.
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Affiliation(s)
- Wenjia Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
- Joint BioEnergy Institute, Emeryville, California 94608
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Angela Bruex
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Christa Barron
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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Dinh HX, Singh D, Periyannan S, Park RF, Pourkheirandish M. Molecular genetics of leaf rust resistance in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2035-2050. [PMID: 32128617 DOI: 10.1007/s00122-020-03570-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
The demand for cereal grains as a main source of energy continues to increase due to the rapid increase in world population. The leaf rust diseases of cereals cause significant yield losses, posing challenges for global food security. The deployment of resistance genes has long been considered as the most effective and sustainable way to control cereal leaf rust diseases. While genetic resistance has reduced the impact of these diseases in agriculture, losses still occur due to the ability of the respective rust pathogens to change and render resistance genes ineffective plus the slow pace at which resistance genes are discovered and characterized. This article highlights novel recently developed strategies based on advances in genome sequencing that have accelerated gene isolation by overcoming the complexity of cereal genomes. The leaf rust resistance genes cloned so far from wheat and barley belong to various protein families, including nucleotide binding site/leucine-rich repeat receptors and transporters. We review recent studies that are beginning to reveal the defense mechanisms conferred by the leaf rust resistance genes identified to date in cereals and their roles in either pattern-triggered immunity or effector-triggered immunity.
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Affiliation(s)
- Hoan X Dinh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Davinder Singh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra, 2601, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia.
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Autophagy-Related 2 Regulates Chlorophyll Degradation under Abiotic Stress Conditions in Arabidopsis. Int J Mol Sci 2020; 21:ijms21124515. [PMID: 32630439 PMCID: PMC7350272 DOI: 10.3390/ijms21124515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/14/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Chloroplasts are extraordinary organelles for photosynthesis and nutrient storage in plants. During leaf senescence or under stress conditions, damaged chloroplasts are degraded and provide nutrients for developing organs. Autophagy is a high-throughput degradation pathway for intracellular material turnover in eukaryotes. Along with chloroplast degradation, chlorophyll, an important component of the photosynthetic machine, is also degraded. However, the chlorophyll degradation pathways under high light intensity and high temperature stress are not well known. Here, we identified and characterized a novel Arabidopsis mutant, sl2 (seedling lethal 2), showing defective chloroplast development and accelerated chlorophyll degradation. Map-based cloning combined with high-throughput sequencing analysis revealed that a 118.6 kb deletion region was associated with the phenotype of the mutant. Complementary experiments confirmed that the loss of function of ATG2 was responsible for accelerating chlorophyll degradation in sl2 mutants. Furthermore, we analyzed chlorophyll degradation under abiotic stress conditions and found that both chloroplast vesiculation and autophagy take part in chlorophyll degradation under high light intensity and high temperature stress. These results enhanced our understanding of chlorophyll degradation under high light intensity and high temperature stress.
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Tanaka T, Nishii Y, Matsuo H, Takahashi T. Easy-to-Use InDel Markers for Genetic Mapping between Col-0 and L er-0 Accessions of Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9060779. [PMID: 32580428 PMCID: PMC7355782 DOI: 10.3390/plants9060779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/16/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Map-based gene cloning has played a key role in many genetic studies using the model plant, Arabidopsis thaliana. In the post- next generation sequencing era, identification of point mutations and their corresponding genes is increasingly becoming a powerful and important approach to define plant gene function. To perform initial mapping experiments efficiently on Arabidopsis mutants, enrichment of easy-to-use and reliable polymorphic DNA markers would be desirable. We present here a list of InDel polymorphic markers between Col-0 and Ler-0 accessions that can be detected in standard agarose gel electrophoresis.
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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Liu X, Liu L, Wang J, Cui H, Chu H, Bi H, Zhao G, Wen J. Genome-Wide Association Study of Muscle Glycogen in Jingxing Yellow Chicken. Genes (Basel) 2020; 11:genes11050497. [PMID: 32366026 PMCID: PMC7290304 DOI: 10.3390/genes11050497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 01/13/2023] Open
Abstract
Glucose metabolism plays an important role in many normal and pathological physiological processes in the body. The breakdown and synthesis of muscle glycogen provides ATP for muscle activities. A genome-wide association study for muscle glycogen was performed in 473 Jingxing yellow chickens to identify significant single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) involved in muscle glycogen metabolism. A total of nine SNPs (p < 1/699341) and three INDELs (p < 1/755733) reached a significant level of potential association. The following results were obtained through a series of analyses, including additive effects and gene function annotation. Two significant SNPs were found in introns 12 and 13 of copine 4 (CPNE4) on chromosome 2. The wild-type and mutant individuals had significant differences in glycogen metabolism at two loci (p < 0.01 for both). Individuals carrying two mutations had increased muscle glycogen content. According to the gene annotation of chromosome 11, there is a significant INDEL in intron 6 of naked cuticle homolog 1 (NKD1). After the INDEL mutation, the glycogen content increased significantly. There was a significant difference between wild-type and mutant individuals (p < 0.01). These mutations likely affecting two genes (CPNE4 and NKD1) may affect glycogen storage in a pleiotropic manner. Gene annotation indicates that CPNE4 and NKD1 may affect the process of glucose metabolism. Our findings contribute to understanding the genetic regulation of muscle glycogen metabolism and provide theoretical support.
