1
|
Skytte Af Sätra J, Garkava-Gustavsson L, Ingvarsson PK. Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden. Heredity (Edinb) 2024; 133:67-77. [PMID: 38834867 PMCID: PMC11286948 DOI: 10.1038/s41437-024-00693-2] [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: 01/26/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
Collapse
Affiliation(s)
- J Skytte Af Sätra
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - L Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - P K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
2
|
Wang X, Wang D, Zhang R, Qin X, Shen X, You C. Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species. Biomolecules 2024; 14:912. [PMID: 39199300 PMCID: PMC11352593 DOI: 10.3390/biom14080912] [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: 06/23/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/01/2024] Open
Abstract
Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of 'ZA', a mutant type of M. baccata. In this study, we compared the differences between 'ZA' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata 'ZA' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata 'ZA', as well as interspecific variations among different individuals. In comparison, the total length of the 'ZA' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the 'ZA' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including 'ZA'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that 'ZA' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.
Collapse
Affiliation(s)
- Xun Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Daru Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Ruifen Zhang
- Qingdao Apple Rootstock Research and Development Center, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China;
| | - Xin Qin
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Xiang Shen
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| | - Chunxiang You
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China; (X.W.); (D.W.); (X.Q.)
| |
Collapse
|
3
|
Minamikawa MF, Kunihisa M, Moriya S, Shimizu T, Inamori M, Iwata H. Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae131. [PMID: 38979105 PMCID: PMC11228094 DOI: 10.1093/hr/uhae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/10/2024]
Abstract
With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).
Collapse
Affiliation(s)
- Mai F Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi, Inage, Chiba, Chiba 263-8522, Japan
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, NARO, Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Minoru Inamori
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| |
Collapse
|
4
|
Li C, Krishnan S, Zhang M, Hu D, Meng D, Riedelsberger J, Dougherty L, Xu K, Piñeros MA, Cheng L. Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310159. [PMID: 38514904 PMCID: PMC11165477 DOI: 10.1002/advs.202310159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Vacuolar malic acid accumulation largely determines fruit acidity, a key trait for the taste and flavor of apple and other fleshy fruits. Aluminum-activated malate transporter 9 (ALMT9/Ma1) underlies a major genetic locus, Ma, for fruit acidity in apple, but how the protein transports malate across the tonoplast is unclear. Here, it is shown that overexpression of the coding sequence of Ma1 (Ma1α) drastically decreases fruit acidity in "Royal Gala" apple, leading to uncovering alternative splicing underpins Ma1's function. Alternative splicing generates two isoforms: Ma1β is 68 amino acids shorter with much lower expression than the full-length protein Ma1α. Ma1β does not transport malate itself but interacts with the functional Ma1α to form heterodimers, creating synergy with Ma1α for malate transport in a threshold manner (When Ma1β/Ma1α ≥ 1/8). Overexpression of Ma1α triggers feedback inhibition on the native Ma1 expression via transcription factor MYB73, decreasing the Ma1β level well below the threshold that leads to significant reductions in Ma1 function and malic acid accumulation in fruit. Overexpression of Ma1α and Ma1β or genomic Ma1 increases both isoforms proportionally and enhances fruit malic acid accumulation. These findings reveal an essential role of alternative splicing in ALMT9-mediated malate transport underlying apple fruit acidity.
Collapse
Affiliation(s)
- Chunlong Li
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China
| | | | - Mengxia Zhang
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dagang Hu
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dong Meng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Janin Riedelsberger
- Center for Bioinformatics, Simulation and Modeling, Department of Bioinformatics, Faculty of EngineeringUniversity of TalcaTalca3460000Chile
| | - Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Miguel A. Piñeros
- Plant Biology Section, School of Integrative Plant Science and Robert W. Holley Center for Agriculture and HealthUSDA‐ARS Cornell UniversityIthacaNY14853USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| |
Collapse
|
5
|
Keller B, Jung M, Bühlmann-Schütz S, Hodel M, Studer B, Broggini GAL, Patocchi A. The genetic basis of apple shape and size unraveled by digital phenotyping. G3 (BETHESDA, MD.) 2024; 14:jkae045. [PMID: 38441135 PMCID: PMC11075547 DOI: 10.1093/g3journal/jkae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 05/08/2024]
Abstract
Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson's correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.
