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Islam MM, Agake SI, Ito T, Habibi S, Yasuda M, Yamada T, Stacey G, Ohkama-Ohtsu N. Involvement of Peptidoglycan Receptor Proteins in Mediating the Growth-Promoting Effects of Bacillus pumilus TUAT1 in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2024; 65:748-761. [PMID: 38372612 PMCID: PMC11138354 DOI: 10.1093/pcp/pcae016] [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: 07/18/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
Bacillus pumilus TUAT1 acts as plant growth-promoting rhizobacteria for various plants like rice and Arabidopsis. Under stress conditions, B. pumilus TUAT1 forms spores with a thick peptidoglycan (PGN) cell wall. Previous research showed that spores were significantly more effective than vegetative cells in enhancing plant growth. In Arabidopsis, lysin motif proteins, LYM1, LYM3 and CERK1, are required for recognizing bacterial PGNs to mediate immunity. Here, we examined the involvement of PGN receptor proteins in the plant growth promotion (PGP) effects of B. pumilus TUAT1 using Arabidopsis mutants defective in PGN receptors. Root growth of wild-type (WT), cerk1-1, lym1-1 and lym1-2 mutant plants was significantly increased by TUAT1 inoculation, but this was not the case for lym3-1 and lym3-2 mutant plants. RNA-seq analysis revealed that the expression of a number of defense-related genes was upregulated in lym3 mutant plants. These results suggested that B. pumilus TUAT1 may act to reduce the defense response, which is dependent on a functional LYM3. The expression of the defense-responsive gene, WRKY29, was significantly induced by the elicitor flg-22, in both WT and lym3 mutant plants, while this induction was significantly reduced by treatment with B. pumilus TUAT1 and PGNs in WT, but not in lym3 mutant plants. These findings suggest that the PGNs of B. pumilus TUAT1 may be recognized by the LYM3 receptor protein, suppressing the defense response, which results in plant growth promotion in a trade-off between defense and growth.
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Affiliation(s)
- Md. Monirul Islam
- Plant Biotechnology and Genetic Engineering Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka 1207, Bangladesh
- United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-shi, Tokyo, 183-8509 Japan
| | - Shin-ichiro Agake
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumicho, Fuchu-shi, Tokyo, 183-8538 Japan
| | - Takehiro Ito
- United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-shi, Tokyo, 183-8509 Japan
| | - Safiullah Habibi
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-shi, Tokyo, 183-8509 Japan
| | - Michiko Yasuda
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumicho, Fuchu-shi, Tokyo, 183-8538 Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-shi, Tokyo, 183-8509 Japan
| | - Tetsuya Yamada
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumicho, Fuchu-shi, Tokyo, 183-8538 Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-shi, Tokyo, 183-8509 Japan
| | - Gary Stacey
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumicho, Fuchu-shi, Tokyo, 183-8538 Japan
- Division of Plant Science and Technology, University of Missouri-Columbia—Bond Life Science Center, 1201 Rollins St., Columbia, MO 65201-4231, USA
| | - Naoko Ohkama-Ohtsu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumicho, Fuchu-shi, Tokyo, 183-8538 Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-shi, Tokyo, 183-8509 Japan
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Liu G, Liu D, Zhang A, Liu H, Mia MS, Mullan D, Yan G. Identification of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near-isogenic lines targeting a 4BS quantitative trait locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:190. [PMID: 37584740 PMCID: PMC10432333 DOI: 10.1007/s00122-023-04438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
KEY MESSAGE This study identified a novel SNP and developed a highly efficient KASP marker for drought tolerance in wheat by genotyping NILs targeting a major QTL for drought tolerance using an SNP array and validation with commercial varieties. Common wheat (Triticum aestivum L.) is an important winter crop worldwide and a typical allopolyploid with a large and complex genome. With global warming, the environmental volatility and incidence of drought in wheat-producing areas will increase. Molecular markers for drought tolerance are urgently needed to enhance drought tolerance breeding. Here, we genotyped four near-isogenic line (NIL) pairs targeting a major QTL qDSI.4B.1 on wheat chromosome arm 4BS for drought tolerance using the 90K SNP Illumina iSelect array and discovered a single nucleotide polymorphism (SNP) (Excalibur_c100336_106) with consistent genotype-phenotype associations among all four NIL pairs and their parents. Then, we converted the SNP into a Kompetitive Allele-Specific PCR (KASP) marker, with an accuracy of 100% for the four NIL pairs and their parents and as high as 81.8% for the 44 tested wheat lines with known phenotypes collected from Australia and China. Two genes near this SNP were suggested as candidate genes for drought tolerance in wheat after checking the Chinese Spring reference genome annotation version 1.1. One gene, TraesCS4B02G085300, encodes an F-box protein reportedly related to the ABA network, a main pathway for drought tolerance, and another gene, TraesCS4B02G085400, encodes a calcineurin-like metallophos-phoesterase transmembrane protein, which participates in Ca2+-dependent phosphorylation regulatory system. Based on this work and previous research on pre-harvest sprouting, we established a quick and efficient general SQV-based approach for KASP marker development, integrating genotyping by SNP arrays (S) using NILs targeting major QTL for a specific trait (Q) and validating them with commercial varieties (V). The identified SNP and developed KASP marker could be applied to marker-assisted selection in drought breeding, and further study of the candidate genes may improve our understanding of drought tolerance in wheat.
