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Santo Domingo M, Orduña L, Navarro D, Mayobre C, Santiago A, Valverde L, Alexiou KG, Matus JT, Pujol M, Garcia-Mas J. The ethylene-responsive transcription factor ERF024 is a novel regulator of climacteric fruit ripening in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38900073 DOI: 10.1111/tpj.16889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/21/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
Fruit ripening is an essential developmental stage in Angiosperms triggered by hormonal signals such as ethylene, a major player in climacteric ripening. Melon is a unique crop showing both climacteric and non-climacteric cultivars, offering an ideal model for dissecting the genetic mechanisms underpinning this process. The major quantitative trait locus ETHQV8.1 was previously identified as a key regulator of melon fruit ripening. Here, we narrowed down ETHQV8.1 to a precise genomic region containing a single gene, the transcription factor CmERF024. Functional validation using CRISPR/Cas9 knock-out plants unequivocally identified CmERF024 as the causal gene governing ETHQV8.1. The erf024 mutants exhibited suppression of ethylene production, leading to a significant delay and attenuation of fruit ripening. Integrative multi-omic analyses encompassing RNA-seq, DAP-seq, and DNase-seq revealed the association of CmERF024 with chromatin accessibility and gene expression dynamics throughout fruit ripening. Our data suggest CmERF024 as a novel regulator of climacteric fruit ripening in melon.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - David Navarro
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Konstantinos G Alexiou
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
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Xin H, Liu X, Chai S, Yang X, Li H, Wang B, Xu Y, Lin S, Zhong X, Liu B, Lu Z, Zhang Z. Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops. THE PLANT CELL 2024; 36:2272-2288. [PMID: 38421027 PMCID: PMC11132967 DOI: 10.1093/plcell/koae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved noncoding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865 to 43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2, and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution.
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Affiliation(s)
- Hongjia Xin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bowen Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuanchao Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengnan Lin
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiaoyun Zhong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Liu
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091China
| | - Zefu Lu
- National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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Wang W, Wei Y, Xu Z, Shen C, Li A, Guan D, Zhang X, Liu B. Evidence Supporting a Role of Alternative Splicing Participates in Melon ( Cucumis melo L.) Fruit Ripening. Int J Mol Sci 2024; 25:5886. [PMID: 38892093 PMCID: PMC11172951 DOI: 10.3390/ijms25115886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/19/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and non-climacteric (PI, PS) melon cultivars to explore alternative splicing (AS) in immature and mature fruit. The results revealed dramatic changes in differential AS genes (DAG) between the young and mature fruit stages, particularly in genes involved in fruit development/ripening, carotenoid and capsaicinoid biosynthesis, and starch and sucrose metabolism. Serine/arginine-rich (SR) family proteins are known as important splicing factors in AS events. From the melon genome, a total of 17 SR members were discovered in this study. These genes could be classified into eight distinct subfamilies based on gene structure and conserved motifs. Promoter analysis detected various cis-acting regulatory elements involved in hormone pathways and fruit development. Interestingly, these SR genes exhibited specific expression patterns in reproductive organs such as flowers and ovaries. Additionally, concurrent with the increase in AS levels in ripening fruit, the transcripts of these SR genes were activated during fruit maturation in both climacteric and non-climacteric melon varieties. We also found that most SR genes were under selection during domestication. These results represent a novel finding of increased AS levels and SR gene expression during fruit ripening, indicating that alternative splicing may play a role in fruit maturation.
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Affiliation(s)
- Wenjiao Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
| | - Yuping Wei
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Zhaoying Xu
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Chengcheng Shen
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.W.); (C.S.)
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Ang Li
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Dailu Guan
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA;
| | - Xuejun Zhang
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Bin Liu
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
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Pujol M, Garcia-Mas J. Regulation of climacteric fruit ripening in melon: recent advances and future challenges. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6224-6236. [PMID: 37399085 DOI: 10.1093/jxb/erad256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Fruit ripening is a complex and highly regulated process where tomato and strawberry have been the model species classically used for studying climacteric and non-climacteric fleshy fruit ripening types, respectively. Melon has emerged as an alternative ripening model because climacteric and non-climacteric cultivars exist, which makes it possible to dissect the regulation of ripening using a genetic approach. Several quantitative trait loci that regulate climacteric fruit ripening have been identified to date, and their combination in both climacteric and non-climacteric genetic backgrounds resulted in lines with different ripening behaviors, demonstrating that the climacteric intensity can be genetically modulated. This review discusses our current knowledge of the physiological changes observed during melon climacteric fruit ripening such as ethylene production, fruit abscission, chlorophyll degradation, firmness, and aroma, as well as their complex genetic control. From pioneer experiments in which ethylene biosynthesis was silenced, to the recent genetic edition of ripening regulators, current data suggest that the climacteric response is determined by the interaction of several loci under quantitative inheritance. The exploitation of the rich genetic diversity of melon will enable the discovery of additional genes involved in the regulation of the climacteric response, ultimately leading to breeding aromatic melon fruits with extended shelf life.