Collapse
Affiliation(s)
- Beat Keller
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Michaela Jung
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Simone Bühlmann-Schütz
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Marius Hodel
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Andrea Patocchi
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| |
Collapse
|
6
|
Zhang W, Han Y, Liao L. Phenomics and transcriptomic profiling of fruit development in distinct apple varieties. Sci Data 2024; 11:390. [PMID: 38627414 PMCID: PMC11021526 DOI: 10.1038/s41597-024-03220-4] [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: 11/27/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Apple is one of the most economically important and popular temperate fruit trees. The domestication of apple has resulted in substantial phenotypic differences, particularly between wild and cultivated varieties. However, the relationship between gene expression and phenotypic variations in apple remains poorly understood. Here, we present a comprehensive dataset featuring five distinct apple varieties, including two wild varieties and three representative cultivated varieties. The dataset comprises of both phenomics data, encompassing twelve fruit quality-related traits continuously measured over two years, and transcriptomic data obtained at different developmental stages with three biological replicates. We performed basic quality control process, gene expression normalization and differential gene expression analysis to demonstrate the utility and reliability of the dataset. Our findings indicate that gene expression strongly related with phenotypic variations in apple. This dataset serves as a valuable resource, encompassing phenomics and transcriptomic data in multiple formats, thereby facilitating further exploration of the relationships between gene expression and phenotypic traits in apple.
Collapse
Affiliation(s)
- Weihan Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Liao Liao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
7
|
Liu X, Song L, Xue B, Chi Z, Wang Y, Wen S, Lv W, Hu Q, Guo Q, Wang S, Wu D, Liang G, Jing D. Organic acid and sugar components accumulation and flavor associated metabolites dynamic changes in yellow- and white-fleshed seedless loquats ( Eriobotrya japonica). Food Chem X 2024; 21:101046. [PMID: 38173902 PMCID: PMC10762357 DOI: 10.1016/j.fochx.2023.101046] [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: 08/08/2023] [Revised: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Triploid loquats are divided into yellow- and white-fleshed cultivars. To better understand taste variations in triploid loquat fruits, we used a UPLC-ESI-QTRAP-MS/MS-based widely targeted metabolomic analysis to examine the metabolic composition of two different color fleshed triploid loquats with a sample size of 54 and external validation method within a confidence level of P<0.05. We identified key flavor-related differentially accumulated metabolites using the variable importance in projection (VIP) value (VIP ≥ 1.0) and fold change ≥ 2 or ≤ 0.5. Furthermore, the results of the HPLC analysis showed that white-fleshed loquats had a low malic acid content. We also performed the UPLC-MS/MS system to investigate the carotenoids contents and lipidome in four triploid cultivars. In the fruits of white-fleshed varieties, the carotenoids contents were significantly downregulated, but the contents of most glycerolphospholipids were increased. Our results reveal the metabolomic changes between the yellow- and white-fleshed cultivars.