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Affiliation(s)
- Guannan Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Aimin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Md Sultan Mia
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Daniel Mullan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
- InterGrain Pty. Ltd., 19 Ambitious Link, Bibra Lake, WA 6163 Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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Wang Y, Li J, Guo P, Liu Q, Ren S, Juan L, He J, Tan X, Yan J. Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase gene increased plant height and promoted secondary cell walls deposition in Arabidopsis. PLANTA 2023; 258:65. [PMID: 37566145 DOI: 10.1007/s00425-023-04222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
MAIN CONCLUSION Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase 1 caused a taller phenotype, promoted secondary cell wall deposition, leaf enlargement, and early flowering, and reduced chlorophyll and anthocyanin accumulation and seed enlargement phenotype in Arabidopsis. Plant height and secondary cell wall (SCW) deposition are important plant traits. Gibberellins (GAs) play important roles in regulating plant height and SCWs deposition. Gibberellin 20-oxidase (GA20ox) is an important enzyme involved in GA biosynthesis. In the present study, we identified a GA synthesis gene in Camellia oleifera. The total length of the CoGA20ox1 gene sequence was 1146 bp, encoding 381 amino acids. Transgenic plants with CoGA20ox1 had a taller phenotype; a seed enlargement phenotype; promoted SCWs deposition, leaf enlargement, and early flowering; and reduced chlorophyll and anthocyanin accumulation. Genetic analysis showed that the mutant ga20ox1-3 Arabidopsis partially rescued the phenotype of CoGA20ox1 overexpression plants. The results showed that CoGA20ox1 participates in the growth and development of C. oleifera. The morphological changes in CoGA20ox1 overexpressed plants provide a theoretical basis for further exploration of GA biosynthesis and analysis of the molecular mechanism in C. oleifera.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Jian'an Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
| | - Purui Guo
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Qian Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Shuangshuang Ren
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Lemei Juan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Jiacheng He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
| | - Jindong Yan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
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Ahmed F, Bappy MNI, Islam MS. Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach. J Genet Eng Biotechnol 2023; 21:43. [PMID: 37024763 PMCID: PMC10079790 DOI: 10.1186/s43141-023-00495-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/18/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18-22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available. RESULTS To identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11-71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways. CONCLUSION These findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.
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Affiliation(s)
- Foeaz Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Md Shariful Islam
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
- Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
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Jing X, Xu L, Huai X, Zhang H, Zhao F, Qiao Y. Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp. Genes (Basel) 2023; 14:genes14010121. [PMID: 36672862 PMCID: PMC9859564 DOI: 10.3390/genes14010121] [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: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.
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Affiliation(s)
- Xiaotong Jing
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Linlin Xu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xinjia Huai
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Hong Zhang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Fengli Zhao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- Correspondence:
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Khatun M, Monir MM, Lou X, Zhu J, Xu H. Genome-wide association studies revealed complex genetic architecture and breeding perspective of maize ear traits. BMC PLANT BIOLOGY 2022; 22:537. [PMID: 36397013 PMCID: PMC9673299 DOI: 10.1186/s12870-022-03913-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Maize (Zea Mays) is one of the world's most important crops. Hybrid maize lines resulted a major improvement in corn production in the previous and current centuries. Understanding the genetic mechanisms of the corn production associated traits greatly facilitate the development of superior hybrid varieties. RESULT In this study, four ear traits associated with corn production of Nested Association Mapping (NAM) population were analyzed using a full genetic model, and further, optimal genotype combinations and total genetic effects of current best lines, superior lines, and superior hybrids were predicted for each of the traits at four different locations. The analysis identified 21-34 highly significant SNPs (-log10P > 5), with an estimated total heritability of 37.31-62.34%, while large contributions to variations was due to dominance, dominance-related epistasis, and environmental interaction effects ([Formula: see text] 14.06% ~ 49.28%), indicating these factors contributed significantly to phenotypic variations of the ear traits. Environment-specific genetic effects were also discovered to be crucial for maize ear traits. There were four SNPs found for three ear traits: two for ear length and weight, and two for ear row number and length. Using the Enumeration method and the stepwise tuning technique, optimum multi-locus genotype combinations for superior lines were identified based on the information obtained from GWAS. CONCLUSIONS Predictions of genetic breeding values showed that different genotype combinations in different geographical regions may be better, and hybrid-line variety breeding with homozygote and heterozygote genotype combinations may have a greater potential to improve ear traits.
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Affiliation(s)
- Mita Khatun
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Md Mamun Monir
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyang Lou
- Department of Biostatistics, University of Florida, Gainesville, FL, 32611, USA
| | - Jun Zhu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Haiming Xu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Liu G, Mullan D, Zhang A, Liu H, Liu D, Yan G. Identification of KASP markers and putative genes for pre-harvest sprouting resistance in common wheat (Triticum aestivum L.). THE CROP JOURNAL 2022. [DOI: 10.1016/j.cj.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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9
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Su C, Cui J, Liu Y, Luan Y. Genome-wide identification and characterization of the tomato F-box associated (FBA) protein family and expression analysis of their responsiveness to Phytophthora infestans. Gene 2022; 821:146335. [PMID: 35182672 DOI: 10.1016/j.gene.2022.146335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/22/2022] [Accepted: 02/11/2022] [Indexed: 11/04/2022]
Abstract
Late blight caused by Phytophthora infestans brings huge economic losses to the production of tomato (Solanum lycopersicum) every year. F-box proteins participate in plants response to phytohormones and biotic stress, whereas as the largest subfamily of F-box superfamily, the detailed information about F-box associated (SlFBA) family in tomato has been rarely reported. In this study, a total of 46 tomato FBA genes were identified based on the latest genome annotation. Phylogenetic analysis revealed that the FBA proteins from tomato and 6 different plant species were clustered into 7 distinct clades. The SlFBA genes were unevenly distributed on 11 chromosomes of tomato, mainly concentrated in the regions with high gene density. Tandem duplications and purification selection contribute to the expansion and evolution of the SlFBA gene family. Transcriptome analysis revealed that the SlFBA genes were differentially expressed in different tissues with obvious tissue-specific expression patterns. There were 18 SlFBA genes differentially expressed in P. infestans-resistant and -susceptible tomato, among which, 3 SlFBA genes might play positive roles in tomato resistance to P. infestans. Taken together, this study systematically analyzed the SlFBA genes family for the first time and identified the candidate SlFBA genes that affect tomato resistance to P. infestans, which provided important genetic and breeding resources for improving tomato resistance to pathogens.
