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Newman TE, Jacques S, Grime C, Mobegi FM, Kamphuis FL, Khentry Y, Lee R, Kamphuis LG. Genetic dissection of domestication traits in interspecific chickpea populations. THE PLANT GENOME 2024; 17:e20408. [PMID: 37961823 DOI: 10.1002/tpg2.20408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
Chickpea (Cicer arietinum) is a pulse crop that provides an integral source of nutrition for human consumption. The close wild relatives Cicer reticulatum and Cicer echinospermum harbor untapped genetic diversity that can be exploited by chickpea breeders to improve domestic varieties. Knowledge of genomic loci that control important chickpea domestication traits will expedite the development of improved chickpea varieties derived from interspecific crosses. Therefore, we set out to identify genomic loci underlying key chickpea domestication traits by both association and quantitative trait locus (QTL) mapping using interspecific F2 populations. Diverse phenotypes were recorded for various agronomic traits. A total of 11 high-confidence markers were detected on chromosomes 1, 3, and 7 by both association and QTL mapping; these were associated with growth habit, flowering time, and seed traits. Furthermore, we identified candidate genes linked to these markers, which advanced our understanding of the genetic basis of domestication traits and validated known genes such as the FLOWERING LOCUS gene cluster that regulates flowering time. Collectively, this study has elucidated the genetic basis of chickpea domestication traits, which can facilitate the development of superior chickpea varieties.
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Affiliation(s)
- Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Christy Grime
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fredrick M Mobegi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fiona L Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Robert Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia
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McLeod L, Barchi L, Tumino G, Tripodi P, Salinier J, Gros C, Boyaci HF, Ozalp R, Borovsky Y, Schafleitner R, Barchenger D, Finkers R, Brouwer M, Stein N, Rabanus-Wallace MT, Giuliano G, Voorrips R, Paran I, Lefebvre V. Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1508-1528. [PMID: 37602679 DOI: 10.1111/tpj.16425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.
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Affiliation(s)
- Louis McLeod
- INRAE, GAFL, Montfavet, France
- INRAE, A2M, Montfavet, France
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Giorgio Tumino
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), Pontecagnano Faiano, Italy
| | | | | | | | - Ramazan Ozalp
- Bati Akdeniz Agricultural Research Institute (BATEM), Antalya, Türkiye
| | - Yelena Borovsky
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
| | - Roland Schafleitner
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Derek Barchenger
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Corre, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | | | - Giovanni Giuliano
- Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Economic Development (ENEA), Rome, Italy
| | - Roeland Voorrips
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Ilan Paran
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
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Goldman IL, Wang Y, Alfaro AV, Brainard S, Oravec MW, McGregor CE, van der Knaap E. Form and contour: breeding and genetics of organ shape from wild relatives to modern vegetable crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1257707. [PMID: 37841632 PMCID: PMC10568141 DOI: 10.3389/fpls.2023.1257707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Shape is a primary determinant of consumer preference for many horticultural crops and it is also associated with many aspects of marketing, harvest mechanics, and postharvest handling. Perceptions of quality and preference often map to specific shapes of fruits, tubers, leaves, flowers, roots, and other plant organs. As a result, humans have greatly expanded the palette of shapes available for horticultural crops, in many cases creating a series of market classes where particular shapes predominate. Crop wild relatives possess organs shaped by natural selection, while domesticated species possess organs shaped by human desires. Selection for visually-pleasing shapes in vegetable crops resulted from a number of opportunistic factors, including modification of supernumerary cambia, allelic variation at loci that control fundamental processes such as cell division, cell elongation, transposon-mediated variation, and partitioning of photosynthate. Genes that control cell division patterning may be universal shape regulators in horticultural crops, influencing the form of fruits, tubers, and grains in disparate species. Crop wild relatives are often considered less relevant for modern breeding efforts when it comes to characteristics such as shape, however this view may be unnecessarily limiting. Useful allelic variation in wild species may not have been examined or exploited with respect to shape modifications, and newly emergent information on key genes and proteins may provide additional opportunities to regulate the form and contour of vegetable crops.
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Affiliation(s)
- Irwin L. Goldman
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yanbing Wang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Andrey Vega Alfaro
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Scott Brainard
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Madeline W. Oravec
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Cecilia Elizabeth McGregor
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Zhou X, Su L, Tang R, Dong Y, Wang F, Li R, Xie Q, Zhang X, Xiao G, Li H. Genome-wide analysis of Hsp40 and Hsp70 gene family in four cotton species provides insights into their involvement in response to Verticillium dahliae and abiotic stress. Front Genet 2023; 14:1120861. [PMID: 36777720 PMCID: PMC9909605 DOI: 10.3389/fgene.2023.1120861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction: Cotton is an important economic crop to provide natural fibers as raw materials to textile industry, and is significantly affected by biotic and abiotic stress during the whole growth stage, in which Verticillium wilt (VW) caused by Verticillium dahliae is one of the most destructive disease to lead to a significant yield reduction. Heat shock proteins (Hsps) are important molecular chaperones, and play crucial roles in plant growth, development, resistance to biotic and abiotic stress. Hsp40 and Hsp70 are two key Hsps in cell chaperone network, however, the function and regulatory mechanism of Hsp40 and Hsp70 members in VW resistance and abiotic stress in cotton are largely unknown. Methods and Results: Herein, a systematic and comprehensive analysis of Hsp40s and Hsp70s in four cotton species of Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense were performed. A total of 291 Hsp40s and 171 Hsp70s identified in four Gossypium species. Sequence analysis revealed that all Hsp40 proteins contained J domain that provides the binding sites to Hsp70. Protein-protein interaction prediction analysis displayed that GhHsp40-55 might interact with GhHsp70-2 and GhHsp70-13, suggesting their potential function as protein complex. Promoter cis-acting element analysis demonstrated that multiple cis-elements related to disease and stress response consists in GhHsp40 and GhHsp70 promoters. Further expression analysis showed that eight GhHsp40s (Hsp40-2,4,8,11,20,23,53,55) and seven GhHsp70s (Hsp70-2,3,6,8,13,19,22) were up-regulated after V. dahliae infection. In addition, five GhHsp40s (Hsp40-2,8,11,53,55) and four GhHsp70s (Hsp70-3,6,8,13) were up-regulated after salt treatment, six GhHsp40s (Hsp40-4,11,20,23) and three GhHsp70s (Hsp70-2,8,19) were up-regulated after drought treatment, four GhHsp40s (Hsp40-2,11,20,23) and four GhHsp70s (Hsp70-3,6,19,22) were up-regulated after temperature treatment, suggesting these Hsps have possible important function in the process of abiotic stress response. Discussion: Our results lay a foundation for understanding the function of Hsp40 and Hsp70 in the resistance against V. dahliae and abiotic stress, and elucidating the regulatory mechanism of the protein complex, evolution and molecular mechanism under stress.