Collapse
Affiliation(s)
- Xinya Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Liqin Song
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Baogui Xue
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
- Jiuquan Forest Fruit Service Center, Jiuquan, Gansu 735000, China
| | - Zhuoheng Chi
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Yuan Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Songqin Wen
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Wenjuan Lv
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qiankun Hu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qigao Guo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Shuming Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Di Wu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Guolu Liang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Danlong Jing
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| |
Collapse
|
8
|
Yang F, Luo J, Guo W, Zhang Y, Liu Y, Yu Z, Sun Y, Li M, Ma F, Zhao T. Origin and early divergence of tandem duplicated sorbitol transporter genes in Rosaceae: insights from evolutionary analysis of the SOT gene family in angiosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:856-872. [PMID: 37983569 DOI: 10.1111/tpj.16533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/30/2023] [Accepted: 10/21/2023] [Indexed: 11/22/2023]
Abstract
Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol transporters (SOTs) play a vital role in facilitating sorbitol allocation from source to sink organs and sugar accumulation in sink organs. While prior research has addressed gene duplications within the SOT gene family in Rosaceae, the precise origin and evolutionary dynamics of these duplications remain unclear, largely due to the complicated interplay of whole genome duplications and tandem duplications. Here, we investigated the synteny relationships among all identified Polyol/Monosaccharide Transporter (PLT) genes in 61 angiosperm genomes and SOT genes in representative genomes within the Rosaceae family. By integrating phylogenetic analyses, we elucidated the lineage-specific expansion and syntenic conservation of PLTs and SOTs across diverse plant lineages. We found that Rosaceae SOTs, as PLT family members, originated from a pair of tandemly duplicated PLT genes within Class III-A. Furthermore, our investigation highlights the role of lineage-specific and synergistic duplications in Amygdaloideae in contributing to the expansion of SOTs in Rosaceae plants. Collectively, our findings provide insights into the genomic origins, duplication events, and subsequent divergence of SOT gene family members. Such insights lay a crucial foundation for comprehensive functional characterizations in future studies.
Collapse
Affiliation(s)
- Fan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiawei Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Wenmeng Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yuxin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yunxiao Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Ze Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yaqiang Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| |
Collapse
|
9
|
Qin X, Hao Q, Wang X, Liu Y, Yang C, Sui M, Zhang Y, Hu Y, Chen X, Mao Z, Mao Y, Shen X. Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species. Funct Integr Genomics 2024; 24:13. [PMID: 38236432 DOI: 10.1007/s10142-024-01291-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Malus baccata (L.) var. gracilis (Rehd.) has high ornamental value and breeding significance, and comparative chloroplast genome analysis was applied to facilitate genetic breeding for desired traits and resistance and provide insight into the phylogeny of this genus. Using data from whole-genome sequencing, a tetrameric chloroplast genome with a length of 159,992 bp and a total GC content of 36.56% was constructed. The M. baccata var. gracilis chloroplast genome consists of a large single-copy sequence (88,100 bp), a short single-copy region (19,186 bp), and two inverted repeat regions, IRa (26,353 bp) and IRb (26,353 bp). This chloroplast genome contains 112 annotated genes, including 79 protein-coding genes (nine multicopy), 29 tRNA genes (eight multicopy), and four rRNA genes (all multicopy). Calculating the relative synonymous codon usage revealed a total of 32 high-frequency codons, and the codons exhibited a biased usage pattern towards A/U as the ending nucleotide. Interspecific sequence comparison and boundary analysis revealed significant sequence variation in the vast single-copy region, as well as generally similar expansion and contraction of the SSC and IR regions for 10 analyzed Malus species. M. baccata var. gracilis and Malus hupehensis were grouped together into one branch based on phylogenetic analysis of chloroplast genome sequences. The chloroplast genome of Malus species provides an important foundation for species identification, genetic diversity analysis, and Malus chloroplast genetic engineering. Additionally, the results can facilitate the use of pendant traits to improve apple tree shape.
Collapse
Affiliation(s)
- Xin Qin
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Qiang Hao
- China National Botanical Garden (North Garden), Beijing, China
| | - Xun Wang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yangbo Liu
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Chen Yang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Mengyi Sui
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yawen Zhang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yanli Hu
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xuesen Chen
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yunfei Mao
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
| | - Xiang Shen
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
| |
Collapse
|
10
|
Ni F, Li Z, Huang J. Worldwide productivity and research trend on fruit quality: a bibliometric study. FRONTIERS IN PLANT SCIENCE 2024; 14:1294989. [PMID: 38264033 PMCID: PMC10803653 DOI: 10.3389/fpls.2023.1294989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Introduction As one of the important sources of food for human beings, fruits have been extensively studied. To better guide basic and applied research, it is urgent to conduct a systematic analysis of these studies based on extensive literature collection. Methods Based on the Web of Science Core Collection database, this study uses R language and CiteSpace to conduct bibliometric analysis and data mining on the literatures related to fruit quality from January 2013 to June 2023. Results The results indicated that among various fruits, tomatoes have been most frequently studied with special interests in photosynthesis, fruit development, and molecular breeding. The research direction primarily focused on fruit resistance and storage characteristics. Among the indicators related to fruit quality, antioxidant activity has the highest co-occurrence with other indicators of fruit quality, especially with nutrients such as anthocyanins, phenolic substances, sugars, and fruit firmness. Discussion Currently, adaptation to stress and antioxidant activity are recognized as prominent research focal points in this field. Fruit morphology, particularly fruit size, irrigation methods, application of molecular technology, and infection prevention, represent potential areas of interests in future research on fruit quality.
