1
|
Nazir MF, Lou J, Wang Y, Zou S, Huang H. Kiwifruit in the Omics Age: Advances in Genomics, Breeding, and Beyond. PLANTS (BASEL, SWITZERLAND) 2024; 13:2156. [PMID: 39124274 PMCID: PMC11313697 DOI: 10.3390/plants13152156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The kiwifruit, Actinidia genus, has emerged as a nutritionally rich and economically significant crop with a history rooted in China. This review paper examines the global journey of the kiwifruit, its genetic diversity, and the role of advanced breeding techniques in its cultivation and improvement. The expansion of kiwifruit cultivation from China to New Zealand, Italy, Chile and beyond, driven by the development of new cultivars and improved agricultural practices, is discussed, highlighting the fruit's high content of vitamins C, E, and K. The genetic resources within the Actinidia genus are reviewed, with emphasis on the potential of this diversity in breeding programs. The review provides extensive coverage to the application of modern omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, which have revolutionized the understanding of the biology of kiwifruit and facilitated targeted breeding efforts. It examines both conventional breeding methods and modern approaches, like marker-assisted selection, genomic selection, mutation breeding, and the potential of CRISPR-Cas9 technology for precise trait enhancement. Special attention is paid to interspecific hybridization and cisgenesis as strategies for incorporating beneficial traits and developing superior kiwifruit varieties. This comprehensive synthesis not only sheds light on the current state of kiwifruit research and breeding, but also outlines the future directions and challenges in the field, underscoring the importance of integrating traditional and omics-based approaches to meet the demands of a changing global climate and market preferences.
Collapse
Affiliation(s)
- Mian Faisal Nazir
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Jinpeng Lou
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Yu Wang
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Shuaiyu Zou
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Hongwen Huang
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
2
|
Qin S, Wei F, Liang Y, Tang D, Lin Q, Miao J, Wei K. Genome-wide analysis of the R2R3-MYB gene family in Spatholobus suberectus and identification of its function in flavonoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1219019. [PMID: 37670861 PMCID: PMC10476624 DOI: 10.3389/fpls.2023.1219019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
Spatholobus suberectus Dunn (S. suberectus), a plant species within the Leguminosae family, has a long history of use in traditional medicines. The dried stem of S. suberectus exhibits various pharmacological activities because it contains various flavonoids. Diverse functions in plants are associated with the R2R3-MYB gene family, including the biosynthesis of flavonoids. Nonetheless, its role remains unelucidated in S. suberectus. Therefore, the newly sequenced S. suberectus genome was utilized to conduct a systematic genome-wide analysis of the R2R3-MYB gene family. The resulting data identified 181 R2R3-SsMYB genes in total, which were then categorized by phylogenetic analysis into 35 subgroups. Among the R2R3-SsMYB genes, 174 were mapped to 9 different chromosomes, and 7 genes were not located on any chromosome. Moreover, similarity in terms of exon-intron structures and motifs was exhibited by most genes in the same subgroup. The expansion of the gene family was primarily driven by segmental duplication events, as demonstrated by collinearity analysis. Notably, most of the duplicated genes underwent purifying selection, which was depicted through the Ka/Ks analysis. In this study, 22 R2R3-SsMYB genes were shown to strongly influence the level of flavonoids. The elevated expression level of these genes was depicted in the tissues with flavonoid accumulation in contrast with other tissues through qRT-PCR data. The resulting data elucidate the structural and functional elements of R2R3-SsMYB genes and present genes that could potentially be utilized for enhancing flavonoid biosynthesis in S. suberectus.
Collapse
Affiliation(s)
- Shuangshuang Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Liang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Danfeng Tang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Quan Lin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jianhua Miao
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Kunhua Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| |
Collapse
|
3
|
Chen T, Cao H, Wang M, Qi M, Sun Y, Song Y, Yang Q, Meng D, Lian N. Integrated transcriptome and physiological analysis revealed core transcription factors that promote flavonoid biosynthesis in apricot in response to pathogenic fungal infection. PLANTA 2023; 258:64. [PMID: 37555984 DOI: 10.1007/s00425-023-04197-x] [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: 04/28/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023]
Abstract
MAIN CONCLUSION Integrated transcriptome and physiological analysis of apricot leaves after Fusarium solani treatment. In addition, we identified core transcription factors and flavonoid-related synthase genes which may function in apricot disease resistance. Apricot (Prunus armeniaca) is an important economic fruit species, whose yield and quality of fruit are limited owing to its susceptibility to diseases. However, the molecular mechanisms underlying the response of P. armeniaca to diseases is still unknown. In this study, we used physiology and transcriptome analysis to characterize responses of P. armeniaca subjected to Fusarium solani. The results showed increasing malondialdehyde (MDA) content, enhanced peroxidase (POD) and catalase (CAT) activity during F. solani infestation. A large number of differentially expressed genes (DEGs), which included 4281 upregulated DEGs and 3305 downregulated DEGs, were detected in P. armeniaca leaves exposed to F. solani infestation. Changes in expression of transcription factors (TFs), including bHLH, AP2/ERF, and WRKY indicated their role in triggering pathogen-responsive genes in P. armeniaca. During the P. armeniaca response to F. solani infestation, the content of total flavonoid was changed, and we identified enzyme genes associated with flavonoid biosynthesis. Ectopic overexpression of PabHLH15 and PabHLH102 in Nicotiana benthamiana conferred elevated resistance to Fspa_1. Moreover, PabHLH15 and PabHLH102 positively interact with the promoter of flavonoid biosynthesis-related genes. A regulatory network of TFs regulating enzyme genes related to flavonoid synthesis affecting apricot disease resistance was constructed. These results reveal the potential underlying mechanisms of the F. solani response of P. armeniaca, which would help improve the disease resistance of P. armeniaca and may cultivate high-quality disease-resistant varieties in the future.