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Affiliation(s)
- Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116033, China
| | - Jun Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yarong Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116033, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116033, China.
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Singh H, Kaur J, Bala R, Srivastava P, Sharma A, Grover G, Dhillon GS, Singh RP, Chhuneja P, Bains NS. Residual effect of defeated stripe rust resistance genes/QTLs in bread wheat against prevalent pathotypes of Puccinia striiformis f. sp. tritici. PLoS One 2022; 17:e0266482. [PMID: 35363829 PMCID: PMC8975100 DOI: 10.1371/journal.pone.0266482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
The periodic breakdowns of stripe rust resistance due to emergence of new virulent and more aggressive pathotypes of Puccinia striiformis f. sp. tritici have resulted in severe epidemics in India. This necessitates the search for new and more durable resistance sources against stripe rust. The three bread wheat cultivars PBW 343 (carries Yr9 and Yr27), PBW 621 (carries Yr17) and HD 2967 (gene not known) were highly popular among the farmers after their release in 2011. But presently all three cultivars are highly susceptible to stripe rust at seedling as well as at adult plant stages as their resistance has been broken down due to emergence of new pathotypes of the pathogen (110S119, 238S119). In previous study, the crosses of PBW 621 with PBW 343 and HD 2967 and evaluation of further generations (up to F4) against pathotype 78S84 resulted in resistant segregants. In the present study, the F5 and F6 RIL populations have been evaluated against new pathotypes of Pst. The RILs categorized based on the disease severity on the P (Penultimate leaf) and F (flag) leaf into three categories i.e., high, moderate and low level of APR (adult plant resistance) having 1–200, 201–400 and >400 values of AUDPC, respectively, upon infection with stripe rust. The various APR components (latent period, lesion growth rate, spore production and uredial density) were studied on each category, i.e., resistant, moderately resistant and susceptible. The values of APR parameters decreased as the level of resistance increased. Based on molecular analysis, the lines (representing different categories of cross PBW 621 X PBW 343) containing the genes Yr9 and Yr17 due to their interactive effect provide resistance. Based on BSA using 35k SNPs and KASP markers association with phenotypic data of the RIL population (PBW 621 X HD 2967) showed the presence of two QTLs (Q.Pst.pau-6B, Q.Pst.pau-5B) responsible for the residual resistance and two SNPs AX-94891670 and AX-94454107 were found to be associated with the trait of interest on chromosome 6B and 5B respectively. The present study concludes that in the population of both the crosses (PBW 621 X PBW 343 and PBW 621 X HD 2967) major defeated gene contributed towards residual resistance by interacting with minor gene/QTLs.
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Affiliation(s)
| | - Jaspal Kaur
- Department of Plant Breeding & Genetics, PAU, Ludhiana, India
- * E-mail:
| | - Ritu Bala
- Department of Plant Breeding & Genetics, PAU, Ludhiana, India
| | - Puja Srivastava
- Department of Plant Breeding & Genetics, PAU, Ludhiana, India
| | - Achla Sharma
- Department of Plant Breeding & Genetics, PAU, Ludhiana, India
| | - Gomti Grover
- Department of Plant Breeding & Genetics, PAU, Ludhiana, India
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
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11
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Kim H, Song E, Kim Y, Choi E, Hwang J, Lee JH. Loss-of-function of ARABIDOPSIS F-BOX PROTEIN HYPERSENSITIVE TO ABA 1 enhances drought tolerance and delays germination. PHYSIOLOGIA PLANTARUM 2021; 173:2376-2389. [PMID: 34687457 DOI: 10.1111/ppl.13588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
ABA is a phytohormone involved in diverse plant events such as seed germination and drought response. An F-box protein functions as a substrate receptor of the SCF complex and is responsible for ubiquitination of target proteins, triggering their subsequent degradation mediated by ubiquitin proteasome system. Here, we have isolated a gene named ARABIDOPSIS F-BOX PROTEIN HYPERSENSITIVE TO ABA 1 (AFA1) that was upregulated by ABA. AFA1 interacted with adaptor proteins of the SCF complex, implying its role as a substrate receptor of the complex. Its loss of function mutants, afa1 seedlings, exhibited ABA-hypersensitivity, including delayed germination in the presence of ABA. Moreover, loss of AFA1 led to increased drought tolerance in adult plants. Microarray data with ABA treatments indicated that 129 and 219 genes were upregulated or downregulated, respectively, by more than three times in afa1 relative to the wild type. Among the upregulated genes in afa1, the expression of 28.7% was induced by more than three times in the presence of ABA, while only 9.3% was repressed to the same extent. These data indicate that AFA1 is involved in the downregulation of many ABA-inducible genes, in accordance with the ABA-hypersensitive phenotype of afa1. Epistasis analysis showed that AFA1 could play a role upstream of ABI4 and ABI5 in the ABA signaling for germination inhibition. Collectively, our findings suggest that AFA1 is a novel F-box protein that negatively regulates ABA signaling.
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Affiliation(s)
- Hani Kim
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Eunyoung Song
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - Yeojin Kim
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University, Busan, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan, Republic of Korea
| | - Jae-Hoon Lee
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
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12
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Fernandez‐Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner‐Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:275-293. [PMID: 33453123 PMCID: PMC8641386 DOI: 10.1111/tpj.15161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
Abstract
Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).