Collapse
Affiliation(s)
- Fei Ni
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- College of Agriculture and Forestry Ecology, Shaoyang University, Shaoyang, China
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| |
Collapse
|
11
|
Zhang RX, Liu Y, Zhang X, Chen X, Sun J, Zhao Y, Zhang J, Yao JL, Liao L, Zhou H, Han Y. Two adjacent NAC transcription factors regulate fruit maturity date and flavor in peach. THE NEW PHYTOLOGIST 2024; 241:632-649. [PMID: 37933224 DOI: 10.1111/nph.19372] [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: 04/25/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023]
Abstract
Although maturity date (MD) is an essential factor affecting fresh fruit marketing and has a pleiotropic effect on fruit taste qualities, the underlying mechanisms remain largely unclear. In this study, we functionally characterized two adjacent NAM-ATAF1/2-CUC2 (NAC) transcription factors (TFs), PpNAC1 and PpNAC5, both of which were associated with fruit MD in peach. PpNAC1 and PpNAC5 were found capable of activating transcription of genes associated with cell elongation, cell wall degradation and ethylene biosynthesis, suggesting their regulatory roles in fruit enlargement and ripening. Furthermore, PpNAC1 and PpNAC5 had pleiotropic effects on fruit taste due to their ability to activate transcription of genes for sugar accumulation and organic acid degradation. Interestingly, both PpNAC1 and PpNAC5 orthologues were found in fruit-producing angiosperms and adjacently arranged in all 91 tested dicots but absent in fruitless gymnosperms, suggesting their important roles in fruit development. Our results provide insight into the regulatory roles of NAC TFs in MD and fruit taste.
Collapse
Affiliation(s)
- Ruo-Xi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yudi Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Xian Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Juanli Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Yun Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jinyun Zhang
- Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Hui Zhou
- Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| |
Collapse
|
12
|
Xu L, Zang E, Sun S, Li M. Main flavor compounds and molecular regulation mechanisms in fruits and vegetables. Crit Rev Food Sci Nutr 2023; 63:11859-11879. [PMID: 35816297 DOI: 10.1080/10408398.2022.2097195] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fruits and vegetables (F&V) are an indispensable part of a healthy diet. The volatile and nonvolatile compounds present in F&V constitute unique flavor substances. This paper reviews the main flavor substances present in F&V, as well as the biosynthetic pathways and molecular regulation mechanisms of these compounds. A series of compounds introduced include aromatic substances, soluble sugars and organic acids, which constitute the key flavor substances of F&V. Esters, phenols, alcohols, amino acids and terpenes are the main volatile aromatic substances, and nonvolatile substances are represented by amino acids, fatty acids and carbohydrates; The combination of these ingredients is the cause of the sour, sweet, bitter, astringent and spicy taste of these foods. This provides a theoretical basis for the study of the interaction between volatile and nonvolatile substances in F&V, and also provides a research direction for the healthy development of food in the future.