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Affiliation(s)
- Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
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Nizan S, Amitzur A, Dahan-Meir T, Benichou JIC, Bar-Ziv A, Perl-Treves R. Mutagenesis of the melon Prv gene by CRISPR/Cas9 breaks papaya ringspot virus resistance and generates an autoimmune allele with constitutive defense responses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4579-4596. [PMID: 37137337 PMCID: PMC10433930 DOI: 10.1093/jxb/erad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]
Abstract
The majority of plant disease resistance (R) genes encode nucleotide binding-leucine-rich repeat (NLR) proteins. In melon, two closely linked NLR genes, Fom-1 and Prv, were mapped and identified as candidate genes that control resistance to Fusarium oxysporum f.sp. melonis races 0 and 2, and to papaya ringspot virus (PRSV), respectively. In this study, we validated the function of Prv and showed that it is essential for providing resistance against PRSV infection. We generated CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] mutants using Agrobacterium-mediated transformation of a PRSV-resistant melon genotype, and the T1 progeny proved susceptible to PRSV, showing strong disease symptoms and viral spread upon infection. Three alleles having 144, 154, and ~3 kb deletions, respectively, were obtained, all of which caused loss of resistance. Interestingly, one of the Prv mutant alleles, prvΔ154, encoding a truncated product, caused an extreme dwarf phenotype, accompanied by leaf lesions, high salicylic acid levels, and defense gene expression. The autoimmune phenotype observed at 25 °C proved to be temperature dependent, being suppressed at 32 °C. This is a first report on the successful application of CRISPR/Cas9 to confirm R gene function in melon. Such validation opens up new opportunities for molecular breeding of disease resistance in this important vegetable crop.
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Affiliation(s)
- Shahar Nizan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Arie Amitzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Tal Dahan-Meir
- Plant and Environmental Sciences, Weizmann Institute of Science, Israel
| | | | - Amalia Bar-Ziv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
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Gao G, Yang F, Wang C, Duan X, Li M, Ma Y, Wang F, Qi H. The transcription factor CmERFI-2 represses CmMYB44 expression to increase sucrose levels in oriental melon fruit. PLANT PHYSIOLOGY 2023; 192:1378-1395. [PMID: 36938625 PMCID: PMC10231561 DOI: 10.1093/plphys/kiad155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/01/2023]
Abstract
Soluble sugar accumulation in fruit ripening determines fleshy fruit quality. However, the molecular mechanism for this process is not yet understood. Here, we showed a transcriptional repressor, CmMYB44 regulates sucrose accumulation and ethylene synthesis in oriental melon (Cucumis. melo var. makuwa Makino) fruit. Overexpressing CmMYB44 suppressed sucrose accumulation and ethylene production. Furthermore, CmMYB44 repressed the transcriptional activation of CmSPS1 (sucrose phosphate synthase 1) and CmACO1 (ACC oxidase 1), two key genes in sucrose and ethylene accumulation, respectively. During the later stages of fruit ripening, the repressive effect of CmMYB44 on CmSPS1 and CmACO1 could be released by overexpressing CmERFI-2 (ethylene response factor I-2) and exogenous ethylene in "HS" fruit (high sucrose accumulation fruit). CmERFI-2 acted upstream of CmMYB44 as a repressor by directly binding the CmMYB44 promoter region, indirectly stimulating the expression level of CmSPS1 and CmACO1. Taken together, we provided a molecular regulatory pathway mediated by CmMYB44, which determines the degree of sucrose and ethylene accumulation in oriental melon fruit and sheds light on transcriptional responses triggered by ethylene sensing that enable the process of fruit ripening.