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Affiliation(s)
- Noe Fernandez‐Pozo
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Timo Metz
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Jake O. Chandler
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
| | - Lydia Gramzow
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | | | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Günter Theißen
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityWageningenThe Netherlands
| | - Gerhard Leubner‐Metzger
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University and Institute of Experimental BotanyAcademy of Sciences of the Czech RepublicOlomoucCzech Republic
| | - Stefan A. Rensing
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
- BIOSS Centre for Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)University of MarburgMarburgGermany
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13
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Muhammad A, Li J, Hu W, Yu J, Khan SU, Khan MHU, Xie G, Wang J, Wang L. Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models. Sci Rep 2021; 11:6767. [PMID: 33762669 PMCID: PMC7990932 DOI: 10.1038/s41598-021-86127-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.
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Affiliation(s)
- Ali Muhammad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Yu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, 311300, China
| | - Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China.
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
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14
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Genome-wide characterization of the hyperaccumulator Sedum alfredii F-box family under cadmium stress. Sci Rep 2021; 11:3023. [PMID: 33542339 PMCID: PMC7862640 DOI: 10.1038/s41598-021-82690-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/22/2021] [Indexed: 12/04/2022] Open
Abstract
The F-box genes, which form one of the largest gene families in plants, are vital for plant growth, development and stress response. However, F-box gene family in Sedum alfredii remains unknown. Comprehensive studies addressing their function responding to cadmium stress is still limited. In the present study, 193 members of the F-box gene (SaFbox) family were identified, which were classified into nine subfamilies. Most of the SaFboxs had highly conserved domain and motif. Various functionally related cis-elements involved in plant growth regulation, stress and hormone responses were located in the upstream regions of SaFbox genes. RNA-sequencing and co-expression network analysis revealed that the identified SaFbox genes would be involved in Cd stress. Expression analysis of 16 hub genes confirmed their transcription level in different tissues. Four hub genes (SaFbox40, SaFbox51, SaFbox136 and SaFbox170) were heterologously expressed in a Cd-sensitive yeast cell to assess their effects on Cd tolerance. The transgenic yeast cells carrying SaFbox40, SaFbox51, SaFbox136, or SaFbox170 were more sensitive and accumulated more cadmium under Cd stress than empty vector transformed control cells. Our results performed a comprehensive analysis of Fboxs in S. alfredii and identified their potential roles in Cd stress response.
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15
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Zhang Y, Liu H, Yan G. Characterization of near-isogenic lines confirmed QTL and revealed candidate genes for plant height and yield-related traits in common wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:4. [PMID: 37309530 PMCID: PMC10231565 DOI: 10.1007/s11032-020-01196-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/14/2020] [Indexed: 06/13/2023]
Abstract
Plant height (PH) is closely associated with yield-related traits and environmental adaptation. Seven pairs of near-isogenic lines (NILs) targeting four QTL on 3AL, 4BL, 4AS, and 7AL wheat chromosome arms were assessed for PH and four yield-related traits including yield per plant (Y/P), grain number per spike (G/S), thousand kernel weight (TKW), and biomass per plant (B/P). Significant differences were observed in the NIL pairs for the measured traits. NIL pairs targeting the 3AL QTL differed significantly in PH, G/S, and TKW; NILs targeting the 4BL QTL differed significantly in PH, Y/P, and B/P; NIL pairs targeting the 4AS QTL differed significantly in all the traits; and NIL pairs targeting the 7AL QTL differed significantly in PH. A 90 K SNP genotyping assay of the NILs detected nineteen SNPs associated with fourteen functional genes. Among them, eight candidate genes are related to Rht proteins, four genes are related to hormone pathways and two genes are related to carbohydrate synthesis and transport. By searching the interval marker physical positions, it was found that the four targeted QTL in this study overlapped with eight previously reported QTL for PH, TKW, biomass, and yield. Correlation analysis revealed that PH significantly and positively correlated with B/P and G/S. The SNP and candidate gene information is potentially useful for marker-assisted selection in breeding programs, and the four targeted QTL are proved to be critical genomic regions controlling the investigated agronomic traits, which can be further fine mapped to identify the underlying genes. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-020-01196-8.
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Affiliation(s)
- Yunxiao Zhang
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
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16
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Yan J, Li X, Zeng B, Zhong M, Yang J, Yang P, Li X, He C, Lin J, Liu X, Zhao X. FKF1 F-box protein promotes flowering in part by negatively regulating DELLA protein stability under long-day photoperiod in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1717-1740. [PMID: 32427421 DOI: 10.1111/jipb.12971] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/18/2020] [Indexed: 05/23/2023]
Abstract
FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1) encodes an F-box protein that regulates photoperiod flowering in Arabidopsis under long-day conditions (LDs). Gibberellin (GA) is also important for regulating flowering under LDs. However, how FKF1 and the GA pathway work in concert in regulating flowering is not fully understood. Here, we showed that the mutation of FKF1 could cause accumulation of DELLA proteins, which are crucial repressors in GA signaling pathway, thereby reducing plant sensitivity to GA in flowering. Both in vitro and in vivo biochemical analyses demonstrated that FKF1 directly interacted with DELLA proteins. Furthermore, we showed that FKF1 promoted ubiquitination and degradation of DELLA proteins. Analysis of genetic data revealed that FKF1 acted partially through DELLAs to regulate flowering under LDs. In addition, DELLAs exerted a negative feedback on FKF1 expression. Collectively, these findings demonstrate that FKF1 promotes flowering partially by negatively regulating DELLA protein stability under LDs, and suggesting a potential mechanism linking the FKF1 to the GA signaling DELLA proteins.