Collapse
Affiliation(s)
- Ling Xu
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Erhuan Zang
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China
| | - Shuying Sun
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Minhui Li
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China
- Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese and Mongolian Medical Research Institute, Hohhot, China
| |
Collapse
|
13
|
Cheng C, Ma N, Zheng Y, Xi L. Editorial: Growth regulation in horticultural plants: new insights in the omics era. FRONTIERS IN PLANT SCIENCE 2023; 14:1305520. [PMID: 37929172 PMCID: PMC10623409 DOI: 10.3389/fpls.2023.1305520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Chenxia Cheng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yi Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
14
|
Ferrão LFV, Dhakal R, Dias R, Tieman D, Whitaker V, Gore MA, Messina C, Resende MFR. Machine learning applications to improve flavor and nutritional content of horticultural crops through breeding and genetics. Curr Opin Biotechnol 2023; 83:102968. [PMID: 37515935 DOI: 10.1016/j.copbio.2023.102968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/31/2023]
Abstract
Over the last decades, significant strides were made in understanding the biochemical factors influencing the nutritional content and flavor profile of fruits and vegetables. Product differentiation in the produce aisle is the natural consequence of increasing consumer power in the food industry. Cotton-candy grapes, specialty tomatoes, and pineapple-flavored white strawberries provide a few examples. Given the increased demand for flavorful varieties, and pressing need to reduce micronutrient malnutrition, we expect breeding to increase its prioritization toward these traits. Reaching this goal will, in part, necessitate knowledge of the genetic architecture controlling these traits, as well as the development of breeding methods that maximize their genetic gain. Can artificial intelligence (AI) help predict flavor preferences, and can such insights be leveraged by breeding programs? In this Perspective, we outline both the opportunities and challenges for the development of more flavorful and nutritious crops, and how AI can support these breeding initiatives.
Collapse
Affiliation(s)
- Luís Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rakshya Dhakal
- Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Raquel Dias
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, United States
| | - Denise Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance Whitaker
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Carlos Messina
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Márcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States.
| |
Collapse
|
15
|
Kemp C. Apple revival: how science is bringing historic varieties back to life. Nature 2023; 622:446-449. [PMID: 37848522 DOI: 10.1038/d41586-023-03229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
|
16
|
Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
Collapse
Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| |
Collapse
|
17
|
Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
Collapse
Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| |
Collapse
|
18
|
Zheng L, Liao L, Duan C, Ma W, Peng Y, Yuan Y, Han Y, Ma F, Li M, Ma B. Allelic variation of MdMYB123 controls malic acid content by regulating MdMa1 and MdMa11 expression in apple. PLANT PHYSIOLOGY 2023; 192:1877-1891. [PMID: 36810940 PMCID: PMC10315266 DOI: 10.1093/plphys/kiad111] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Acidity is a key determinant of fruit organoleptic quality. Here, a candidate gene for fruit acidity, designated MdMYB123, was identified from a comparative transcriptome study of two Ma1Ma1 apple (Malus domestica) varieties, "Qinguan (QG)" and "Honeycrisp (HC)" with different malic acid content. Sequence analysis identified an A→T SNP, which was located in the last exon, resulting in a truncating mutation, designated mdmyb123. This SNP was significantly associated with fruit malic acid content, accounting for 9.5% of the observed phenotypic variation in apple germplasm. Differential MdMYB123- and mdmyb123-mediated regulation of malic acid accumulation was observed in transgenic apple calli, fruits, and plantlets. Two genes, MdMa1 and MdMa11, were up- and down-regulated in transgenic apple plantlets overexpressing MdMYB123 and mdmyb123, respectively. MdMYB123 could directly bind to the promoter of MdMa1 and MdMa11, and induce their expression. In contrast, mdmyb123 could directly bind to the promoters of MdMa1 and MdMa11, but with no transcriptional activation of both genes. In addition, gene expression analysis in 20 different apple genotypes based on SNP locus from "QG" × "HC" hybrid population confirmed a correlation between A/T SNP with expression levels of MdMa1 and MdMa11. Our finding provides valuable functional validation of MdMYB123 and its role in the transcriptional regulation of both MdMa1 and MdMa11, and apple fruit malic acid accumulation.