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Affiliation(s)
- Xin Zhou
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Ling Su
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Rui Tang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Yuxuan Dong
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Xianliang Zhang
- National Key Laboratory of Cotton Biology, Institute of Cotton Research (CAAS), Anyang, China,*Correspondence: Xianliang Zhang, ; Guanghui Xiao, ; Hongbin Li,
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China,*Correspondence: Xianliang Zhang, ; Guanghui Xiao, ; Hongbin Li,
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China,*Correspondence: Xianliang Zhang, ; Guanghui Xiao, ; Hongbin Li,
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Borah P, Ni F, Ying W, Zhuang H, Chong SL, Hu XG, Yang J, Lin EP, Huang H. Genome-wide identification and characterization of OVATE family proteins in Betula luminifera reveals involvement of BlOFP3 and BlOFP5 genes in leaf development. FRONTIERS IN PLANT SCIENCE 2022; 13:950936. [PMID: 36311104 PMCID: PMC9613114 DOI: 10.3389/fpls.2022.950936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Ovate family proteins (OFP) are plant-specific transcription factors involved in regulating morphologies of the lateral organs, plant growth and development. However, the functional roles of OFP genes in Betula luminifera, an important timber tree species, are not well studied. In this study, we identified 20 BlOFP genes and analyzed their phylogenetic relationship, gene structure, conserved motifs, and cis-elements. Further, expression analysis indicates that BlOFP genes were up-regulated in leaves on the one-year-old branch compared to leaves on the current-year branch and bract, except BlOFP7, BlOFP11, BlOFP14 and BlOFP12. The overexpression of BlOFP3 and BlOFP5 in Arabidopsis thaliana not only resulted in a slower growth rate but also produced sawtooth shape, flatter and darker green rosette leaves. Further investigation showed that the leaf thickness of the transgenic plants was more than double that of the wild type, which was caused by the increasement in the number and size of palisade tissue cells. Furthermore, the expression analysis also indicated that the expressions of several genes related to leaf development were significantly changed in the transgene plants. These results suggested the significant roles of BlOFP3 and BlOFP5 in leaf development. Moreover, protein-protein interaction studies showed that BlOFP3 interacts with BlKNAT5, and BlOFP5 interacts with BlKNAT5, BlBLH6 and BlBLH7. In conclusion, our study demonstrates that BlOFP3 and BlOFP5 were involved in leaf shape and thickness regulation by forming a complex with BlKNAT5, BlBLH6 and BlBLH7. In addition, our study serves as a guide for future functional genomic studies of OFP genes of the B. luminifera.
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Affiliation(s)
- Priyanka Borah
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Fei Ni
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiyang Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Hebi Zhuang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Sun-Li Chong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Xian-Ge Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Er-pei Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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Luo Y, Yang S, Luo X, Li J, Li T, Tang X, Liu F, Zou X, Qin C. Genome-wide analysis of OFP gene family in pepper (Capsicum annuum L.). Front Genet 2022; 13:941954. [PMID: 36246640 PMCID: PMC9563708 DOI: 10.3389/fgene.2022.941954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Ovate family proteins (OFPs) are transcriptional inhibitors that regulate plant growth and development and play important roles in the synthesis of secondary cell walls during pollen development. This study identified the pepper OFP gene family based on the genome-wide analysis and used bioinformatics methods to provide a fundamental profile of the gene family. 74 OFP genes with typical Ovate domain were identified in cultivated pepper Zunla-1, wild pepper Chiltepin and CM334. Chromosome mapping revealed that CazOFP genes were unevenly distributed on 11 chromosomes and Chr00 in Zunla-1, CacOFP genes on 12 chromosomes in Chiltepin, and CamOFP genes on 12 chromosomes and two Scaffflods in CM334. Gene structure analysis revealed that CaOFP genes possessed 1-3 exons, and the analysis of physicochemical properties suggested that CaOFPs were hydrophilic. Many cis-acting elements were identified in the promoter region of CaOFP genes, including ABRE, ARE, Box 4, G-box, TC-rich, and TCT-motif. The expression patterns of pepper at different growth stages showed that CaOFP genes were actively involved in the growth and fruit development of pepper, and CazOFP16 and CazOFP17 were actively involved in response to multiple hormones and stress events. qRT-PCR was also used to verify the expression of CazOFP gene in two developmental stages of seven pepper varieties with different fruit shapes, and it was found that CaOFP genes may be involved in the formation of fruit type in pepper. This study provides theoretical and practical evidence for future research on the OFP gene family.
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Affiliation(s)
- Yin Luo
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Shimei Yang
- Engineering Research Center of Zunyi Pepper Germplasm Resources Conservation and Breeding Cultivation of Guizhou Province, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi, China
| | - Xirong Luo
- Engineering Research Center of Zunyi Pepper Germplasm Resources Conservation and Breeding Cultivation of Guizhou Province, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi, China
| | - Jing Li
- Engineering Research Center of Zunyi Pepper Germplasm Resources Conservation and Breeding Cultivation of Guizhou Province, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi, China
| | - Tangyan Li
- Engineering Research Center of Zunyi Pepper Germplasm Resources Conservation and Breeding Cultivation of Guizhou Province, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi, China
| | - Xiangqun Tang
- Key Lab of Zunyi Crop Gene Resource and Germplasm Innovation, Zunyi Academy of Agricultural Sciences, Zunyi, China
| | - Feng Liu
- Longping Branch, College of Biology, Hunan University, Changsha, China
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuexiao Zou
- Longping Branch, College of Biology, Hunan University, Changsha, China
- College of Horticulture, Hunan Agricultural University, Changsha, China
- *Correspondence: Xuexiao Zou, ; Cheng Qin,
| | - Cheng Qin
- Engineering Research Center of Zunyi Pepper Germplasm Resources Conservation and Breeding Cultivation of Guizhou Province, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi, China
- *Correspondence: Xuexiao Zou, ; Cheng Qin,
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An Y, Xia X, Jing T, Zhang F. Identification of gene family members and a key structural variation reveal important roles of OVATE genes in regulating tea ( Camellia sinensis) leaf development. FRONTIERS IN PLANT SCIENCE 2022; 13:1008408. [PMID: 36212328 PMCID: PMC9539550 DOI: 10.3389/fpls.2022.1008408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
OVATE genes are a new class of transcriptional repressors with important regulatory roles in plant growth and development. Through genome-wide analysis of the OVATE gene family of tea plants, 26 and 13 family members were identified in cultivated and ancient tea plants, respectively. Syntenic results showed that OVATE gene family in cultivated tea plants may have experienced a special expansion event. Based on phylogenetic tree analysis, all OVATE genes were divided into four groups, and the third group had the largest number, reaching 16. Transcriptome data from different organs and populations indicated that many OVATE family members were highly expressed in young shoots and leaves, and their expression levels gradually decreased as tea leaves developed. Finally, the expression trends of the six key candidate genes were verified by RT-qPCR, which were consistent with the transcriptome results, indicating that the ovate gene family plays an important role in regulating the process of tea leaf development. In addition, we identified a key structural variation with a length of 184 bp, and the population genotyping showed that it was closely related to the area of tea leaves. Our research provides an important clue for further exploring the function of ovate gene family in tea plants and the development mechanism of tea leaves.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- CIMMYT-JAAS Joint Center for Wheat Diseases/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing) Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
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8
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Ergon Å, Milvang ØW, Skøt L, Ruttink T. Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes. Mol Genet Genomics 2022; 297:1587-1600. [PMID: 36001174 DOI: 10.1007/s00438-022-01942-x] [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: 03/01/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
Abstract
MAIN CONCLUSION Through selective genotyping of pooled phenotypic extremes, we identified a number of loci and candidate genes putatively controlling timing of stem elongation in red clover. We have identified candidate genes controlling the timing of stem elongation prior to flowering in red clover (Trifolium pratense L.). This trait is of ecological and agronomic significance, as it affects fitness, competitivity, climate adaptation, forage and seed yield, and forage quality. We genotyped replicate pools of phenotypically extreme individuals (early and late-elongating) within cultivar Lea using genotyping-by-sequencing in pools (pool-GBS). After calling and filtering SNPs and GBS locus haplotype polymorphisms, we estimated allele frequencies and searched for markers with significantly different allele frequencies in the two phenotypic groups using BayeScan, an FST-based test utilizing replicate pools, and a test based on error variance of replicate pools. Of the three methods, BayeScan was the least stringent, and the error variance-based test the most stringent. Fifteen significant markers were identified in common by all three tests. The candidate genes flanking the markers include genes with potential roles in the vernalization, autonomous, and photoperiod regulation of floral transition, hormonal regulation of stem elongation, and cell growth. These results provide a first insight into the potential genes and mechanisms controlling transition to stem elongation in a perennial legume, which lays a foundation for further functional studies of the genetic determinants regulating this important trait.