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Affiliation(s)
- Jindong Yan
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Bingjie Zeng
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Ming Zhong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Jiaxin Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Piao Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Xin Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Chongsheng He
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Jianzhong Lin
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
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17
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Rodríguez-Alvarez CI, López-Vidriero I, Franco-Zorrilla JM, Nombela G. Basal differences in the transcriptional profiles of tomato leaves associated with the presence/absence of the resistance gene Mi-1 and changes in these differences after infestation by the whitefly Bemisia tabaci. BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:463-479. [PMID: 31813394 DOI: 10.1017/s0007485319000828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The tomato Mi-1 gene mediates plant resistance to whitefly Bemisia tabaci, nematodes, and aphids. Other genes are also required for this resistance, and a model of interaction between the proteins encoded by these genes was proposed. Microarray analyses were used previously to identify genes involved in plant resistance to pests or pathogens, but scarcely in resistance to insects. In the present work, the GeneChip™ Tomato Genome Array (Affymetrix®) was used to compare the transcriptional profiles of Motelle (bearing Mi-1) and Moneymaker (lacking Mi-1) cultivars, both before and after B. tabaci infestation. Ten transcripts were expressed at least twofold in uninfested Motelle than in Moneymaker, while other eight were expressed half or less. After whitefly infestation, differences between cultivars increased to 14 transcripts expressed more in Motelle than in Moneymaker and 14 transcripts less expressed. Half of these transcripts showed no differential expression before infestation. These results show the baseline differences in the tomato transcriptomic profile associated with the presence or absence of the Mi-1 gene and provide us with valuable information on candidate genes to intervene in either compatible or incompatible tomato-whitefly interactions.
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Affiliation(s)
- Clara I Rodríguez-Alvarez
- Department of Plant Protection Institute for Agricultural Sciences (ICA), Spanish National Research Council (CSIC), Serrano 115 Dpdo., Madrid28006, Spain
| | - Irene López-Vidriero
- Genomics Unit, Centro Nacional de Biotecnología (CNB), Spanish National Research Council (CSIC), Darwin 3, Madrid28049, Spain
| | - José M Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología (CNB), Spanish National Research Council (CSIC), Darwin 3, Madrid28049, Spain
| | - Gloria Nombela
- Department of Plant Protection Institute for Agricultural Sciences (ICA), Spanish National Research Council (CSIC), Serrano 115 Dpdo., Madrid28006, Spain
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18
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Li L, Li B, Xie C, Zhang T, Borassi C, Estevez JM, Li X, Liu X. Arabidopsis RAD23B regulates pollen development by mediating degradation of KRP1. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4010-4019. [PMID: 32242227 DOI: 10.1093/jxb/eraa167] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
The ubiquitin (Ub)/26S proteasome system (UPS) plays a key role in plant growth, development, and survival by directing the turnover of numerous regulatory proteins. In the UPS, the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains function as hubs for ubiquitin-mediated protein degradation. Radiation sensitive 23 (RAD23), which has been identified as a UBL/UBA protein, contributes to the progression of the cell cycle, stress responses, ER proteolysis, and DNA repair. Here, we report that pollen development is arrested at the microspore stage in a rad23b null mutant. We demonstrate that RAD23B can directly interact with KIP-related protein 1 (KRP1) through its UBL-UBA domains. In addition, plants overexpressing KRP1 have defects in pollen development, which is a phenotype similar to the rad23b mutant. RAD23B promotes the degradation of KRP1 in vivo, which is accumulated following treatment with the proteasome inhibitor MG132. Our results indicate that RAD23B plays an important in pollen development by controlling the turnover of the key cell cycle protein, KRP1.
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Affiliation(s)
- Lan Li
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Bin Li
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Chong Xie
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Teng Zhang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Cecilia Borassi
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP, Argentina
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Xiushan Li
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Xuanming Liu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
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19
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Luo D, Qu L, Zhong M, Li X, Wang H, Miao J, Liu X, Zhao X. Vascular plant one-zinc finger 1 (VOZ1) and VOZ2 negatively regulate phytochrome B-mediated seed germination in Arabidopsis. Biosci Biotechnol Biochem 2020; 84:1384-1393. [DOI: 10.1080/09168451.2020.1740971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Seed germination is regulated by light. Phytochromes (Phys) act as red and far-red light photoreceptors to mediate seed germination. However, the mechanism of this process is not well understood. In this study, we found that the Arabidopsis thaliana mutants vascular plant one-zinc finger 1 (voz1) and voz2 showed higher seed germination percentage than wild type when PhyB was inactivated by far-red light. In wild type, VOZ1 and VOZ2 expression were downregulated after seed imbibition, repressed by PhyB, and upregulated by Phytochrome-interacting factor 1 (PIF1), a key negative regulator of seed germination. Red light irradiation and the voz1voz2 mutation caused increased expression of Gibberellin 3-oxidase 1 (GA3ox1), a gibberellin (GA) biosynthetic gene. We also found that VOZ2 is bound directly to the promoter of GA3ox1 in vitro and in vivo. Our findings suggest that VOZs play a negative role in PhyB-mediated seed germination, possibly by directly regulating GA3ox1 expression.