Collapse
Affiliation(s)
- Litong Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
| | - Chenbo Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenfang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunjing Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yangyang Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| |
Collapse
|
19
|
Xu J, Zhang W, Zhang P, Sun W, Han Y, Li L. A comprehensive analysis of copy number variations in diverse apple populations. BMC Genomics 2023; 24:256. [PMID: 37170226 PMCID: PMC10176694 DOI: 10.1186/s12864-023-09347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/16/2022] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND As an important source of genetic variation, copy number variation (CNV) can alter the dosage of DNA segments, which in turn may affect gene expression level and phenotype. However, our knowledge of CNV in apple is still limited. Here, we obtained high-confidence CNVs and investigated their functional impact based on genome resequencing data of two apple populations, cultivars and wild relatives. RESULTS In this study, we identified 914,610 CNVs comprising 14,839 CNV regions (CNVRs) from 346 apple accessions, including 289 cultivars and 57 wild relatives. CNVRs summed to 71.19 Mb, accounting for 10.03% of the apple genome. Under the low linkage disequilibrium (LD) with nearby SNPs, they could also accurately reflect the population structure of apple independent of SNPs. Furthermore, A total of 3,621 genes were covered by CNVRs and functionally involved in biological processes such as defense response, reproduction and metabolic processes. In addition, the population differentiation index ([Formula: see text]) analysis between cultivars and wild relatives revealed 127 CN-differentiated genes, which may contribute to trait differences in these two populations. CONCLUSIONS This study was based on identification of CNVs from 346 diverse apple accessions, which to our knowledge was the largest dataset for CNV analysis in apple. Our work presented the first comprehensive CNV map and provided valuable resources for understanding genomic variations in apple.
Collapse
Affiliation(s)
- Jinsheng Xu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weihan Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weicheng Sun
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China.
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Li Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
20
|
Grabska J, Beć KB, Ueno N, Huck CW. Analyzing the Quality Parameters of Apples by Spectroscopy from Vis/NIR to NIR Region: A Comprehensive Review. Foods 2023; 12:foods12101946. [PMID: 37238763 DOI: 10.3390/foods12101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Spectroscopic methods deliver a valuable non-destructive analytical tool that provides simultaneous qualitative and quantitative characterization of various samples. Apples belong to the world's most consumed crops and with the current challenges of climate change and human impacts on the environment, maintaining high-quality apple production has become critical. This review comprehensively analyzes the application of spectroscopy in near-infrared (NIR) and visible (Vis) regions, which not only show particular potential in evaluating the quality parameters of apples but also in optimizing their production and supply routines. This includes the assessment of the external and internal characteristics such as color, size, shape, surface defects, soluble solids content (SSC), total titratable acidity (TA), firmness, starch pattern index (SPI), total dry matter concentration (DM), and nutritional value. The review also summarizes various techniques and approaches used in Vis/NIR studies of apples, such as authenticity, origin, identification, adulteration, and quality control. Optical sensors and associated methods offer a wide suite of solutions readily addressing the main needs of the industry in practical routines as well, e.g., efficient sorting and grading of apples based on sweetness and other quality parameters, facilitating quality control throughout the production and supply chain. This review also evaluates ongoing development trends in the application of handheld and portable instruments operating in the Vis/NIR and NIR spectral regions for apple quality control. The use of these technologies can enhance apple crop quality, maintain competitiveness, and meet the demands of consumers, making them a crucial topic in the apple industry. The focal point of this review is placed on the literature published in the last five years, with the exceptions of seminal works that have played a critical role in shaping the field or representative studies that highlight the progress made in specific areas.