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Affiliation(s)
- Åshild Ergon
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
| | - Øystein W Milvang
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Leif Skøt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, B-9090 Melle, Belgium
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9
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Research Progress on the Leaf Morphology, Fruit Development and Plant Architecture of the Cucumber. PLANTS 2022; 11:plants11162128. [PMID: 36015432 PMCID: PMC9415855 DOI: 10.3390/plants11162128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022]
Abstract
Cucumber (Cucumis sativus L.) is an annual climbing herb that belongs to the Cucurbitaceae family and is one of the most important economic crops in the world. The breeding of cucumber varieties with excellent agronomic characteristics has gained more attention in recent years. The size and shape of the leaves or fruit and the plant architecture are important agronomic traits that influence crop management and productivity, thus determining the crop yields and consumer preferences. The growth of the plant is precisely regulated by both environmental stimuli and internal signals. Although significant progress has been made in understanding the plant morphological regulation of Arabidopsis, rice, and maize, our understanding of the control mechanisms of the growth and development of cucumber is still limited. This paper reviews the regulation of phytohormones in plant growth and expounds the latest progress in research regarding the genetic regulation pathways in leaf development, fruit size and shape, branching, and plant type in cucumber, so as to provide a theoretical basis for improving cucumber productivity and cultivation efficiency.
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10
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Wang H, Zhang D, Zhou X, Zhou G, Zong W, Chen L, Chang Y, Wu X. Transcription Factor AtOFP1 Involved in ABA-Mediated Seed Germination and Root Growth through Modulation of ROS Homeostasis in Arabidopsis. Int J Mol Sci 2022; 23:ijms23137427. [PMID: 35806432 PMCID: PMC9267126 DOI: 10.3390/ijms23137427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/05/2023] Open
Abstract
Ovate family proteins (OFPs) are valued as a family of transcription factors that are unique to plants, and they play a pluripotent regulatory role in plant growth and development, including secondary-cell-wall synthesis, DNA repair, gibberellin synthesis, and other biological processes, via their interaction with TALE family proteins. In this study, CHIP-SEQ was used to detect the potential target genes of AtOFP1 and its signal-regulation pathways. On the other hand, Y2H and BIFC were employed to prove that AtOFP1 can participate in ABA signal transduction by interacting with one of the TALE family protein called AtKNAT3. ABA response genes are not only significantly upregulated in the 35S::HAOFP1 OE line, but they also show hypersensitivity to ABA in terms of seed germination and early seedling root elongation. In addition, the AtOFP1-regulated target genes are mainly mitochondrial membranes that are involved in the oxidative–phosphorylation pathway. Further qRT-PCR results showed that the inefficient splicing of the respiratory complex I subunit genes NAD4 and NAD7 may lead to ROS accumulation in 35S::HA-AtOFP1 OE lines. In conclusion, we speculated that the overexpression of AtOFP1 may cause the ABA hypersensitivity response by increasing the intracellular ROS content generated from damage to the intima systems of mitochondria.
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Affiliation(s)
- Hemeng Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (H.W.); (D.Z.)
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Dongrui Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (H.W.); (D.Z.)
| | - Xi’nan Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Ganghua Zhou
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China;
| | - Wenbo Zong
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Jilin University, Changchun 130021, China;
| | - Lingling Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ying Chang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (H.W.); (D.Z.)
- Correspondence: (Y.C.); (X.W.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (Y.C.); (X.W.)
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11
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Chakrabarti M, Nagabhyru P, Schardl CL, Dinkins RD. Differential gene expression in tall fescue tissues in response to water deficit. THE PLANT GENOME 2022; 15:e20199. [PMID: 35322562 DOI: 10.1002/tpg2.20199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Tall fescue (Festuca arundinacea Schreb.) is a popular pasture and turf grass particularly known for drought resistance, allowing for its persistence in locations that are unfavorable for other cool-season grasses. Also, its seed-borne fungal symbiont (endophyte) Epichloë coenophiala, which resides in the crown and pseudostem, can be a contributing factor in its drought tolerance. Because it contains the apical meristems, crown survival under drought stress is critical to plant survival as well as the endophyte. In this study, we subjected tall fescue plants with their endophyte to water-deficit stress or, as controls with normal watering, then compared plant transcriptome responses in four vegetative tissues: leaf blades, pseudostem, crown, and roots. A transcript was designated a differentially expressed gene (DEG) if it exhibited at least a twofold expression difference between stress and control samples with an adjusted p value of .001. Pathway analysis of the DEGs across all tissue types included photosynthesis, carbohydrate metabolism, phytohormone biosynthesis and signaling, cellular organization, and a transcriptional regulation. While no specific pathway was observed to be differentially expressed in the crown, genes encoding auxin response factors, nuclear pore anchors, structural maintenance of chromosomes, and class XI myosin proteins were more highly differentially expressed in crown than in the other vegetative tissues, suggesting that regulation in expression of these genes in the crown may aid in survival of the meristems in the crown.
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Affiliation(s)
- Manohar Chakrabarti
- Dep. of Plant and Soil Sciences, Univ. of Kentucky, Lexington, KY, 40546-0312, USA
| | - Padmaja Nagabhyru
- Dep. of Plant Pathology, Univ. of Kentucky, Lexington, KY, 40546-0312, USA
| | | | - Randy D Dinkins
- USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY, 40546-0091, USA
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12
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Nookaraju A, Pandey SK, Ahlawat YK, Joshi CP. Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:493. [PMID: 35214825 PMCID: PMC8880547 DOI: 10.3390/plants11040493] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOXTF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.
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Affiliation(s)
- Akula Nookaraju
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Kaveri Seed Company Limited, Secunderabad 500003, Telangana, India
| | - Shashank K. Pandey
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
| | - Yogesh K. Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Chandrashekhar P. Joshi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
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13
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Zhang C, Cui L, Fang J. Genome-wide association study of the candidate genes for grape berry shape-related traits. BMC PLANT BIOLOGY 2022; 22:42. [PMID: 35057757 PMCID: PMC8772106 DOI: 10.1186/s12870-022-03434-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In the breeding of new horticultural crops, fruit shape is an important selection characteristic. A variety of fruit shapes appeared during the gradual process of selection and domestication. However, few studies have been conducted on grape berry shape, especially studies related to mining candidate genes. To discover candidate genes related to grape berry shape, the present study first took the berry shape parameters analyzed by Tomato Analyzer as the target traits and used a genome-wide association analysis to analyze candidate genes. RESULTS In total, 122 single-nucleotide polymorphism (SNP) loci had significant correlations with multiple berry shape traits in both years, and some candidate genes were further mined. These genes were mainly related to LRR receptor-like serine/threonine-protein kinase (At1g05700 and At1g07650), transcription factors (GATA transcription factor 23-like, transcription factor VIP1, transcription initiation factor TFIID, and MADS-box transcription factor 6), ubiquitin ligases (F-box protein SKIP19 and RING finger protein 44), and plant hormones (indole-3-acetic acid-amido synthetase GH3.6 and ethylene-responsive transcription factor ERF061). In addition, some important SNP loci were associated with multiple berry-shape traits. The study further revealed some genes that control multiple traits simultaneously, indicating that these berry shape traits are subject to the coordinated regulation of some genes in controlling berry shape. CONCLUSIONS In the present work, we identified interesting genetic determinants of grape berry shape-related traits. The identification of molecular markers that are closely related to these berry-shape traits is of great significance for breeding specific berry-shaped grape varieties.
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Affiliation(s)
- Chuan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Liwen Cui
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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14
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Maurya D, Mukherjee A, Akhtar S, Chattopadhyay T. Development and validation of the OVATE gene-based functional marker to assist fruit shape selection in tomato. 3 Biotech 2021; 11:474. [PMID: 34777931 DOI: 10.1007/s13205-021-03029-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/12/2021] [Indexed: 01/14/2023] Open
Abstract
Fruit size, shape and colour are important determinants of fruit quality in tomato. Among the different genetic factors, the OVATE gene is a key regulator of fruit elongation in tomato. The loss-of-function recessive ovate allele results from a functional single nucleotide polymorphism (SNP) in the second exon of the gene to produce fruit elongation and variable fruit shapes in different genetic backgrounds. The mutation has also been associated with increased fruit firmness, a desirable trait for processing purpose of tomato. However, the recessive nature of this important mutant allele makes its identification and utilization in breeding programme difficult. Hence, we developed the OVATE gene-based functional marker using the tetra-primer amplification refractory mutation system (T-ARMS) strategy. The developed functional marker was capable of identifying the allelic status at OVATE locus in a co-dominant manner, using routine polymerase chain reaction (PCR) followed by standard agarose gel electrophoresis. Trait-marker association of the developed functional marker was validated in the F2 segregants bearing elongated and non-elongated fruits. Thus, the functional marker developed and validated in this study will assist the tomato breeders in identification and introgression of the desired allelic version of the OVATE gene in a time-, labour- and cost-effective manner. Moreover, identification of the allelic status at the OVATE locus will help in exploring its interacting partners and modifiers for detailed understanding of the fascinating genetics behind fruit shape variation in tomato. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03029-7.