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Affiliation(s)
- Dan Luo
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Shenzhen Institute, Hunan University, Shenzhen, China
| | - Lina Qu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Shenzhen Institute, Hunan University, Shenzhen, China
| | - Ming Zhong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Shenzhen Institute, Hunan University, Shenzhen, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Shenzhen Institute, Hunan University, Shenzhen, China
| | - Han Wang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
| | - Jiahui Miao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Shenzhen Institute, Hunan University, Shenzhen, China
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Lu L, Liu H, Wu Y, Yan G. Development and Characterization of Near-Isogenic Lines Revealing Candidate Genes for a Major 7AL QTL Responsible for Heat Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1316. [PMID: 32983205 PMCID: PMC7485290 DOI: 10.3389/fpls.2020.01316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/11/2020] [Indexed: 05/22/2023]
Abstract
Wheat is one of the most important food crops in the world, but as a cool-season crop, it is more prone to heat stress, which severely affects crop production and grain quality. Heat tolerance in wheat is a quantitative trait, and the genes underlying reported quantitative trait loci (QTL) have rarely been identified. Near-isogenic lines (NILs) with a common genetic background but differing at a particular locus could turn quantitative traits into a Mendelian factor; therefore, they are suitable material for identifying candidate genes for targeted locus/loci. In this study, we developed and characterized NILs from two populations Cascades × Tevere and Cascades × W156 targeting a major 7AL QTL responsible for heat tolerance. Molecular marker screening and phenotyping for SPAD chlorophyll content and grain-yield-related traits confirmed four pairs of wheat NILs that contrasted for heat-stress responses. Genotyping the NILs using a 90K Infinium iSelect SNP array revealed five single nucleotide polymorphism (SNP) markers within the QTL interval that were distinguishable between the isolines. Seven candidate genes linked to the SNPs were identified as related to heat tolerance, and involved in important processes and pathways in response to heat stress. The confirmed multiple pairs of NILs and identified candidate genes in this study are valuable resources and information for further fine-mapping to clone major genes for heat tolerance.
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Affiliation(s)
- Lu Lu
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hui Liu
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Hui Liu, ; Guijun Yan,
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guijun Yan
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Hui Liu, ; Guijun Yan,
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Yang P, Li Y, He C, Yan J, Zhang W, Li X, Xiang F, Zuo Z, Li X, Zhu Y, Liu X, Zhao X. Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure. J Proteomics 2019; 214:103621. [PMID: 31863931 DOI: 10.1016/j.jprot.2019.103621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 12/20/2022]
Abstract
The conversion of light energy into chemical energy in leaves is very important for plant growth and development. During this process, chlorophylls and their derivatives are indispensable as their fundamental role in the energy absorption and transduction activities. Chlorophyll variation mutants are important materials for studying chlorophyll metabolism, chloroplast biogenesis, photosynthesis and related physiological processes. Here, a chlorophyll-reduced mutant (crm1) was isolated from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Compared to wild type, crm1 showed yellow leaves, reduced chlorophyll content, fewer thylakoid stacks and retarded growth. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 4575 proteins were identified from the chloroplast of Brassica napus leaves, and 466 of which displayed differential accumulations between wild type and crm1. The differential abundance proteins were found to be involved in chlorophyll metabolism, photosynthesis, phagosome and proteasome. Our results suggest that the decreased abundance of chlorophyll biosynthetic enzymes, proteins involved in photosynthesis might account for the reduced chlorophyll content, impaired thylakoid structure, and reduction of plant productivity. The increased abundance of proteins involved in phagosome and proteasome pathways might allow plants to adapt the proteome to environmental conditions to ensure growth and survival due to chlorophyll reduction. BIOLOGICAL SIGNIFICANCE: Photosynthesis, which consists of light and dark reactions, is fundamental to biomass production. Chloroplast is regarded as the main site for photosynthesis. During photosynthesis, the pigment chlorophyll is essential for light harvesting and energy transfer. This work provides new insights into protein expression patterns, and enables the identification of many attractive candidates for investigation of chlorophyll biosynthesis, chloroplast structure and photosynthesis in Brassica napus. These findings may be applied to improve the photosynthetic efficiency by genetic engineering in crops.
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Affiliation(s)
- Piao Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Yaxing Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chongsheng He
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Jindong Yan
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Wei Zhang
- Hunan Agricultural University, College of Agronnomy, Changsha, Hunan 410128, China
| | - Xin Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Fujiang Xiang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Yonghua Zhu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
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22
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Cao-Pham AH, Urano D, Ross-Elliott TJ, Jones AM. Nudge-nudge, WNK-WNK (kinases), say no more? THE NEW PHYTOLOGIST 2018; 220:35-48. [PMID: 29949669 DOI: 10.1111/nph.15276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/01/2018] [Indexed: 05/09/2023]
Abstract
Contents Summary 35 I Overview of animal and plant WNK kinases 35 II. Structure: domains and topology 36 III. Phylogeny-evolutionary relationships 41 IV. Plant WNK kinase distribution and regulation of WNK expression and activity 41 V. Functions of WNK family members in physiology and development 41 VI. Say no more? Still many questions to be answered 45 Acknowledgements 46 References 46 SUMMARY: WITH NO LYSINE (WNK) kinases are serine/threonine kinases uniquely characterized by an anomalous placement of a catalytic lysine, hence their moniker. In animals, WNK protein kinases play critical roles in protein trafficking of components that mediate renal ion transport processes and regulate osmoregulation of cell volume. In plants, the WNK kinase gene family is larger and more diverse. Recent studies revealed WNK kinase roles in orchestrating the trafficking of an ion channel, a lipid kinase complex in animals, and a heterotrimeric G protein signaling component in plants that is necessary for signal transduction. For this reason, new attention is geared toward investigating the mechanisms adopted by WNK kinases to nudge intracellular proteins to their destinations. In this review, the functions of WNK kinases in protein trafficking are derived from what we have learned from the model organism Arabidopsis thaliana. To place this new idea in context, we provide the predicted WNK kinase structures, their predicted expression patterns, a speculated evolutionary pathway, and the regulatory roles of plant WNKs in transport processes and other physiologies. We brazenly predict that the WNK kinases in both plants and animals will soon be recognized as a nexus for trafficking-based signal transduction.