Collapse
Affiliation(s)
- Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nami Ueno
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| |
Collapse
|
21
|
Lin Q, Chen J, Liu X, Wang B, Zhao Y, Liao L, Allan AC, Sun C, Duan Y, Li X, Grierson D, Verdonk JC, Chen K, Han Y, Bi J. A metabolic perspective of selection for fruit quality related to apple domestication and improvement. Genome Biol 2023; 24:95. [PMID: 37101232 PMCID: PMC10131461 DOI: 10.1186/s13059-023-02945-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits collected from 292 wild and cultivated accessions representing various consumption types. RESULTS We find decreased amounts of certain metabolites, including tannins, organic acids, phenolic acids, and flavonoids as the wild accessions transition to cultivated apples, while lysolipids increase in the "Golden Delicious" to "Ralls Janet" pedigree, suggesting better storage. We identify a total of 222,877 significant single-nucleotide polymorphisms that are associated with 2205 apple metabolites. Investigation of a region from 2.84 to 5.01 Mb on chromosome 16 containing co-mapping regions for tannins, organic acids, phenolic acids, and flavonoids indicates the importance of these metabolites for fruit quality and nutrition during breeding. The tannin and acidity-related genes Myb9-like and PH4 are mapped closely to fruit weight locus fw1 from 3.41 to 3.76 Mb on chromosome 15, a region under selection during domestication. Lysophosphatidylethanolamine (LPE) 18:1, which is suppressed by fatty acid desaturase-2 (FAD2), is positively correlated to fruit firmness. We find the fruit weight is negatively correlated with salicylic acid and abscisic acid levels. Further functional assays demonstrate regulation of these hormone levels by NAC-like activated by Apetala3/Pistillata (NAP) and ATP binding cassette G25 (ABCG25), respectively. CONCLUSIONS This study provides a metabolic perspective for selection on fruit quality during domestication and improvement, which is a valuable resource for investigating mechanisms controlling apple metabolite content and quality.
Collapse
Affiliation(s)
- Qiong Lin
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, 6708 PD The Netherlands
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Jing Chen
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xuan Liu
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, 430070 China
| | - Yaoyao Zhao
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Liao Liao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland Mail Centre, Auckland, 1142 New Zealand
| | - Chongde Sun
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Yuquan Duan
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xuan Li
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Donald Grierson
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
- Plant and Science Crop Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Julian C. Verdonk
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, 6708 PD The Netherlands
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Yuepeng Han
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Jinfeng Bi
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| |
Collapse
|
22
|
Wang JH, Gu KD, Zhang QY, Yu JQ, Wang CK, You CX, Cheng L, Hu DG. Ethylene inhibits malate accumulation in apple by transcriptional repression of aluminum-activated malate transporter 9 via the WRKY31-ERF72 network. THE NEW PHYTOLOGIST 2023. [PMID: 36747049 DOI: 10.1111/nph.18795] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Malic acid accumulation in the vacuole largely determines acidity and perception of sweetness of apple. It has long been observed that reduction in malate level is associated with increase in ethylene production during the ripening process of climacteric fruits, but the molecular mechanism linking ethylene to malate reduction is unclear. Here, we show that ethylene-modulated WRKY transcription factor 31 (WRKY31)-Ethylene Response Factor 72 (ERF72)-ALUMINUM ACTIVATED MALATE TRANSPORTER 9 (Ma1) network regulates malate accumulation in apple fruit. ERF72 binds to the promoter of ALMT9, a key tonoplast transporter for malate accumulation of apple, transcriptionally repressing ALMT9 expression in response to ethylene. WRKY31 interacts with ERF72, suppressing its transcriptional inhibition activity on ALMT9. In addition, WRKY31 directly binds to the promoters of ERF72 and ALMT9, transcriptionally repressing and activating ERF72 and ALMT9, respectively. The expression of WRKY31 decreases in response to ethylene, lowering the transcription of ALMT9 directly and via its interactions with ERF72. These findings reveal that the regulatory complex WRKY31 forms with ERF72 responds to ethylene, linking the ethylene signal to ALMT9 expression in reducing malate transport into the vacuole during fruit ripening.