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Affiliation(s)
- Xiaojing Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.L.); (L.L.); (J.W.); (H.C.); (G.Z.)
| | - Lu Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.L.); (L.L.); (J.W.); (H.C.); (G.Z.)
| | - Jie Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.L.); (L.L.); (J.W.); (H.C.); (G.Z.)
| | - Huanxian Cui
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.L.); (L.L.); (J.W.); (H.C.); (G.Z.)
| | - Huanhuan Chu
- Yantai Dadi Animal Husbrandry Co., Ltd., Yantai 1265100, China; (H.C.); (H.B)
| | - Huijuan Bi
- Yantai Dadi Animal Husbrandry Co., Ltd., Yantai 1265100, China; (H.C.); (H.B)
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.L.); (L.L.); (J.W.); (H.C.); (G.Z.)
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.L.); (L.L.); (J.W.); (H.C.); (G.Z.)
- Correspondence:
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Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing. PLoS One 2020; 15:e0219884. [PMID: 32275655 PMCID: PMC7147731 DOI: 10.1371/journal.pone.0219884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/11/2019] [Indexed: 12/05/2022] Open
Abstract
Among the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the ‘Ruby-3’, ‘Yongfeng male’, ‘Kuilv male’, and ‘Hongbei male’ genomes, respectively, compared with the reference genome sequence of cv ‘Hongyang’. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit.
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Li L, Qi Z, Chai L, Chen Z, Wang T, Zhang M, You M, Peng H, Yao Y, Hu Z, Xin M, Guo W, Sun Q, Ni Z. The semidominant mutation w5 impairs epicuticular wax deposition in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1213-1225. [PMID: 31965231 DOI: 10.1007/s00122-020-03543-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/10/2020] [Indexed: 05/14/2023]
Abstract
The semidominant EMS-induced mutant w5 affects epicuticular wax deposition and mapped to an approximately 194-kb region on chromosome 7DL. Epicuticular wax is responsible for the glaucous appearance of plants and protects against many biotic and abiotic stresses. In wheat (Triticum aestivum L.), β-diketone is a major component of epicuticular wax in adult plants and contributes to the glaucousness of the aerial organs. In the present study, we identified an ethyl methanesulfonate-induced epicuticular wax-deficient mutant from the elite wheat cultivar Jimai22. Compared to wild-type Jimai22, the mutant lacked β-diketone and failed to form the glaucous coating on all aerial organs. The mutant also had significantly increased in cuticle permeability, based on water loss and chlorophyll efflux. Genetic analysis indicated that the mutant phenotype is controlled by a single, semidominant gene on the long arm of chromosome 7D, which was not allelic to the known wax gene loci W1-W4, and was therefore designated W5. W5 was finely mapped to an ~ 194-kb region (flanked by the molecular markers SSR2 and STARP11) that harbored four annotated genes according to the reference genome of Chinese Spring (RefSeq v1.0). Collectively, these data will broaden the knowledge of the genetic basis underlying epicuticular wax deposition in wheat.
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Affiliation(s)
- Linghong Li
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongqi Qi
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Mingyi Zhang
- Dryland Agricultural Research Centre, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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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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Liu S, An Y, Tong W, Qin X, Samarina L, Guo R, Xia X, Wei C. Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research. BMC Genomics 2019; 20:935. [PMID: 31805860 PMCID: PMC6896268 DOI: 10.1186/s12864-019-6347-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.
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Affiliation(s)
- Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Xiuju Qin
- Guangxi LuYI Institute of Tea Tree Species, 17 Jinji Road, Guilin, China
| | - Lidia Samarina
- Department of Biotechnology, Russian Research Institute of Floriculture and Subtropical Crops, Sochi, Russia
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, China.