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Affiliation(s)
- Deepak Maurya
- Department of Horticulture (Vegetable and Floriculture), Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Arnab Mukherjee
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Shirin Akhtar
- Department of Horticulture (Vegetable and Floriculture), Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Tirthartha Chattopadhyay
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
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15
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Gala HP, Lanctot A, Jean-Baptiste K, Guiziou S, Chu JC, Zemke JE, George W, Queitsch C, Cuperus JT, Nemhauser JL. A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana. THE PLANT CELL 2021; 33:2197-2220. [PMID: 33822225 PMCID: PMC8364244 DOI: 10.1093/plcell/koab101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/31/2021] [Indexed: 05/20/2023]
Abstract
Root architecture is a major determinant of plant fitness and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied examples of plant organogenesis, yet there are still many unanswered questions about its earliest steps. Among the challenges faced in capturing these first molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. Single-cell sequencing methods afford the opportunity to isolate the specific transcriptional changes occurring in cells undergoing this fate transition. Using this approach, we successfully captured the transcriptomes of initiating lateral root primordia in Arabidopsis thaliana and discovered many upregulated genes associated with this process. We developed a method to selectively repress target gene transcription in the xylem pole pericycle cells where lateral roots originate and demonstrated that the expression of several of these targets is required for normal root development. We also discovered subpopulations of cells in the pericycle and endodermal cell files that respond to lateral root initiation, highlighting the coordination across cell files required for this fate transition.
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Affiliation(s)
- Hardik P. Gala
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Amy Lanctot
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Jonah C. Chu
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Joseph E. Zemke
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Wesley George
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Josh T. Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Author for correspondence: (J.T.C.); (J.L.N.)
| | - Jennifer L. Nemhauser
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Author for correspondence: (J.T.C.); (J.L.N.)
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16
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Kumar A, Anju T, Kumar S, Chhapekar SS, Sreedharan S, Singh S, Choi SR, Ramchiary N, Lim YP. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. Int J Mol Sci 2021; 22:8093. [PMID: 34360856 PMCID: PMC8348985 DOI: 10.3390/ijms22158093] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Thattantavide Anju
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sushil Kumar
- Department of Botany, Govt. Degree College, Kishtwar 182204, Jammu and Kashmir, India;
| | - Sushil Satish Chhapekar
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Sajana Sreedharan
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sonam Singh
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Su Ryun Choi
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Yong Pyo Lim
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
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17
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Wang T, Li Y, Song S, Qiu M, Zhang L, Li C, Dong H, Li L, Wang J, Li L. EMBRYO SAC DEVELOPMENT 1 affects seed setting rate in rice by controlling embryo sac development. PLANT PHYSIOLOGY 2021; 186:1060-1073. [PMID: 33734397 PMCID: PMC8195536 DOI: 10.1093/plphys/kiab106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 05/16/2023]
Abstract
Seed setting rate is one of the critical factors that determine rice yield. Grain formation is a complex biological process, whose molecular mechanism is yet to be improved. Here we investigated the function of an OVATE family protein, Embryo Sac Development 1 (ESD1), in the regulation of seed setting rate in rice (Oryza sativa) by examining its loss-of-function mutants generated via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) technology. ESD1 was predominantly expressed at Stage 6 of panicle development, especially in the ovules. esd1 mutants displayed reduced seed setting rates with normal stamen development and pollen tube growth but abnormal pistil group. Investigation of embryo sacs revealed that during the mitosis of functional megaspores, some egg cells degraded during differentiation in esd1 mutants, thereby hindering subsequent fertilization process and reducing seed setting rate. In addition, the transcriptional level of O. sativa anaphase-promoting complex 6, a reported embryo sac developing gene, was significantly reduced in esd1 mutants. These results support that ESD1 is an important modulator of ESD and seed setting rate in rice. Together, this finding demonstrates that ESD1 positively regulates the seed setting rate by controlling ESD in rice and has implications for the improvement of rice yield.
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Affiliation(s)
- Tiankang Wang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yixing Li
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Shufeng Song
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Mudan Qiu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Licheng Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Chengxia Li
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Hao Dong
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Lei Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Jianlong Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Li Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Author for communication:
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18
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Wang H, Chen JG, Chang Y. Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2021; 12:650109. [PMID: 33959141 PMCID: PMC8095670 DOI: 10.3389/fpls.2021.650109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis, and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis-acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.
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Affiliation(s)
- Hemeng Wang
- Northeast Agricultural University, Harbin, China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ying Chang
- Northeast Agricultural University, Harbin, China
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19
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Zhou H, Ma R, Gao L, Zhang J, Zhang A, Zhang X, Ren F, Zhang W, Liao L, Yang Q, Xu S, Otieno Ogutu C, Zhao J, Yu M, Jiang Q, Korban SS, Han Y. A 1.7-Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:192-205. [PMID: 32722872 PMCID: PMC7769229 DOI: 10.1111/pbi.13455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/16/2020] [Indexed: 05/06/2023]
Abstract
Flat peaches have become popular worldwide due to their novelty and convenience. The peach flat fruit trait is genetically controlled by a single gene at the S locus, but its genetic basis remains unclear. Here, we report a 1.7-Mb chromosomal inversion downstream of a candidate gene encoding OVATE Family Protein, designated PpOFP1, as the causal mutation for the peach flat fruit trait. Genotyping of 727 peach cultivars revealed an occurrence of this large inversion in flat peaches, but absent in round peaches. Ectopic overexpression of PpOFP1 resulted in oval-shaped leaves and shortened siliques in Arabidopsis, suggesting its role in repressing cell elongation. Transcriptional activation of PpOFP1 by the chromosomal inversion may repress vertical elongation in flat-shaped fruits at early stages of development, resulting in the flat fruit shape. Moreover, PpOFP1 can interact with fruit elongation activator PpTRM17, suggesting a regulatory network controlling fruit shape in peach. Additionally, screening of peach wild relatives revealed an exclusive presence of the chromosomal inversion in P. ferganensis, supporting that this species is the ancestor of the domesticated peach. This study provides new insights into mechanisms underlying fruit shape evolution and molecular tools for genetic improvement of fruit shape trait in peach breeding programmes.