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Affiliation(s)
- Anh H Cao-Pham
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Daisuke Urano
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 117604, Singapore
| | - Timothy J Ross-Elliott
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alan M Jones
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Ryder N, Dorn KM, Huitsing M, Adams M, Ploegstra J, DeHaan L, Larson S, Tintle NL. Transcriptome assembly and annotation of johnsongrass ( Sorghum halepense) rhizomes identify candidate rhizome-specific genes. PLANT DIRECT 2018; 2:e00065. [PMID: 31245728 PMCID: PMC6508516 DOI: 10.1002/pld3.65] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 05/25/2023]
Abstract
Rhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum halepense (johnsongrass) is an aggressive perennial grass that relies on a robust rhizome system to persist through winters and reproduce asexually from its rootstock nodes. This study aimed to sequence and assemble expressed transcripts within the johnsongrass rhizome. A de novo transcriptome assembly was generated from a single johnsongrass rhizome meristem tissue sample. A total of 141,176 probable protein-coding sequences from the assembly were identified and assigned gene ontology terms using Blast2GO. Estimated expression analysis and BLAST results were used to reduce the assembly to 64,447 high-confidence sequences. The johnsongrass assembly was compared to Sorghum bicolor, a related nonrhizomatous species, along with an assembly of similar rhizome tissue from the perennial grain crop Thinopyrum intermedium. The presence/absence analysis yielded a set of 98 expressed johnsongrass contigs that are likely associated with rhizome development.
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Affiliation(s)
- Nathan Ryder
- Departments of Biology and StatisticsDordt CollegeSioux CenterIowa
| | - Kevin M. Dorn
- Department of Plant PathologyKansas State UniversityManhattanKansas
| | - Mark Huitsing
- Departments of Biology and StatisticsDordt CollegeSioux CenterIowa
| | - Micah Adams
- Departments of Biology and StatisticsDordt CollegeSioux CenterIowa
| | - Jeff Ploegstra
- Departments of Biology and StatisticsDordt CollegeSioux CenterIowa
| | | | - Steve Larson
- USDA‐ARS, Forage and Range Research LaboratoryUtah State UniversityLoganUtah
| | - Nathan L. Tintle
- Departments of Biology and StatisticsDordt CollegeSioux CenterIowa
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He R, Li X, Zhong M, Yan J, Ji R, Li X, Wang Q, Wu D, Sun M, Tang D, Lin J, Li H, Liu B, Liu H, Liu X, Zhao X, Lin C. A photo-responsive F-box protein FOF2 regulates floral initiation by promoting FLC expression in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:788-801. [PMID: 28608936 DOI: 10.1111/tpj.13607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/08/2017] [Accepted: 05/13/2017] [Indexed: 05/09/2023]
Abstract
Floral initiation is regulated by various genetic pathways in response to light, temperature, hormones and developmental status; however, the molecular mechanisms underlying the interactions between different genetic pathways are not fully understood. Here, we show that the photoresponsive gene FOF2 (F-box of flowering 2) negatively regulates flowering. FOF2 encodes a putative F-box protein that interacts specifically with ASK14, and its overexpression results in later flowering under both long-day and short-day photoperiods. Conversely, transgenic plants expressing the F-box domain deletion mutant of FOF2 (FOF2ΔF), or double loss of function mutant of FOF2 and FOL1 (FOF2-LIKE 1) present early flowering phenotypes. The late flowering phenotype of the FOF2 overexpression lines is suppressed by the flc-3 loss-of-function mutation. Furthermore, FOF2 mRNA expression is regulated by autonomous pathway gene FCA, and the repressive effect of FOF2 in flowering can be overcome by vernalization. Interestingly, FOF2 expression is regulated by light. The protein level of FOF2 accumulates in response to light, whereas it is degraded under dark conditions via the 26S proteasome pathway. Our findings suggest a possible mechanistic link between light conditions and the autonomous floral promotion pathway in Arabidopsis.
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Affiliation(s)
- Reqing He
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Xinmei Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Ming Zhong
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Jindong Yan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Ronghuan Ji
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qin Wang
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Dan Wu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Mengsi Sun
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Jianzhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Hongyu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaoying Zhao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
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Kim YY, Cui MH, Noh MS, Jung KW, Shin JS. The FBA motif-containing protein AFBA1 acts as a novel positive regulator of ABA response in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:574-586. [PMID: 28184867 DOI: 10.1093/pcp/pcx003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
ABA plays a critical role in regulating seed germination and stomatal movement in response to drought stress. Screening ABA-responsive genes led to the identification of a novel Arabidopsis gene encoding a protein which contained a conserved F-box-associated (FBA) domain, subsequently named ABA-responsive FBA domain-containing protein 1 (AFBA1). Expression of ProAFBA1:GUS revealed that this gene was mainly expressed in guard cells. Expression of AFBA1 increased following the application of exogenous ABA and exposure to salt (NaCl) and drought stresses. Seed germination of the loss-of-function mutant (afba1) was insensitive to ABA, salt or mannitol, whereas AFBA1-overexpressing (Ox) seeds were more sensitive to these stresses than the wild-type seeds. The afba1 plants showed decreased drought tolerance, increased water loss rate and ABA-insensitive stomatal movement compared with the wild-type. In contrast, AFBA1-Ox plants exhibited enhanced drought tolerance and a rapid ABA-induced stomatal closure response. The expression of genes encoding serine/threonine protein phosphatases that are known negative regulators of ABA signaling increased in afba1 plants but decreased in AFBA1-Ox plants. AFBA1 was also found to be localized in the nucleus and to interact with an R2R3-type transcription factor, MYB44, leading to the suggestion that it functions in the stabilization of MYB44. Based on these results, we suggest that AFBA1 functions as a novel positive regulator of ABA responses, regulating the expression of genes involved in ABA signal transduction in Arabidopsis through its interaction with positive regulators of ABA signaling including MYB44, and increasing their stability during ABA-mediated responses.