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Wang P, Yao FJ, Lu LX, Fang M, Zhang YM, Khan AA, Kong XH, Yu J, Jiang WZ, Kitamoto Y, Honda Y. Map-based cloning of genes encoding key enzymes for pigment synthesis in Auricularia cornea. Fungal Biol 2019; 123:843-853. [PMID: 31627860 DOI: 10.1016/j.funbio.2019.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/10/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
Color is an important quality attribute of fungi, and a useful marker for classification, genetic, and molecular research. However, there is much debate over which enzymes play key regulatory roles in pigment synthesis pathways among different fungi and even within the same species. Auricularia cornea is the most widely cultivated mushroom in the genus Auricularia; 1.834 million tons of this mushroom were produced in 2016 in China. Thus, systematic studies on its color inheritance and the genes encoding key enzymes for pigment synthesis have high scientific and economic value. In this study, the white strain ACW001 and the purple strain ACP004 of A. cornea were used as dikaryotic parents. Selfing populations of ACW001 and ACP004 were constructed with their monokaryotic strains. The fruiting body color of the two populations was consistent with that of their parents, confirming that the two parents were color homozygotes. All strains in the hybrid population of the two parents produced purple fruiting bodies. A robust hybrid strain (ACW001-33×ACP004-33) was selected from the hybrid population, and 87 monokaryotic strains of ACW001-33×ACP004-33 were obtained as a mapping population. Finally, a testcross population was constructed by crossing the mapping population with the test strain ACW001-9. The color genotype of each monokaryotic strain in the mapping population was identified by a fruiting test. The genomes of the two monokaryotic strains ACW001-33 and ACP004-33 were sequenced, and then simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker primers were developed. Then, 88 pairs of primers that could distinguish the genotypes of the mapping population were used to construct a genetic linkage map. The genetic linkage map consisted of 12 linkage groups (LGs) spanning 1315.2 cM. The color control locus was preliminarily located at 24.5 cM of the 11th LG. Fine-mapping primers were designed based on sequence differences between ACW001-33 and ACP004-33 in the primary location region. Four color control candidate genes were located in an 8.2-kb region of ACW001-33_contig733 and a 9.2-kb region of ACP004-33_contig802. Homologous alignment and prediction of conserved domain analyses indicated that two of the color control candidate genes encoded proteins with unknown function, and the other two, ACP004_g11815 and ACP004_g11816, encoded glutamyl aminotransferases. These two genes were consecutively arranged on ACP004-33_contig802, and were likely to encode key enzymes in the γ-glutamine-4-hydroxy-benzoate (GHB) pigment synthesis pathway. Primers were designed from the flanking sequences of the two genes and used to analyze the testcross population. Products were amplified only from the 30 testcross strains with purple fruiting bodies, confirming the accuracy of the localization results. We discuss the deficiencies and advantages of map-based cloning in fungi vs. plants, and summarize the steps and requirements of the map-based cloning method for fungi. This study has provided novel ideas and methods for locating functional genes in fungi.
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Affiliation(s)
- Peng Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Fang-Jie Yao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China; College of Horticulture, Jilin Agricultural University, Changchun, 130118, China.
| | - Li-Xin Lu
- College of Horticulture, Jilin Agricultural University, Changchun, 130118, China
| | - Ming Fang
- College of Horticulture, Jilin Agricultural University, Changchun, 130118, China
| | - You-Min Zhang
- College of Horticulture, Jilin Agricultural University, Changchun, 130118, China.
| | - Asif Ali Khan
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Xiang-Hui Kong
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Jing Yu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Wan-Zhu Jiang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Yutaka Kitamoto
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto, 6068502, Japan
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Hickey LT, N Hafeez A, Robinson H, Jackson SA, Leal-Bertioli SCM, Tester M, Gao C, Godwin ID, Hayes BJ, Wulff BBH. Breeding crops to feed 10 billion. Nat Biotechnol 2019; 37:744-754. [PMID: 31209375 DOI: 10.1038/s41587-019-0152-9] [Citation(s) in RCA: 349] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
Crop improvements can help us to meet the challenge of feeding a population of 10 billion, but can we breed better varieties fast enough? Technologies such as genotyping, marker-assisted selection, high-throughput phenotyping, genome editing, genomic selection and de novo domestication could be galvanized by using speed breeding to enable plant breeders to keep pace with a changing environment and ever-increasing human population.