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Affiliation(s)
- Hui Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural CropsInstitute of HorticultureAnhui Academy of Agricultural SciencesHefeiChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Ruijuan Ma
- Institute of HorticultureJiangsu Academy of Agricultural SciencesNanjingChina
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNYUSA
| | - Jinyun Zhang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural CropsInstitute of HorticultureAnhui Academy of Agricultural SciencesHefeiChina
| | - Aidi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Xiujun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Fei Ren
- Institute of Forestry and PomologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Weihan Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei ProvinceCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Qiurui Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
| | - Shengli Xu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Department of Natural Resources and Environmental SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Jianbo Zhao
- Institute of Forestry and PomologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Mingliang Yu
- Institute of HorticultureJiangsu Academy of Agricultural SciencesNanjingChina
| | - Quan Jiang
- Institute of Forestry and PomologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
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Boudichevskaia A, Ruban A, Thiel J, Fiebig A, Houben A. Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides. Int J Mol Sci 2020; 21:ijms21207596. [PMID: 33066598 PMCID: PMC7593951 DOI: 10.3390/ijms21207596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 11/30/2022] Open
Abstract
Some eukaryotes exhibit dramatic genome size differences between cells of different organs, resulting from programmed elimination of chromosomes. Here, we present the first transcriptome analysis of programmed chromosome elimination using laser capture microdissection (LCM)-based isolation of the central meristematic region of Aegilops speltoides embryos where B chromosome (B) elimination occurs. The comparative RNA-seq analysis of meristematic cells of embryos with (Bplus) and without Bs (B0) allowed the identification of 14,578 transcript isoforms (35% out of 41,615 analyzed transcript isoforms) that are differentially expressed during the elimination of Bs. A total of 2908 annotated unigenes were found to be up-regulated in Bplus condition. These genes are either associated with the process of B chromosome elimination or with the presence of B chromosomes themselves. GO enrichment analysis categorized up-regulated transcript isoforms into 27 overrepresented terms related to the biological process, nine terms of the molecular function aspect and three terms of the cellular component category. A total of 2726 annotated unigenes were down-regulated in Bplus condition. Based on strict filtering criteria, 341 B-unique transcript isoforms could be identified in central meristematic cells, of which 70 were functionally annotated. Beside others, genes associated with chromosome segregation, kinetochore function and spindle checkpoint activity were retrieved as promising candidates involved in the process of B chromosome elimination.
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Affiliation(s)
- Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466 OT Gatersleben, Germany; (A.R.); (J.T.); (A.F.)
- KWS SAAT SE & Co. KGaA, 37574 Einbeck, Germany
- Correspondence: (A.B.); (A.H.)
| | - Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466 OT Gatersleben, Germany; (A.R.); (J.T.); (A.F.)
- KWS SAAT SE & Co. KGaA, 37574 Einbeck, Germany
| | - Johannes Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466 OT Gatersleben, Germany; (A.R.); (J.T.); (A.F.)
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466 OT Gatersleben, Germany; (A.R.); (J.T.); (A.F.)
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466 OT Gatersleben, Germany; (A.R.); (J.T.); (A.F.)
- Correspondence: (A.B.); (A.H.)
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21
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Ding B, Hu C, Feng X, Cui T, Liu Y, Li L. Systematic analysis of the OFP genes in six Rosaceae genomes and their roles in stress response in Chinese pear ( Pyrus bretschneideri). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2085-2094. [PMID: 33088052 PMCID: PMC7548309 DOI: 10.1007/s12298-020-00866-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 05/13/2023]
Abstract
OVATE family proteins (OFPs) are the plant-specific transcription factors, and have significant functions in regulating plant growth, development and resistance. The OFP genes have been investigated in several plants, but they still lack a systematic analysis of OFP genes in Chinese pear and some other five Rosaceae genomes. Here, 28 PbrOFPs were identified within Chinese pear and compared them with those of other five Rosaceae genomes. Evolutionary tree revealed that all OFP genes from six Rosaceae genomes were divided into eight groups. Seventeen conserved microsynteny regions were detected in Chinese pear genome, suggested that these PbrOFP genes might be considered to have originated from the large-scale duplication events., indicating these PbrOFP genes might contain specialized regulatory mechanisms in these tissues, such as flower, ovary and fruit. Remarkably, two PbrOFP genes (Pbr010426.1 and Pbr010427.1) were up-regulated under Venturia nashicola treatment, and five PbrOFP genes were up-regulated under PEG treatment, suggesting that these genes might play crucial roles in defence to environmental stresses. Our data presented a systematic analysis and might aid in the selection of appropriate PbrOFPs for further functional studies in Chinese pear, especially in response to the mechanism of biotic and abiotic stresses.
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Affiliation(s)
- Baopeng Ding
- College of Horticulture, Shanxi Agriculture University, Jinzhong, China
| | - Chaohui Hu
- College of Horticulture, Shanxi Agriculture University, Jinzhong, China
| | - Xinxin Feng
- College of Horticulture, Shanxi Agriculture University, Jinzhong, China
| | - Tingting Cui
- College of Horticulture, Shanxi Agriculture University, Jinzhong, China
| | - Yi Liu
- College of Horticulture, Shanxi Agriculture University, Jinzhong, China
| | - Liulin Li
- College of Horticulture, Shanxi Agriculture University, Jinzhong, China
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 DOI: 10.21203/rs.3.rs-17010/v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. RESULTS We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. CONCLUSIONS This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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23
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 PMCID: PMC7437933 DOI: 10.1186/s12864-020-06972-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. Results We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. Conclusions This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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Yang T, Sun Y, Wang Y, Zhou L, Chen M, Bian Z, Lian Y, Xuan L, Yuan G, Wang X, Wang C. AtHSPR is involved in GA- and light intensity-mediated control of flowering time and seed set in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3543-3559. [PMID: 32157303 PMCID: PMC7475253 DOI: 10.1093/jxb/eraa128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/05/2020] [Indexed: 05/15/2023]
Abstract
Flowering is a dynamic and synchronized process, the timing of which is finely tuned by various environmental signals. A T-DNA insertion mutant in Arabidopsis HEAT SHOCK PROTEIN-RELATED (AtHSPR) exhibited late-flowering phenotypes under both long-day (LD) and short-day (SD) conditions compared to the wild-type, while over-expression of AtHSPR promoted flowering. Exogenous application of gibberellin (GA) partially rescued the late-flowering mutant phenotype under both LD and SD conditions, suggesting that AtHSPR is involved in GA biosynthesis and/or the GA signaling that promotes flowering. Under SD or low-light conditions, the Athspr mutant exhibited late flowering together with reduced pollen viability and seed set, defective phenotypes that were partially rescued by GA treatment. qRT-PCR assays confirmed that GA biosynthetic genes were down-regulated, that GA catabolic genes were up-regulated, and that the levels of bioactive GA and its intermediates were decreased in Athspr under both SD and low-light/LD, further suggesting that AtHSPR could be involved in the GA pathway under SD and low-light conditions. Furthermore, AtHSPR interacted in vitro with OFP1 and KNAT5, which are transcriptional repressors of GA20ox1 in GA biosynthesis. Taken together, our findings demonstrate that AtHSPR plays a positive role in GA- and light intensity-mediated regulation of flowering and seed set.
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Affiliation(s)
- Tao Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yan Sun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongli Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lina Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mengya Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiyuan Bian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuke Lian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lijuan Xuan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guoqiang Yuan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xinyu Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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Zhang J, Miao H, Xie B, Wang J, Jia C, Zhang J, Xu B, Jin Z, Liu J. Genomic and Transcriptional Analysis of Banana Ovate Family Proteins Reveals Their Relationship with Fruit Development and Ripening. Biochem Genet 2020; 58:412-429. [PMID: 32144551 DOI: 10.1007/s10528-020-09951-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 02/01/2020] [Indexed: 01/19/2023]
Abstract
Ovate Family Proteins (OFPs) belong to a plant-specific transcription factor family. They have been found to have significant roles in growth and development in Arabidopsis and tomato; however, little is known regarding their role in banana. Thus, a genome-wide study of OFP genes in banana was conducted for the first time in the present study. The results demonstrated that 49 OFP family members are unequally distributed across 11 chromosomes. Phylogenetic analysis grouped these genes into two subfamilies and eight subgroups, which was confirmed by the conserved motif and gene structure analysis. Furthermore, MaOFPs genes duplicates were found to have originated from whole-genome duplication (WGD). The expression patterns of the genes in the various tissues and at different fruit development and ripening stages in the BaXi Jiao (BX) and Feng Jiao (FJ), banana cultivars were elucidated using transcriptome analysis. Using co-expression network analysis, MaOFP1 was found to interact not only with MaMADS36 but also with hormone response proteins. These findings improve our understanding of the functions of MaOFPs genes in the control of plant hormone signal transduction pathways during banana growth and ripening, which should inform the genetic improvement of important agricultural characters.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Biyu Xie
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
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Characterization of the OFP Gene Family and its Putative Involvement of Tuberous Root Shape in Radish. Int J Mol Sci 2020; 21:ijms21041293. [PMID: 32075122 PMCID: PMC7072887 DOI: 10.3390/ijms21041293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/21/2022] Open
Abstract
The shape of the tuberous root, a very important quality trait, varies dramatically among radish cultivars. Ovate family proteins (OFPs) are plant-specific proteins that regulate multiple aspects of plant growth and development. To investigate the possible role of OFPs in radish tuberous root formation, 35 putative RsOFPs were identified from radish, and their expression patterns were detected during tuberous root development in six different radish cultivars. Phylogenetically, RsOFP2.3 clustered together with AtOFP1 and other members of this family that are known to regulate organ shape. Moreover, RsOFP2.3 expression was negatively correlated with tuberous root elongation after the cortex splitting stage, which made this gene the top candidate for the involvement of tuberous root shape. To further characterize the function of RsOFP2.3, it was ectopically expressed in Arabidopsis. RsOFP2.3 overexpression in Arabidopsis led to multiple phenotypical changes, especially the decreased length and increased width of the hypocotyl. Furthermore, RsOFP2.3 expression was induced by all the five classic plant hormones except ethylene, and it was most sensitive to exogenous gibberellic acid treatment. We also found that RsOFP2.3 was localized in the cytoplasm. Taken together, our results suggested the possible involvement for RsOFP2.3 in suppressing radish tuberous root elongation and that it encodes a functional protein which mainly inhibits the elongation of Arabidopsis aerial organs.