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Affiliation(s)
- Yun Young Kim
- Division of Life Sciences, Korea University, Seoul 136-701, Korea
| | - Mei Hua Cui
- Division of Life Sciences, Korea University, Seoul 136-701, Korea
- School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Min Soo Noh
- Division of Life Sciences, Korea University, Seoul 136-701, Korea
| | - Kwang Wook Jung
- Division of Life Sciences, Korea University, Seoul 136-701, Korea
- DuPont Pioneer Hi-Bred, DuPont (Korea) Inc., Gangnam-gu, Seoul 135-719, Korea
| | - Jeong Sheop Shin
- Division of Life Sciences, Korea University, Seoul 136-701, Korea
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He R, Yu D, Li X, Duan G, Zhang Y, Tang D, Zhao X, Liu X. F-box gene FOA2 regulates GA- and ABA- mediated seed germination in Arabidopsis. SCIENCE CHINA-LIFE SCIENCES 2016; 59:1192-1194. [PMID: 27612866 DOI: 10.1007/s11427-016-0098-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Reqing He
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Dashi Yu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Xinmei Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Guifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Yunxuan Zhang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaoying Zhao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China.
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China. .,State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China.
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27
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Xie M, Wu D, Duan G, Wang L, He R, Li X, Tang D, Zhao X, Liu X. AtWNK9 is regulated by ABA and dehydration and is involved in drought tolerance in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 77:73-83. [PMID: 24561249 DOI: 10.1016/j.plaphy.2014.01.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
WNK (with no lysine [K]) kinases play important regulatory roles in flowering, as well as salt and osmotic stress tolerance in plants. Here, we report that AtWNK9, a member of the Arabidopsis WNK gene family, was induced by exogenous abscisic acid (ABA) treatment and dehydration stress. Overexpression of AtWNK9 from the cauliflower mosaic virus 35S promoter in Arabidopsis resulted in increased sensitivity to ABA, strong inhibition of primary root elongation, increased proline accumulation, reduced stomatal aperture, and a reduced rate of water loss. In addition, plant survival under drought stress was improved compared to wild type. In contrast, a mutant with a T-DNA insertion in AtWNK9 showed reduced ABA sensitivity and an increased rate of water loss; further, it showed increased susceptibility to drought stress. The transcription of a number of ABA signaling components, including ABI1, ERA1, ABI3, and ABF3, was up-regulated in AtWNK9 transgenic plants and down-regulated in the wnk9 mutant in response to ABA. Some ABA-responsive and biosynthetic genes, as well as other drought-related genes, were altered at various levels in AtWNK9 transgenic plants and wnk9 mutants under dehydration stress. Overall, these findings suggest that AtWNK9 plays a positive role in ABA signaling and improves drought tolerance in transgenic Arabidopsis.
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Affiliation(s)
- Minmin Xie
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Dan Wu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Guifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Liqun Wang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Reqing He
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Xiushan Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Xiaoying Zhao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China.
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China; State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China.
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28
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Chen R, Guo W, Yin Y, Gong ZH. A novel F-box protein CaF-box is involved in responses to plant hormones and abiotic stress in pepper (Capsicum annuum L.). Int J Mol Sci 2014; 15:2413-30. [PMID: 24518684 PMCID: PMC3958859 DOI: 10.3390/ijms15022413] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 11/19/2022] Open
Abstract
The F-box protein family is characterized by an F-box motif that has been shown to play an important role in regulating various developmental processes and stress responses. In this study, a novel F-box-containing gene was isolated from leaves of pepper cultivar P70 (Capsicum annuum L.) and designated CaF-box. The full-length cDNA is 2088 bp and contains an open reading frame of 1914 bp encoding a putative polypeptide of 638 amino acids with a mass of 67.8 kDa. CaF-box was expressed predominantly in stems and seeds, and the transcript was markedly upregulated in response to cold stress, abscisic acid (ABA) and salicylic acid (SA) treatment, and downregulated under osmotic and heavy metal stress. CaF-box expression was dramatically affected by salt stress, and was rapidly increased for the first hour, then sharply decreased thereafter. In order to further assess the role of CaF-box in the defense response to abiotic stress, a loss-of-function experiment in pepper plants was performed using a virus-induced gene silencing (VIGS) technique. Measurement of thiobarbituric acid reactive substances (TBARS) and electrolyte leakage revealed stronger lipid peroxidation and cell death in the CaF-box-silenced plants than in control plants, suggesting CaF-box plays an important role in regulating the defense response to abiotic stress resistance in pepper plants.
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Affiliation(s)
- Rugang Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Weili Guo
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yanxu Yin
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Choi CM, Gray WM, Mooney S, Hellmann H. Composition, roles, and regulation of cullin-based ubiquitin e3 ligases. THE ARABIDOPSIS BOOK 2014; 12:e0175. [PMID: 25505853 PMCID: PMC4262284 DOI: 10.1199/tab.0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation. The largest group of E3 ligases known in plants is represented by CULLIN-REALLY INTERESTING NEW GENE (RING) E3 ligases (CRLs). In recent years, a great amount of knowledge has been generated to reveal the critical roles of these enzymes across all aspects of plant life. This review provides an overview of the different classes of CRLs in plants, their specific complex compositions, the variety of biological processes they control, and the regulatory steps that can affect their activities.
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Affiliation(s)
| | | | | | - Hanjo Hellmann
- Washington State University, Pullman, Washington
- Address correspondence to
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Navarro-Quezada A, Schumann N, Quint M. Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves. PLoS One 2013; 8:e68672. [PMID: 23904908 PMCID: PMC3719486 DOI: 10.1371/journal.pone.0068672] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/07/2013] [Indexed: 12/21/2022] Open
Abstract
F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.
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Affiliation(s)
- Aura Navarro-Quezada
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nadine Schumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Marcel Quint
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
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