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Affiliation(s)
- Ge Gao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Fan Yang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Cheng Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Xiaoyu Duan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Meng Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Feng Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
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Nonaka S, Ito M, Ezura H. Targeted modification of CmACO1 by CRISPR/Cas9 extends the shelf-life of Cucumis melo var. reticulatus melon. Front Genome Ed 2023; 5:1176125. [PMID: 37304010 PMCID: PMC10249633 DOI: 10.3389/fgeed.2023.1176125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
The gaseous plant hormone ethylene is a regulator of fruit shelf-life, one of the essential traits in fruits. Extending fruit shelf-life reduces food loss, thereby expected to contribute to food security. The enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) is the final step of the ethylene production pathway. Its suppression via antisense technology has been demonstrated to extend the shelf-life of melon, apple, and papaya. Genome editing technology is an innovative technique for plant breeding. Because the genome editing technology would not leave the exogenous genes in the final crop products, the crops via genome editing can be considered non-genetically modified yields; compared to conventional breeding, such as mutation breeding, the breeding term would be expected to be relatively short. These points include the advantage of this technique in utilization for commercial applications. We attempted to extend the shelf-life of the Japanese luxury melon (Cucumis melo var. reticulatus, 'Harukei-3') via modification of the ethylene synthesis pathway with the genome editing technology, CRISPR/Cas9 system. The Melonet-DB (https://melonet-db.dna.affrc.go.jp/ap/top) showed that the melon genome had the five CmACOs and the gene CmACO1 predominantly expressed in harvested fruits. From this information, CmACO1 was expected to be a key gene for shelf-life in melons. Based on this information, the CmACO1 was selected as the target of the CRISPR/Cas9 system and introduced the mutation. The final product of this melon did not have any exogenous genes. The mutation was inherited for at least two generations. In the T2 generation, the fruit phenotypes 14 days after harvest were as follows: ethylene production was reduced to one-tenth that of the wild type, pericarp colour remained green, and higher fruit firmness. Early fermentation of the fresh fruit was observed in the wild-type fruit but not in the mutant. These results show that CmACO1 knockout via CRISPR/Cas9 extended the melon's shelf-life. Moreover, our results suggest that genome editing technology would reduce food loss and contribute to food security.
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Affiliation(s)
- Satoko Nonaka
- Tskuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Agricultural Sciences, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Maki Ito
- College of Agro-Biological Resources, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroshi Ezura
- Tskuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Agricultural Sciences, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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8
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Chaudhry A, Hassan AU, Khan SH, Abbasi A, Hina A, Khan MT, Abdelsalam NR. The changing landscape of agriculture: role of precision breeding in developing smart crops. Funct Integr Genomics 2023; 23:167. [PMID: 37204621 DOI: 10.1007/s10142-023-01093-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Food plants play a crucial role in human survival, providing them essential nutrients. However, traditional breeding methods have not been able to keep up with the demands of the growing population. The improvement of food plants aims to increase yield, quality, and resistance to biotic and abiotic stresses. With CRISPR/Cas9, researchers can identify and edit key genes conferring desirable qualities in agricultural plants, including increased yield, enhanced product quality attributes, and increased tolerance to biotic and abiotic challenges. These modifications have enabled the creation of "smart crops" that exhibit rapid climatic adaptation, resistance to extreme weather conditions and high yield and quality. The use of CRISPR/Cas9 combined with viral vectors or growth regulators has made it possible to produce more efficient modified plants with certain conventional breeding methods. However, ethical and regulatory aspects of this technology must be carefully considered. Proper regulation and application of genome editing technology can bring immense benefits to agriculture and food security. This article provides an overview of genetically modified genes and conventional as well as emerging tools, including CRISPR/Cas9, that have been utilized to enhance the quality of plants/fruits and their products. The review also discusses the challenges and prospects associated with these techniques.
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Affiliation(s)
- Amna Chaudhry
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Ahtsham Ul Hassan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University, Murree, 47150, Pakistan.
| | - Aiman Hina
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Muhammad Tajammal Khan
- Institute of Botany, University of the Punjab, Lahore, 54590, Pakistan
- Division of Science and Technology, Department of Botany, University of Education, Lahore, Pakistan
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
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Huang Q, Lin B, Cao Y, Zhang Y, Song H, Huang C, Sun T, Long C, Liao J, Zhuo K. CRISPR/Cas9-mediated mutagenesis of the susceptibility gene OsHPP04 in rice confers enhanced resistance to rice root-knot nematode. FRONTIERS IN PLANT SCIENCE 2023; 14:1134653. [PMID: 36998699 PMCID: PMC10043372 DOI: 10.3389/fpls.2023.1134653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/28/2023] [Indexed: 06/17/2023]
Abstract
CRISPR crops carrying a mutation in susceptibility (S) genes provide an effective strategy for controlling plant disease, because they could be 'transgene-free' and commonly have more broad-spectrum and durable type of resistance. Despite their importance, CRISPR/Cas9-mediated editing of S genes for engineering resistance to plant-parasitic nematode (PPN) disease has not been reported. In this study, we employed the CRISPR/Cas9 system to specifically induce targeted mutagenesis of the S gene rice copper metallochaperone heavy metal-associated plant protein 04 (OsHPP04), and successfully obtained genetically stable homozygous rice mutants with or without transgenic elements. These mutants confer enhanced resistance to the rice root-knot nematode (Meloidogyne graminicola), a major plant pathogenic nematode in rice agriculture. Moreover, the plant immune responses triggered by flg22, including reactive oxygen species burst, defence-related genes expression and callose deposition, were enhanced in the 'transgene-free' homozygous mutants. Analysis of rice growth and agronomic traits of two independent mutants showed that there are no obvious differences between wild-type plants and mutants. These findings suggest that OsHPP04 may be an S gene as a negative regulator of host immunity and genetic modification of S genes through the CRISPR/Cas9 technology can be used as a powerful tool to generate PPN resistant plant varieties.