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Afsharyan NP, Sannemann W, Léon J, Ballvora A. Effect of epistasis and environment on flowering time in barley reveals a novel flowering-delaying QTL allele. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:893-906. [PMID: 31781747 PMCID: PMC6977191 DOI: 10.1093/jxb/erz477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 10/07/2019] [Indexed: 05/25/2023]
Abstract
Flowering time is a complex trait and has a key role in crop yield and adaptation to environmental stressors such as heat and drought. This study aimed to better understand the interconnected dynamics of epistasis and environment and look for novel regulators. We investigated 534 spring barley MAGIC DH lines for flowering time at various environments. Analysis of quantitative trait loci (QTLs), epistatic interactions, QTL × environment (Q×E) interactions, and epistasis × environment (E×E) interactions were performed with single SNP and haplotype approaches. In total, 18 QTLs and 2420 epistatic interactions were detected, including intervals harboring major genes such as Ppd-H1, Vrn-H1, Vrn-H3, and denso/sdw1. Epistatic interactions found in field and semi-controlled conditions were distinctive. Q×E and E×E interactions revealed that temperature influenced flowering time by triggering different interactions between known and newly detected regulators. A novel flowering-delaying QTL allele was identified on chromosome 1H (named 'HvHeading') and was shown to be engaged in epistatic and environment interactions. Results suggest that investigating epistasis, environment, and their interactions, rather than only single QTLs, is an effective approach for detecting novel regulators. We assume that barley can adapt flowering time to the environment via alternative routes within the pathway.
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Affiliation(s)
- Nazanin P Afsharyan
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Wiebke Sannemann
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
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28
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Yu J, Conrad AO, Decroocq V, Zhebentyayeva T, Williams DE, Bennett D, Roch G, Audergon JM, Dardick C, Liu Z, Abbott AG, Staton ME. Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach. FRONTIERS IN PLANT SCIENCE 2020; 11:180. [PMID: 32180783 PMCID: PMC7059448 DOI: 10.3389/fpls.2020.00180] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/06/2020] [Indexed: 05/07/2023]
Abstract
Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Anna O. Conrad
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States
| | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Universite de Bordeaux, Villenave d'Ornon, France
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, the Pennsylvania State University, University Park, PA, United States
| | - Daniel E. Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Guillaume Roch
- GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA, Montfavet, France
| | - Jean-Marc Audergon
- GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA, Montfavet, France
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Albert G. Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Margaret E. Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
- Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
- *Correspondence: Margaret E. Staton,
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Pan Y, Wang Y, McGregor C, Liu S, Luan F, Gao M, Weng Y. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1-21. [PMID: 31768603 DOI: 10.1007/s00122-019-03481-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/11/2019] [Indexed: 05/28/2023]
Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
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Affiliation(s)
- Yupeng Pan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Shi Liu
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Feishi Luan
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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30
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Cruz MV, Mori GM, Oh DH, Dassanayake M, Zucchi MI, Oliveira RS, Souza APD. Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae). Mol Ecol 2019; 29:344-362. [PMID: 31834961 DOI: 10.1111/mec.15330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/31/2022]
Abstract
Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
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Affiliation(s)
- Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | | | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, USA
| | | | - Rafael Silva Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | - Anete Pereira de Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
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31
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Knauer S, Javelle M, Li L, Li X, Ma X, Wimalanathan K, Kumari S, Johnston R, Leiboff S, Meeley R, Schnable PS, Ware D, Lawrence-Dill C, Yu J, Muehlbauer GJ, Scanlon MJ, Timmermans MCP. A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. Genome Res 2019; 29:1962-1973. [PMID: 31744902 PMCID: PMC6886502 DOI: 10.1101/gr.250878.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.
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Affiliation(s)
- Steffen Knauer
- Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Marie Javelle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Xiaoli Ma
- Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Kokulapalan Wimalanathan
- Interdepartmental Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Robyn Johnston
- Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Samuel Leiboff
- Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Robert Meeley
- DuPont Pioneer, Agricultural Biotechnology, Johnston, Iowa 50131, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Carolyn Lawrence-Dill
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA.,Interdepartmental Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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32
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Maeda H, Akagi T, Onoue N, Kono A, Tao R. Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon. PLANT & CELL PHYSIOLOGY 2019; 60:2464-2477. [PMID: 31350891 PMCID: PMC6839372 DOI: 10.1093/pcp/pcz139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.
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Affiliation(s)
- Haruka Maeda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Akagi
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, Japan
| | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan
| | - Atsushi Kono
- Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan
| | - Ryutaro Tao
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Genome-wide identification, expression, and interaction analysis for ovate family proteins in peach. Mol Biol Rep 2019; 46:3755-3764. [PMID: 31028569 DOI: 10.1007/s11033-019-04817-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/12/2019] [Indexed: 10/26/2022]
Abstract
Ovate family proteins (OFPs), which are involved in aspects of plant development and growth, is a class of plant-specific transcription factors. Although OFPs have been reported in some species, little is known about their evolution, structure, fruit developmental expression, and interactions among OFP members in peach (Prunus persica). In this study, 15 peach OFP (PpOFP) genes were identified. Phylogenetic analysis showed that 716 OFPs from 32 species were divided into 15 subgroups; 10 subgroups (Ia, Ib, Ic, Id, Ie, If, Ig, Ih, Ii, and Ij) were composed of dicotyledonous plants only and five (IIa, IIb, IIc, IId, and IIe) were composed of monocotyledonous plants only. Structure analysis showed that the OFP genes in monocotyledonous and dicotyledonous plants had no introns. Chromosomal localization analysis showed that 15 PpOFP genes were unevenly mapped on seven chromosomes. Furthermore, eight of the 15 PpOFP genes were cloned successfully by the RT-PCR method. To some extent, eight PpOFPs were expressed in all the detected peach tissues. In addition, analysis by Y2H and BiFC technologies indicated that both PpOFP4 and PpOFP5 formed homodimers with themselves, and PpOFP5 interacted with PpOFP7 or PpOFP8 to form heterodimers. These results serve as the theoretical basis for the analysis of the biological function and regulation of peach OFP transcription factors in the growth, development and other conditions, as well as evolution studies of OFP transcription factors in higher plants.
