Kiwifruit in the Omics Age: Advances in Genomics, Breeding, and Beyond
Abstract
:1. Introduction
2. Kiwifruit Genetic Resources
No. | Species (Genotype) | Distribution | Ploidy | Male/Female | Wild/Cultivated | Flesh Color | Features |
---|---|---|---|---|---|---|---|
1 | A. callosa | Guangxi, China Wuhan, China | 2x, 4x | Female | Cultivated | Jade green | Fruit size varies from medium to large with a very delicate and slightly acidic flavor |
2 | A. diversicolora | Sichuan, China | 2x | Female | Wild | Variable leaf color. Found in temperate forests. Small, tart fruits used in local culinary dishes | |
3 | A. jiangxiensis | Jiangxi, China | 2x | Female | Wild | Green | |
4 | A. arguta | Guangxi, China Heilongjiang, China | 4x, 8x | Female | - | Green | Smooth-skinned, apple-like fruit. High genetic variability, used in interspecific breeding |
5 | A. pentapetala | Guangxi, China | 2x | Female | - | Small, sweet fruits with a unique penta-petalous flower structure. Grows in forested areas | |
6 | A. macrosperma | Zhejiang, China | 4x | Female | Wild | Orange | Oval fruits with relatively thicker skin and large seeds |
7 | A. guilinensis | Guangxi, China | 2x | Female | - | Green | Produces medium-sized fruits with smooth skin. Known for its rich flavor and high nutritional content |
8 | A. latifolia | Shanxi, China Hubei, China Sichuan, China Guangxi, China | 2x | Female | Cultivated | Jade green | High vitamin C content. Cultivated for its nutritional value and adaptability |
9 | A. carnosifolia | Guangxi, China | Male | Wild | |||
10 | A. hemsleyana | Guangxi, China | 2x | Female | Wild | Yellow green | Cylindrical fruits with smooth skin |
11 | A. tetramera | Guangdong, China | 4x | Female | Wild | Small fruit. Adapted to mountainous regions. Known for its distinct flavor and smooth skin | |
12 | A. Eriantha | Jiangxi, China Wuhan, China Guangxi, China | 2x | Female | Cultivated | Jade green | High vitamin C content; easy peeling. Used for its smooth skin and nutritional benefits |
13 | A. valvata | Hunan, China | 4x | Female | Wild | ||
14 | A. cylindrica | Guangxi, China | 2x | Female | - | Light green | Produces cylindrical fruits. Known for its unique shape and taste. Evergreen species |
15 | A. polygamya | Yunnan, China | 4x | Female | Cultivated | ||
16 | A. indochinensis | Guangxi, China | 2x | Female | Cultivated | Green | Sub-globose fruit with smooth skin |
17 | A. melliana | Guangxi, China | 2x | Female | Cultivated | Green | |
18 | A. persicina | Guangxi, China | 2x | Female | - | Green | Produces peach-like fruits. Known for its unique flavor. Cultivated in various regions |
19 | A. longicarpa | Sichuan, China | 2x | Female | - | Produces long fruits. Known for its unique shape and taste | |
20 | A. rongshuiensis | Guangxi, China | 2x | Female | - | Fruits are cylindrical and tomentose | |
21 | A. wantianensis | Guangxi, China | 2x | Female | - | Fruits are typically small and ovoid, with smooth skin | |
22 | A. chrysantha | Guangxi, China | 4x | Female | Wild | Green | Oval-shaped fruits are maroon–brown to greenish-brown |
23 | A. rubricaulis | Guangxi, China Sichuan, China | 2x | Female | Cultivated | Small, oval fruits with yellow–red flesh color | |
24 | A. glaucophylla | Guangxi, China | 2x | Female | Wild | Green | Evergreen species with glaucous leaves |
25 | A. liangguangensis | Guangxi, China | 2x | Female | Cultivated | Dark green | |
26 | A. chinensis × A. eriantha | Guangxi, China | Female | Cultivated | Green | ||
27 | A. albicalyx | Guangxi, China | 2x | Female | Wild | Evergreen species with unique foliage | |
28 | A. styracifolia | Fujian, China | 2x | Female | Cultivated | Berry-like fruits with smooth skin | |
29 | A. deliciosa | Southeastern China | 6x | Female | Cultivated | Green | Large, oval fruit with fuzzy skin and more tangy taste. Green-fleshed variety grown globally |
3. Modern Omics Approaches
3.1. Genomics
Authors | Year | Key Findings |
---|---|---|