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Affiliation(s)
- Qiuling Huang
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Borong Lin
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yuqing Cao
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yu Zhang
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Handa Song
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Chunhui Huang
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Tianling Sun
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Changwen Long
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Jinling Liao
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Kan Zhuo
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
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10
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Liu J, Qiao Y, Li C, Hou B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1095967. [PMID: 36909440 PMCID: PMC9996081 DOI: 10.3389/fpls.2023.1095967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fruits are derived from flowers and play an important role in human food, nutrition, and health. In general, flowers determine the crop yield, and ripening affects the fruit quality. Although transcription factors (TFs) only account for a small part of plant transcriptomes, they control the global gene expression and regulation. The plant-specific NAC (NAM, ATAF, and CUC) TFs constitute a large family evolving concurrently with the transition of both aquatic-to-terrestrial plants and vegetative-to-reproductive growth. Thus, NACs play an important role in fruit yield and quality by determining shoot apical meristem (SAM) inflorescence and controlling ripening. The present review focuses on the various properties of NACs together with their function and regulation in flower formation and fruit ripening. Hitherto, we have a better understanding of the molecular mechanisms of NACs in ripening through abscisic acid (ABA) and ethylene (ETH), but how NACs regulate the expression of the inflorescence formation-related genes is largely unknown. In the future, we should focus on the analysis of NAC redundancy and identify the pivotal regulators of flowering and ripening. NACs are potentially vital manipulation targets for improving fruit quantity and quality.
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Affiliation(s)
- Jianfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Qiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Thorough Characterization of ETHQB3.5, a QTL Involved in Melon Fruit Climacteric Behavior and Aroma Volatile Composition. Foods 2023; 12:foods12020376. [PMID: 36673468 PMCID: PMC9858179 DOI: 10.3390/foods12020376] [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: 11/25/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The effect of the QTL involved in climacteric ripening ETHQB3.5 on the fruit VOC composition was studied using a set of Near-Isogenic Lines (NILs) containing overlapping introgressions from the Korean accession PI 16375 on the chromosome 3 in the climacteric 'Piel de Sapo' (PS) genetic background. ETHQB3.5 was mapped in an interval of 1.24 Mb that contained a NAC transcription factor. NIL fruits also showed differences in VOC composition belonging to acetate esters, non-acetate esters, and sulfur-derived families. Cosegregation of VOC composition (23 out of 48 total QTLs were mapped) and climacteric ripening was observed, suggesting a pleiotropic effect of ETHQB3.5. On the other hand, other VOCs (mainly alkanes, aldehydes, and ketones) showed a pattern of variation independent of ETHQB3.5 effects, indicating the presence of other genes controlling non-climacteric ripening VOCs. Network correlation analysis and hierarchical clustering found groups of highly correlated compounds and confirmed the involvement of the climacteric differences in compound classes and VOC differences. The modification of melon VOCs may be achieved with or without interfering with its physiological behavior, but it is likely that high relative concentrations of some type of ethylene-dependent esters could be achieved in climacteric cultivars.
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Santo Domingo M, Mayobre C, Pereira L, Argyris J, Valverde L, Martín-Hernández AM, Garcia-Mas J, Pujol M. Fruit Morphology and Ripening-Related QTLs in a Newly Developed Introgression Line Collection of the Elite Varieties 'Védrantais' and 'Piel de Sapo'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223120. [PMID: 36432848 PMCID: PMC9694011 DOI: 10.3390/plants11223120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 05/28/2023]
Abstract
Melon is an economically important crop with widely diverse fruit morphology and ripening characteristics. Its diploid sequenced genome and multiple genomic tools make this species suitable to study the genetic architecture of fruit traits. With the development of this introgression line population of the elite varieties 'Piel de Sapo' and 'Védrantais', we present a powerful tool to study fruit morphology and ripening traits that can also facilitate characterization or pyramidation of QTLs in inodorous melon types. The population consists of 36 lines covering almost 98% of the melon genome, with an average of three introgressions per chromosome and segregating for multiple fruit traits: morphology, ripening and quality. High variability in fruit morphology was found within the population, with 24 QTLs affecting six different traits, confirming previously reported QTLs and two newly detected QTLs, FLQW5.1 and FWQW7.1. We detected 20 QTLs affecting fruit ripening traits, six of them reported for the first time, two affecting the timing of yellowing of the rind (EYELLQW1.1 and EYELLQW8.1) and four at the end of chromosome 8 affecting aroma, abscission and harvest date (EAROQW8.3, EALFQW8.3, ABSQW8.3 and HARQW8.3). We also confirmed the location of several QTLs, such as fruit-quality-related QTLs affecting rind and flesh appearance and flesh firmness.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
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