Collapse
Affiliation(s)
- Ting Chen
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Hongyan Cao
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Mengying Wang
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Meng Qi
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | | | - Yangbo Song
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016, China
| | - Qing Yang
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Dong Meng
- Beijing Forestry University, Beijing, 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
4
|
Liu F, Sun X, Wang L, Zhou K, Yao Q, Zhan RL. Transcriptomic and proteomic analyses of Mangifera indica in response to Xanthomonas critis pv. mangiferaeindicae. Front Microbiol 2023; 14:1220101. [PMID: 37469435 PMCID: PMC10352610 DOI: 10.3389/fmicb.2023.1220101] [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: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Mango is an important tropical fruit with the reputation of "Tropical Fruit King." It is widely cultivated in tropical and subtropical regions. Mango bacterial leaf spot, which is caused by Xanthomonas critis pv. mangiferaeindicae (Xcm), poses a great threat to the development of mango planting industry. In this study, we used RNA sequencing and data-independent acquisition techniques to compare the transcriptome and proteome of the highly resistant cultivar "Renong No.1" (RN) and the highly susceptible cultivar "Keitt" (KT) in response to Xcm infection at different stages (0, 2, and 6 days). A total of 14,397 differentially expressed genes (DEGs) were identified in the transcriptome of the two varieties, and 4,400 and 8,926 genes were differentially expressed in RN and KT, respectively. Among them, 217 DEGs were related to plant hormone signaling pathway, and 202 were involved in the maintenance of cellular redox homeostasis. A total of 3,438 differentially expressed proteins (DEPs) were identified in the proteome of the two varieties. Exactly 1,542 and 1,700 DEPs were detected in RN and KT, respectively. In addition, 39 DEPs were related to plant hormone signaling pathway, whereas 68 were involved in the maintenance of cellular redox homeostasis. Through cross-validation of the two omics, 1,470 genes were found to be expressed in both groups, and a large number of glutathione metabolism-related genes, such as HSP26-A, G6PD4, and GPX2, were up-regulated in both omics. Peroxisome-related genes, such as LACS6, LACS9, PED1, GLO4, and HACL, were up-regulated or down-regulated in both omics. ABCB11, SAPK2, MYC2, TAG7, PYL1, and other genes related to indole-3-acetic acid and abscisic acid signal transduction and plant-pathogen interaction were up-regulated or down-regulated in both omics. We also used weighted gene co-expression network analysis to combine physiological and biochemical data (superoxide dismutase and catalase activity changes) with transcriptome and proteome data and finally identified three hub genes/proteins (SAG113, SRK2A, and ABCB1) that play an important role in plant hormone signal transduction. This work was the first study of gene/protein changes in resistant and susceptible mango varieties, and its results improved our understanding of the molecular mechanism of mango resistance to Xcm.
Collapse
Affiliation(s)
- Feng Liu
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Xin Sun
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Lulu Wang
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Kaibing Zhou
- College of Horticulture, Hainan University, Haikou, China
| | - Quansheng Yao
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Ru-lin Zhan
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| |
Collapse
|
5
|
Han Z, Zhang C, Zhang H, Duan Y, Zou Z, Zhou L, Zhu X, Fang W, Ma Y. CsMYB Transcription Factors Participate in Jasmonic Acid Signal Transduction in Response to Cold Stress in Tea Plant ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212869. [PMID: 36365324 PMCID: PMC9654479 DOI: 10.3390/plants11212869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 05/31/2023]
Abstract
Low-temperature stress is an increasing problem for the cultivation of tea (Camellia sinensis), with adverse effects on plant growth and development and subsequent negative impacts on the tea industry. Methyl jasmonate (MeJA), as a plant inducer, can improve the cold-stress tolerance in tea plants. R2R3-MYB transcription factors (TFs) are considered potentially important regulators in the resistance to cold stress in plants. However, the molecular mechanisms, by which MYB TFs via the jasmonic acid pathway respond to cold stress in the tea plant, remain unknown. In this study, physiological and biochemical assays showed that exogenous MeJA application could effectively promote ROS scavenging in the tea plant under cold stress, maintaining the stability of the cell membrane. Sixteen R2R3-MYB TFs genes were identified from the tea plant genome database. Quantitative RT-PCR analysis showed that three CsMYB genes were strongly induced under a combination of MeJA and cold-stress treatment. Subcellular localization assays suggest CsMYB45, CsMYB46, and CsMYB105 localized in the nucleus. Exogenous MeJA treatment enhanced the overexpression of CsMYB45, CsMYB46, and CsMYB105 in E. coli and improved the growth and survival rates of recombinant cells compared to an empty vector under cold stress. Yeast two-hybrid and bimolecular fluorescence complementation experiments confirmed that CsMYB46 and CsMYB105 interacted with CsJAZ3, CsJAZ10, and CsJAZ11 in the nucleus. Taken together, these results highlight that CsMYB45, CsMYB46, and CsMYB105 are not only key components in the cold-stress signal response pathway but also may serve as points of confluence for cold stress and JA signaling pathways. Furthermore, our findings provide new insight into how MYB TFs influence cold tolerance via the jasmonic acid pathway in tea and provide candidate genes for future functional studies and breeding.
Collapse
Affiliation(s)
- Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongwei Zou
- Department of Biology, Faculty of Science, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - Lin Zhou
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|