Crowhurst et al. [45] | 2008 | Identification of genes involved in flavor, health, color, and ripening through a cross-species EST database. This facilitated the understanding of genetic control over these traits and allowed for targeted breeding strategies. |
Huang et al. [18] | 2014 | Demonstrated the benefits of natural hybridization and introgression in enhancing cultivar traits such as disease resistance, fruit quality, and yield. |
Zhang et al. [49] | 2015 | Demonstrated the benefits of natural hybridization and introgression in enhancing cultivar traits such as disease resistance, fruit quality, and yield. |
Wu et al. [60] | 2019 | Presented a high-quality genome sequence of A. chinensis, enhancing the precision of genetic studies and breeding programs. |
Tahir et al. [51] | 2020 | Identification of QTLs linked to resistance against Pseudomonas syringae pv. Actinidiae (Psa), aiding in the development of canker-resistant kiwifruit varieties. |
Yue et al. [54] | 2020 | Establishment of the Kiwifruit Genome Database, a resource that consolidates genomic data to support research and breeding programs. |
Popowski et al. [48] | 2021 | Creation of a high-density genetic map, enabling the identification of QTLs for important traits such as fruit size and resistance to diseases, which is crucial for marker-assisted selection. |
Lu et al. [46] | 2022 | Identification of a single nucleotide mutation controlling fruit flesh color, aiding in association mapping and breeding for desirable fruit traits. |
Yao et al. [61] | 2022 | Conducted genome sequencing and comparative analysis of A. eriantha, enriching the genetic pool for breeding programs. |
Li et al. [50] | 2023 | Development of a high-density genetic map and identification of QTLs associated with growth traits, facilitating the breeding of kiwifruit with optimized growth characteristics. |
Wang et al. [52] | 2023 | Development of a comprehensive SNP genotyping array, enabling detailed genetic mapping and QTL analysis for traits like fruit quality and yield. |
Akagi et al. [56] | 2023 | Discovery of recurrent neo-sex chromosome evolution, providing insights into the genetic mechanisms of sex chromosome development in kiwifruit. |
Xia et al. [58] | 2023 | Achieved a chromosome-scale genome assembly, providing a high-resolution genetic resource for breeding and research. |
Yue et al. [55] | 2024 | Detailed study on the origin and evolution of the Y chromosome in kiwifruit, enhancing the understanding of sex determination mechanisms. |
3.2. Transcriptomics
3.3. Proteomics
3.4. Metabolomics
Author et al., Year | Key Pathways Identified | Key Traits Under Study | Proteins/Metabolites Identified | Methods Used |
---|---|---|---|---|
Günther et al., 2011 [104] | Methylsulfanyl-volatiles pathways | Volatiles | Methylsulfanyl-volatiles | Headspace analysis |
McGhie, 2013 [110] | Secondary metabolite components | Metabolites | Secondary metabolites | Not specified |
Commisso et al., 2019 [103] | Tryptophan decarboxylase pathways | Development of kiwifruits | Tryptophan-derived metabolites | Untargeted and targeted metabolomics |
Shin et al., 2020 [93] | Ethylene response pathways | Fruit ripening | Ethylene biosynthesis enzymes and cell wall-modifying proteins | Proteomic analysis |
Xiong et al., 2020 [97] | Developmental stage pathways | Nutritional components | Sugars, organic acids, and amino acids | Metabolomic and transcriptomic approaches |
Yu et al., 2020 [99] | Flavonoids and anthocyanin pathways | Gene analyses of kiwifruit and kiwiberry | Flavonoids and anthocyanins | Metabolomics study |
Wang et al., 2021 [89] | AcMYB16 role in response to Pseudomonas syringae pv. actinidiae | Disease response | AcMYB16 and defense-related proteins | Transcriptomic and proteomic profiling |
Zhang et al., 2021 [90] | Mechanisms of chilling injury | Chilling injury | Heat shock proteins and oxidative stress-related proteins | Label-free proteome techniques |