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34
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Yang H, Akagi T, Kawakatsu T, Tao R. Gene networks orchestrated by MeGI: a single-factor mechanism underlying sex determination in persimmon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:97-111. [PMID: 30556936 PMCID: PMC6850717 DOI: 10.1111/tpj.14202] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 05/20/2023]
Abstract
Separating male and female sex organs is one of the main strategies used to maintain genetic diversity within a species. However, the genetic determinants and their regulatory mechanisms have been identified in only a few species. In dioecious persimmons, the homeodomain transcription factor, MeGI, which is the target of a Y chromosome-encoded small-RNA, OGI, can determine floral sexuality. The basic features of this system are conserved in the monoecious hexaploid Oriental persimmon, in which an additional epigenetic regulation of MeGI determines floral sexuality. The downstream regulatory pathways of MeGI remain uncharacterized. In this study, we examined transcriptomic data for male and female flowers from monoecious persimmon cultivars to unveil the gene networks orchestrated by MeGI. A network visualization and cistrome assessment suggested that class-1 KNOTTED-like homeobox (KNOX)/ovate family protein (OFP)/growth regulating factors (GRFs) and short vegetative phase (SVP) genes mediate the differences in gynoecium and androecium development between male and female flowers, respectively. The expression of these genes is directly controlled by MeGI. The gene networks also suggested that some cytokinin, auxin, and gibberellin signaling genes function cooperatively in the KNOX/OFP/GRF pathway during gynoecium differentiation. Meanwhile, SVP may repress PI expression in developing androecia. Overall, our results suggest that MeGI evolved the ability to promote gynoecium development and suppress androecium development by regulating KNOX/OFP/GRF and SVP expression levels, respectively. These insights may help to clarify the molecular mechanism underlying the production of unisexual flowers, while also elucidating the physiological background enabling a single-factor system to establish dioecy in plants.
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Affiliation(s)
- Ho‐Wen Yang
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
| | - Takashi Akagi
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
- Japan Science and Technology Agency (JST)PRESTOKawaguchi‐shiSaitama332‐0012Japan
| | - Taiji Kawakatsu
- Division of BiotechnologyInstitute of Agrobiological SciencesNational Agriculture and Food Research OrganizationTsukubaIbaraki305‐8602Japan
| | - Ryutaro Tao
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
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Zhou S, Hu Z, Li F, Tian S, Zhu Z, Li A, Chen G. Overexpression of SlOFP20 affects floral organ and pollen development. HORTICULTURE RESEARCH 2019; 6:125. [PMID: 31754432 PMCID: PMC6856366 DOI: 10.1038/s41438-019-0207-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 05/06/2023]
Abstract
The OVATE gene was initially identified in tomato and serves as a key regulator of fruit shape. There are 31 OFP members in the tomato genome. However, their roles in tomato growth and reproductive development are largely unknown. Here, we cloned the OFP transcription factor SlOFP20. Tomato plants overexpressing SlOFP20 displayed several phenotypic defects, including an altered floral architecture and fruit shape and reduced male fertility. SlOFP20 overexpression altered the expression levels of some brassinosteroid (BR)-associated genes, implying that SlOFP20 may play a negative role in the BR response, similar to its ortholog OsOFP19 in rice. Moreover, the transcript accumulation of gibberellin (GA)-related genes was significantly affected in the transgenic lines. SlOFP20 may play an important role in the crosstalk between BR and GA. The pollen germination assay suggested that the pollen germination rate of SlOFP20-OE plants was distinctly lower than that of WT plants. In addition, the tomato pollen-associated genes SlCRK1, SlPMEI, LePRK3, SlPRALF, and LAT52 were all suppressed in the transgenic lines. Our data imply that SlOFP20 may affect floral organ and pollen development by modulating BR and GA signaling in tomato.
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Affiliation(s)
- Shengen Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Fenfen Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Shibing Tian
- Institute of Vegetable Research, Chongqing Academy of Agricultural Sciences, Chongqing, People’s Republic of China
| | - Zhiguo Zhu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Anzhou Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People’s Republic of China
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Dangwal M, Das S. Identification and Analysis of OVATE Family Members from Genome of the Early Land Plants Provide Insights into Evolutionary History of OFP Family and Function. J Mol Evol 2018; 86:511-530. [PMID: 30206666 DOI: 10.1007/s00239-018-9863-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023]
Abstract
Mosses, liverworts, hornworts and lycophytes represent transition stages between the aquatic to terrestrial/land plants. Several morphological and adaptive novelties driven by genomic components including emergence and expansion of new or existing gene families have played a critical role during and after the transition, and contributed towards successful colonization of terrestrial ecosystems. It is crucial to decipher the evolutionary transitions and natural selection on the gene structure and function to understand the emergence of phenotypic and adaptive diversity. Plants at the "transition zone", between aquatic and terrestrial ecosystem, are also the most vulnerable because of climate change and may contain clues for successful mitigation of the challenges of climate change. Identification and comparative analyses of such genetic elements and gene families are few in mosses, liverworts, hornworts and lycophytes. Ovate family proteins (OFPs) are plant-specific transcriptional repressors and are acknowledged for their roles in important growth and developmental processes in land plants, and information about the functional aspects of OFPs in early land plants is fragmentary. As a first step towards addressing this gap, a comprehensive in silico analysis was carried out utilizing publicly available genome sequences of Marchantia polymorpha (Mp), Physcomitrella patens (Pp), Selaginella moellendorffii (Sm) and Sphagnum fallax (Sf). Our analysis led to the identification of 4 MpOFPs, 19 PpOFPs, 6 SmOFPs and 3 SfOFPs. Cross-genera analysis revealed a drastic change in the structure and physiochemical properties in OFPs suggesting functional diversification and genomic plasticity during the evolutionary course. Knowledge gained from this comparative analysis will form the framework towards deciphering and dissection of their developmental and adaptive role/s in early land plants and could provide insights into evolutionary strategies adapted by land plants.
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Affiliation(s)
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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Cai M, Huang H, Ni F, Tong Z, Lin E, Zhu M. RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation. PeerJ 2018; 6:e5427. [PMID: 30155351 PMCID: PMC6108316 DOI: 10.7717/peerj.5427] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/20/2018] [Indexed: 01/09/2023] Open
Abstract
Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.
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Affiliation(s)
- Miaomiao Cai
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Fei Ni
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Zaikang Tong
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Erpei Lin
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Zhang L, Sun L, Zhang X, Zhang S, Xie D, Liang C, Huang W, Fan L, Fang Y, Chang Y. OFP1 Interaction with ATH1 Regulates Stem Growth, Flowering Time and Flower Basal Boundary Formation in Arabidopsis. Genes (Basel) 2018; 9:genes9080399. [PMID: 30082666 PMCID: PMC6116164 DOI: 10.3390/genes9080399] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 11/16/2022] Open
Abstract
Ovate Family Protein1 (OFP1) is a regulator, and it is suspected to be involved in plant growth and development. Meanwhile, Arabidopsis Thaliana Homeobox (ATH1), a BEL1-like homeodomain (HD) transcription factor, is known to be involved in regulating stem growth, flowering time and flower basal boundary development in Arabidopsis. Previous large-scale yeast two-hybrid studies suggest that ATH1 possibly interact with OFP1, but this interaction is yet unverified. In our study, the interaction of OFP1 with ATH1 was verified using a directional yeast two-hybrid system and bimolecular fluorescence complementation (BiFC). Our results also demonstrated that the OFP1-ATH1 interaction is mainly controlled by the HD domain of ATH1. Meanwhile, we found that ATH1 plays the role of transcriptional repressor to regulate plant development and that OFP1 can enhance ATH1 repression function. Regardless of the mechanism, a putative functional role of ATH1-OFP1 may be to regulate the expression of the both the GA20ox1 gene, which is involved in gibberellin (GA) biosynthesis and control of stem elongation, and the Flowering Locus C (FLC) gene, which inhibits transition to flowering. Ultimately, the regulatory functional mechanism of OFP1-ATH1 may be complicated and diverse according to our results, and this work lays groundwork for further understanding of a unique and important protein⁻protein interaction that influences flowering time, stem development, and flower basal boundary development in plants.