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Affiliation(s)
- Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
| | | | | | - Scott A Jackson
- Center for Applied Genetic Technologies, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, Department of Plant Pathology, University of Georgia, Athens, GA, USA
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Ian D Godwin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
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Peng K, Zhang GL, Yu T, Cao Y, Yu YS, Chen H, Lei CZ, Lan XY, Zhao YM. Detection of InDel variations within seven candidate genes and their associations with phenotypic traits in three cattle breeds. Anim Biotechnol 2019; 31:463-471. [PMID: 31159648 DOI: 10.1080/10495398.2019.1620258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Xinjiang brown cattle, Red steppe cattle, and Yunling cattle are indigenous cultivated cattle breeds in Chinese frontier provinces, and they produce high-grade beef and milk products, however, their genetic diversity in many important genes related to excellent meat and milk production is still unknown. Our previous studies have found that several candidate genes (e.g., SREBP1c and PAX7) were associated with bovine economically important phenotypic traits, but none has been reported in the above-mentioned three cattle breeds. Since the InDel (insertion/deletion) marker becomes a useful tool applied in the animal molecular breeding, herein, we firstly found that the InDel variations of seven candidate genes in these cattle. Results showed that the genotypic and allelic distributions of these seven genes were remarkably different among these three cattle (p < 0.05 or p < 0.01). Furthermore, the InDel variations of SREBP1c and PAX7 genes were significantly associated with eight phenotypic traits in Xinjiang brown cattle (p < 0.05 or p < 0.01), respectively, suggesting that they can become the useful DNA markers.
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Affiliation(s)
- Kun Peng
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Guo-Liang Zhang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
| | - Ting Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yang Cao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
| | - Yong-Sheng Yu
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yu-Min Zhao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
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Xu W, He H, Zheng L, Xu JW, Lei CZ, Zhang GM, Dang RH, Niu H, Qi XL, Chen H, Huang YZ. Detection of 19-bp deletion within PLAG1 gene and its effect on growth traits in cattle. Gene 2018; 675:144-149. [DOI: 10.1016/j.gene.2018.06.041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/10/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022]
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49
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Itoh RD, Ishikawa H, Nakajima KP, Moriyama S, Fujiwara MT. Isolation and analysis of a stromule-overproducing Arabidopsis mutant suggest the role of PARC6 in plastid morphology maintenance in the leaf epidermis. PHYSIOLOGIA PLANTARUM 2018; 162:479-494. [PMID: 28984364 DOI: 10.1111/ppl.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/24/2017] [Accepted: 10/02/2017] [Indexed: 05/10/2023]
Abstract
Stromules, or stroma-filled tubules, are thin extensions of the plastid envelope membrane that are most frequently observed in undifferentiated or non-mesophyll cells. The formation of stromules is developmentally regulated and responsive to biotic and abiotic stress; however, the physiological roles and molecular mechanisms of the stromule formation remain enigmatic. Accordingly, we attempted to obtain Arabidopsis thaliana mutants with aberrant stromule biogenesis in the leaf epidermis. Here, we characterize one of the obtained mutants. Plastids in the leaf epidermis of this mutant were giant and pleomorphic, typically having one or more constrictions that indicated arrested plastid division, and usually possessed one or more extremely long stromules, which indicated the deregulation of stromule formation. Genetic mapping, whole-genome resequencing-aided exome analysis, and gene complementation identified PARC6/CDP1/ARC6H, which encodes a vascular plant-specific, chloroplast division site-positioning factor, as the causal gene for the stromule phenotype. Yeast two-hybrid assay and double mutant analysis also identified a possible interaction between PARC6 and MinD1, another known chloroplast division site-positioning factor, during the morphogenesis of leaf epidermal plastids. To the best of our knowledge, PARC6 is the only known A. thaliana chloroplast division factor whose mutations more extensively affect the morphology of plastids in non-mesophyll tissue than in mesophyll tissue. Therefore, the present study demonstrates that PARC6 plays a pivotal role in the morphology maintenance and stromule regulation of non-mesophyll plastids.
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Affiliation(s)
- Ryuuichi D Itoh
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Hiroki Ishikawa
- Department of Biology, Graduate School of Science and Technology, Sophia University, Tokyo, Japan
| | - Kohdai P Nakajima
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Shota Moriyama
- Department of Biology, Graduate School of Science and Technology, Sophia University, Tokyo, Japan
| | - Makoto T Fujiwara
- Department of Biology, Graduate School of Science and Technology, Sophia University, Tokyo, Japan
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Fan L, Chae E, Gust AA, Nürnberger T. Isolation of Novel MAMP‐like Activities and Identification of Cognate Pattern Recognition Receptors in
Arabidopsis thaliana
Using Next‐Generation Sequencing (NGS)–Based Mapping. ACTA ACUST UNITED AC 2018; 2:173-189. [DOI: 10.1002/cppb.20056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Li Fan
- Center of Plant Molecular Biology (ZMBP), Eberhard‐Karls‐University Tübingen Tübingen Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology Tübingen Germany
| | - Andrea A. Gust
- Center of Plant Molecular Biology (ZMBP), Eberhard‐Karls‐University Tübingen Tübingen Germany
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard‐Karls‐University Tübingen Tübingen Germany
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