Tian et al., 2021 [92] | Regulatory pathways of ripening and quality | Postharvest ripening | Ethylene-responsive proteins and ripening-associated metabolites | Proteomics and metabolomics |
Rowan et al., 2021 [96] | Metabolite variability | Orchard variability of two cultivars | Primary metabolites and secondary metabolites | Metabolomics |
Zhao et al., 2021 [100] | Aroma profile pathways | Aroma in three kiwifruit varieties | Volatile organic compounds (VOCs) | HS-SPME-GC-MS and GC-IMS coupled with DSA |
Lan et al., 2021 [102] | Aroma chemical composition | Common kiwifruit cultivars in China | Aroma-related metabolites | Not specified |
Liang et al., 2021 [107] | Physicochemical, nutritional, and bioactive properties | Pulp and peel from 15 kiwifruit cultivars | Nutritional and bioactive metabolites | - |
Starowicz et al., 2022 [105] | VOCs in kiwiberries | Kiwiberries | Volatile organic compounds (VOCs) | HS-SPME/GC-MS |
Choi et al., 2022 [109] | Metabolites and antioxidant activities | Green ‘Hayward’ and gold ‘Haegeum’ kiwifruits | Antioxidant metabolites | Ethylene treatment |
Wang et al., 2022 [73] | Flavor formation pathways | Kiwifruit | Flavor-related metabolites | Integrative analyses of metabolome and genome-wide transcriptome |
Qu et al., 2023 [86] | Potential mechanisms of SA in triggering resistance | Resistance to Pseudomonas syringae pv. actinidiae | Pathogenesis-related proteins and SA-responsive proteins | 4D proteome investigation |
Li et al., 2023 [91] | Amyloplast biogenesis and differentiation | Amyloplast development | Starch biosynthesis enzymes and amyloplast-specific proteins | Proteome analysis |
Li et al., 2023 [98] | Auxin pathways in postharvest resistance | Postharvest resistance to Botrytis cinerea | Auxin-responsive proteins and resistance-related metabolites | Widely targeted metabolomics analysis |
Wang et al., 2023 [101] | Volatile profiles of kiwifruits with soft rot | Soft rot in kiwifruits | Volatile organic compounds (VOCs) | E-nose and HS-SPME/GC–MS |
Bi et al., 2023 [106] | Forchlorfenuron pathways | Kiwifruit development | Forchlorfenuron-responsive metabolites | Metabolomics |
Shu et al., 2023 [69] | Major quality regulations | Red-flesh kiwifruit | Quality-related metabolites | Metabolic map |
Xiong et al., 2023 [111] | Color formation pathways | Yellow-fleshed kiwifruit | Color-related metabolites | Integrative analysis of metabolome and transcriptome |
Valasiadis et al., 2024 [87] | High and low dry matter pathways | Dry matter content in kiwifruit | Metabolites related to sugar and acid content | Spatiotemporal multi-omics approach |
Polychroniadou et al., 2024 [88] | Calcium-related pathways | Ripening processes | Calcium-binding proteins and pectin methylesterase | Cross-omics approach |
4. Kiwifruit Breeding
4.1. Conventional and Molecular Breeding
4.2. Marker-Assisted Selection
4.3. Genomic Selection
4.4. Enhancing Kiwifruit Breeding through Mutation Breeding and CRISPR-Cas9 Technologies
4.5. Interspecific Hybridization
4.6. Cisgenesis and Genome Editing
5. Key Traits for Improvement
6. Conclusions and Future Directions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Author et al., Year | Key Pathways Identified | Key Traits Under Study | Genes/Markers Identified | Methods Used |
---|---|---|---|---|
Li et al., 2015 [78] | Phytohormones, sugars, starch, and L-ascorbic acid metabolism | Fruit quality and anthocyanin accumulation | - | Transcriptome sequencing and gene expression profiling |
Kamboj et al., 2020 [79] | Molecular polymorphism | Diversity analysis and genotype identification | RAPD markers | Diversity analysis and genotype identification |
Zhang et al., 2020 [80] | Ripening-related ester biosynthesis | Fruit ripening and ester content | AdFAD1, AdALDH2, AdAT17, AdNAC5, AdDof4 | Co-expression network analysis |
Wu et al., 2020 [63] | Phytohormone pathways | Fruit development | CPPU, IAA | Transcriptome sequencing and phytohormone analysis |