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Affiliation(s)
- Liguo Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Lili Sun
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Xiaofei Zhang
- College of Mathematics and Information Sciences, Guangxi University, Nanning 530004, China.
| | - Shuquan Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Dongwei Xie
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Chunbo Liang
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Wengong Huang
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Lijuan Fan
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Yuyan Fang
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Ying Chang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Pickersgill B. Parallel vs. Convergent Evolution in Domestication and Diversification of Crops in the Americas. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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40
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Liu J, Zhang J, Wang J, Zhang J, Miao H, Jia C, Wang Z, Xu B, Jin Z. MuMADS1 and MaOFP1 regulate fruit quality in a tomato ovate mutant. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:989-1001. [PMID: 28944538 PMCID: PMC5902769 DOI: 10.1111/pbi.12843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/11/2017] [Accepted: 09/20/2017] [Indexed: 05/11/2023]
Abstract
Fruit ripening and quality are common botanical phenomena that are closely linked and strictly regulated by transcription factors. It was previously discovered that a banana MADS-box protein named MuMADS1 interacted with an ovate family protein named MaOFP1 to regulate banana fruit ripening. To further investigate the role of MuMADS1 and MaOFP1 in the regulation of fruit quality, a combination of genetic transformation and transcriptional characterization was used. The results indicated that the co-expression of MuMADS1 and MaOFP1 in the ovate mutant could compensate for fruit shape and inferior qualities relating to fruit firmness, soluble solids and sugar content. The number of differentially expressed genes (DEGs) was 1395 in WT vs. ovate, with 883 up-regulated and 512 down-regulated genes, while the numbers of DEGs gradually decreased with the transformation of MuMADS1 and MaOFP1 into ovate. 'Starch and sucrose metabolism' constituted the primary metabolic pathway, and the gene numbers in this pathway were obviously different when MuMADS1 and MaOFP1 were integrated into ovate. A series of metabolic genes involved in cell wall biosynthesis were up-regulated in the WT vs. ovate, which probably resulted in the firmer texture and lower sugar contents in the ovate fruit. These results demonstrate that MuMADS1 and MaOFP1 are coregulators of fruit quality, facilitating the dissection of the molecular mechanisms underlying fruit quality formation.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jing Zhang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jingyi Wang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Hongxia Miao
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Caihong Jia
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Zhuo Wang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Biyu Xu
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Key Laboratory of Genetic Improvement of BananasHainan ProvinceHaikou Experimental StationChinese Academy of Tropical Agricultural SciencesHaikouChina
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Rao X, Dixon RA. Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses. FRONTIERS IN PLANT SCIENCE 2018; 9:399. [PMID: 29670638 PMCID: PMC5893761 DOI: 10.3389/fpls.2018.00399] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 03/13/2018] [Indexed: 05/17/2023]
Abstract
Secondary cell walls mediate many crucial biological processes in plants including mechanical support, water and nutrient transport and stress management. They also provide an abundant resource of renewable feed, fiber, and fuel. The grass family contains the most important food, forage, and biofuel crops. Understanding the regulatory mechanism of secondary wall formation in grasses is necessary for exploiting these plants for agriculture and industry. Previous research has established a detailed model of the secondary wall regulatory network in the dicot model species Arabidopsis thaliana. Grasses, branching off from the dicot ancestor 140-150 million years ago, display distinct cell wall morphology and composition, suggesting potential for a different secondary wall regulation program from that established for dicots. Recently, combined application of molecular, genetic and bioinformatics approaches have revealed more transcription factors involved in secondary cell wall biosynthesis in grasses. Compared with the dicots, grasses exhibit a relatively conserved but nevertheless divergent transcriptional regulatory program to activate their secondary cell wall development and to coordinate secondary wall biosynthesis with other physiological processes.
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Affiliation(s)
- Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN, United States
- *Correspondence: Xiaolan Rao,
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN, United States
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Rymen B, Kawamura A, Schäfer S, Breuer C, Iwase A, Shibata M, Ikeda M, Mitsuda N, Koncz C, Ohme-Takagi M, Matsui M, Sugimoto K. ABA Suppresses Root Hair Growth via the OBP4 Transcriptional Regulator. PLANT PHYSIOLOGY 2017; 173:1750-1762. [PMID: 28167701 PMCID: PMC5338652 DOI: 10.1104/pp.16.01945] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/03/2017] [Indexed: 05/20/2023]
Abstract
Plants modify organ growth and tune morphogenesis in response to various endogenous and environmental cues. At the cellular level, organ growth is often adjusted by alterations in cell growth, but the molecular mechanisms underlying this control remain poorly understood. In this study, we identify the DNA BINDING WITH ONE FINGER (DOF)-type transcription regulator OBF BINDING PROTEIN4 (OBP4) as a repressor of cell growth. Ectopic expression of OBP4 in Arabidopsis (Arabidopsis thaliana) inhibits cell growth, resulting in severe dwarfism and the repression of genes involved in the regulation of water transport, root hair development, and stress responses. Among the basic helix-loop-helix transcription factors known to control root hair growth, OBP4 binds the ROOT HAIR DEFECTIVE6-LIKE2 (RSL2) promoter to repress its expression. The accumulation of OBP4 proteins is detected in expanding root epidermal cells, and its expression level is increased by the application of abscisic acid (ABA) at concentrations sufficient to inhibit root hair growth. ABA-dependent induction of OBP4 is associated with the reduced expression of RSL2 Furthermore, ectopic expression of OBP4 or loss of RSL2 function results in ABA-insensitive root hair growth. Taken together, our results suggest that OBP4-mediated transcriptional repression of RSL2 contributes to the ABA-dependent inhibition of root hair growth in Arabidopsis.
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Affiliation(s)
- Bart Rymen
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Ayako Kawamura
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Sabine Schäfer
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Christian Breuer
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Akira Iwase
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Michitaro Shibata
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Miho Ikeda
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Nobutaka Mitsuda
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Csaba Koncz
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Masaru Ohme-Takagi
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Minami Matsui
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.)
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.)
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
| | - Keiko Sugimoto
- RIKEN CSRS, Yokohama 230-0045, Japan (B.R., A.K., C.B., A.I., M.S., M.M., K.S.);
- Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (S.S., C.K.);
- Graduate School of Science and Engineering (M.I.) and Institute for Environmental Science and Technology (M.O.-T.), Saitama University, Saitama 338-8570, Japan;
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan (M.I., N.M., M.O.-T.); and
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, H-6724 Szeged, Hungary (C.K.)
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Montero-Pau J, Blanca J, Esteras C, Martínez-Pérez EM, Gómez P, Monforte AJ, Cañizares J, Picó B. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing. BMC Genomics 2017; 18:94. [PMID: 28100189 PMCID: PMC5241963 DOI: 10.1186/s12864-016-3439-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
Background Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. Results We report the Genotyping-by-sequencing analysis of a RIL population developed from the inter subspecific cross Zucchini x Scallop (ssp. pepo x ssp. ovifera). Several thousands of SNP markers were identified and genotyped, followed by the construction of a high-density linkage map based on 7,718 SNPs (average of 386 markers/linkage group) covering 2,817.6 cM of the whole genome, which is a great improvement with respect to previous maps. A QTL analysis was performed using phenotypic data obtained from the RIL population from three environments. In total, 48 consistent QTLs for vine, flowering and fruit quality traits were detected on the basis of a multiple-environment analysis, distributed in 33 independent positions in 15 LGs, and each QTL explained 1.5–62.9% of the phenotypic variance. Eight major QTLs, which could explain greater than 20% of the phenotypic variation were detected and the underlying candidate genes identified. Conclusions Here we report the first SNP saturated map in the species, anchored to the physical map. Additionally, several consistent QTLs related to early flowering, fruit shape and length, and rind and flesh color are reported as well as candidate genes for them. This information will enhance molecular breeding in C. pepo and will assist the gene cloning underlying the studied QTLs, helping to reveal the genetic basis of the studied processes in squash. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3439-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Montero-Pau
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Cristina Esteras
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Eva Ma Martínez-Pérez
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Pedro Gómez
- Instituto de Investigación y Formación Agraria y Pesquera (IFAPA). Área de Mejora y Biotecnología de cultivos. Camino San Nicolás 1, 04745, La Mojonera, Almería, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Joaquín Cañizares
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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