Zambounis et al., 2020 [64] | Pathogen response pathways | Disease resistance | PR, CHI | RNA sequencing-based transcriptome analysis |
Qiu et al., 2020 [76] | Coloration and quality pathways | Coloration and fruit quality | MYB, DFR | Transcriptome and metabolome analyses |
Lin et al., 2020 [66] | Hydrogen sulfide signaling pathways | Ripening delay | PG, EXP | Transcriptome analysis |
Liang et al., 2020 [70] | Phenolic synthesis pathways | Fruit development and ripening | CHS, F3H | Gene expression profiling |
Salazar et al., 2021 [65] | Ethylene signaling pathways | Fruit ripening | ETR, EIN | Transcriptome analysis |
Brian et al., 2021 [81] | Floral bud and flower development, fruit development and maturation, and ethylene-induced fruit ripening | Transcriptional control of floral bud, flower, and fruit development, and ethylene response | AP2/ERF, bHLH, MYB | Network analysis and transcriptome profiling |
Yang et al., 2021 [82] | Nitric oxide regulation during fruit softening | Fruit ripening inhibition | Genes related to nitric oxide regulation | Transcriptome profiling |
Sun et al., 2021 [83] | Cellulose degradation, trehalose synthesis, starch degradation, and cold response | Freezing tolerance and low-temperature response | beta-GC, TPS5, BAM3.1, CBF3, MYC2, MYB44 | Transcriptome profiling and WGCNA |
Tu et al., 2021 [72] | Chlorophyll degradation pathways | Chlorophyll degradation | CAB, SGR | Transcriptome analysis |
Burdon et al., 2021 [68] | Maturation pathways | Fruit maturation | MYB, MADS-box | Transcriptomic analysis |
Salazar et al., 2021 [77] | Transcriptomic pathways | Tissue-specific transcriptomics | AP2/ERF, bHLH | De novo transcriptome sequencing |
Huan et al., 2021 [74] | Starch degradation and fermentation pathways | Alcoholic off-flavor development | AMY, PDC | Transcriptome analysis |
Wang et al., 2022 [73] | Flavor formation pathways | Flavor formation | LOX, ADH | Metabolome and genome-wide transcriptome analyses |
Tao et al., 2022 [84] | Stress responses, phytohormone signal transduction, and plant growth and development | TIFY gene family functions | TIFY gene family (JAZ, ZML, TIFY, PPD) | Genome-wide identification and characterization |
Xiong et al., 2022 | mRNA editing post-pathogen infection | Pathogen stress response | MORF genes | Genome-wide analysis |
Jia et al., 2022 [85] | Flavonoid biosynthesis and chalcone synthase gene family | Parthenocarpy in seedless kiwifruit | Chalcone synthase (CHS) gene family | Full-length transcriptome sequencing |
Shu et al., 2023 [69] | Metabolic regulatory networks during development and ripening | Kiwifruit quality improvement | Various genes related to metabolic regulation | Metabolomic and transcriptomic analyses |
Niu et al., 2023 [67] | Phenolic synthesis and phytohormone pathways | Chilling injury mitigation | PAL, PR1 | Transcriptome analysis |
Shu et al., 2023 [69] | Metabolic pathways | Fruit quality | ANS, DFR | Metabolic mapping |
Guo et al., 2024 [71] | Comparative gene expression pathways | Gene expression differences | WRKY, NAC | Comparative transcriptome analysis |
Wang, Y.; et al. 2024 [75] | Cell wall metabolism pathways | Postharvest softening | XTH, PME | Transcriptomic analysis |
Yang et al., 2024 [62] | Metabolomic and transcriptomic pathways | Postharvest ripening | ACS, ACO | Integrated metabolomic and transcriptomic analyses |
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Nazir, M.F.; Lou, J.; Wang, Y.; Zou, S.; Huang, H. Kiwifruit in the Omics Age: Advances in Genomics, Breeding, and Beyond. Plants 2024, 13, 2156. https://doi.org/10.3390/plants13152156
Nazir MF, Lou J, Wang Y, Zou S, Huang H. Kiwifruit in the Omics Age: Advances in Genomics, Breeding, and Beyond. Plants. 2024; 13(15):2156. https://doi.org/10.3390/plants13152156
Chicago/Turabian StyleNazir, Mian Faisal, Jinpeng Lou, Yu Wang, Shuaiyu Zou, and Hongwen Huang. 2024. "Kiwifruit in the Omics Age: Advances in Genomics, Breeding, and Beyond" Plants 13, no. 15: 2156. https://doi.org/10.3390/plants13152156