Collapse
Affiliation(s)
- Jia-Hui Wang
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Kai-Di Gu
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Quan-Yan Zhang
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, 276000, China
| | - Jian-Qiang Yu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Chu-Kun Wang
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Lailiang Cheng
- Section of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| |
Collapse
|
23
|
Mollah MDA, Zhang X, Zhao L, Jiang X, Ogutu CO, Peng Q, Belal MAA, Yang Q, Cai Y, Nishawy E, Cherono S, Wang L, Han Y. Two vacuolar invertase inhibitors PpINHa and PpINH3 display opposite effects on fruit sugar accumulation in peach. FRONTIERS IN PLANT SCIENCE 2022; 13:1033805. [PMID: 36589059 PMCID: PMC9795002 DOI: 10.3389/fpls.2022.1033805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/01/2022] [Indexed: 06/12/2023]
Abstract
Soluble sugars are an important determinant of fruit taste, but their accumulation mechanisms remain elusive. In this study, we report two vacuolar invertase inhibitor genes involved in sugar accumulation in peach, PpINHa and PpINH3. Transient overexpression of PpINH3 in peach fruits resulted in an increase in sugar content, while the opposite trend was detected for PpINHa. Unexpectedly, PpINH3 and PpINHa both had no physical interaction with vacuolar invertase (VIN). Moreover, the PpVIN genes had no or extremely low expression in fruits at the ripening stage. These results suggested that the regulatory role of PpINHa and PpINH3 in sugar accumulation is unlikely due to their interaction with PpVINs. Additionally, overexpression of PpINHa and PpINH3 had an impact on transcription of genes related to fruit sugar metabolism and transport, which is likely responsible for their regulatory role in fruit sugar accumulation. Altogether, these results indicated an important role of PpINHs in fruit accumulation in peach. Our study provides new insights into molecular mechanisms underlying sugar accumulation, which could be useful for genetic improvement of fruit taste in breeding programs of peach and other fruit crops.
Collapse
Affiliation(s)
- Md Dulal Ali Mollah
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Xian Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Li Zhao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
| | - Xiaohan Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Collins O. Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Mohammad A. A. Belal
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Qiurui Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Yaming Cai
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Elsayed Nishawy
- Genetic Resource Department, Egyptian Deserts Gene Bank, Desert Research Center, Cairo, Egypt
| | - Sylvia Cherono
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing, ;China
| | - Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences (CAS), Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
24
|
Yu J, Tseng Y, Pham K, Liu M, Beckles DM. Starch and sugars as determinants of postharvest shelf life and quality: some new and surprising roles. Curr Opin Biotechnol 2022; 78:102844. [PMID: 36410153 DOI: 10.1016/j.copbio.2022.102844] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 11/21/2022]
Abstract
Starch and sugars account for most of the dry weight of horticultural crops and in many species, are known determinants of quality. However, we posit that these carbohydrates often have less-obvious roles in plant tissues with direct implications for the postharvest quality and produce shelf life. The latter has not been given as much attention, but with the recent interest in reducing the scale of postharvest waste and loss, we highlight how dynamic changes in the spatial-temporal accumulation of carbohydrates, can influence myriads of biological processes affecting postharvest attributes. Versatile roles, some surprising, that carbohydrates play in determining produce of high value to consumers, are highlighted, and gene targets for biotechnological improvement are specified.
Collapse
Affiliation(s)
- Jingwei Yu
- SUSTech-PKU Joint Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yute Tseng
- Department of Plant Sciences, University of California Davis, One Shields Avenue, CA 95616, USA; Graduate Group of Horticulture & Agronomy, University of California Davis, One Shields Avenue, CA 95616, USA
| | - Kien Pham
- Department of Plant Sciences, University of California Davis, One Shields Avenue, CA 95616, USA; Graduate Group of Horticulture & Agronomy, University of California Davis, One Shields Avenue, CA 95616, USA
| | - Margaret Liu
- Department of Plant Sciences, University of California Davis, One Shields Avenue, CA 95616, USA; Graduate Group of Horticulture & Agronomy, University of California Davis, One Shields Avenue, CA 95616, USA
| | - Diane M Beckles
- Department of Plant Sciences, University of California Davis, One Shields Avenue, CA 95616, USA.
| |
Collapse
|
25
|
Ban S, El-Sharkawy I, Zhao J, Fei Z, Xu K. An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1609-1625. [PMID: 35861682 DOI: 10.1111/tpj.15911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/03/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Somatic mutations may alter important traits in tree fruits, such as fruit color, size and maturation date. Autumn Gala (AGala), a somatic mutation from apple cultivar Gala, matures 4 weeks later than Gala. To understand the mechanisms underlying the delayed maturation, RNA-seq analyses were conducted with fruit sampled at 13 (Gala) and 16 (AGala) time-points during their growth and development. Weighted gene co-expression network analysis (WGCNA) of 23 372 differentially expressed genes resulted in 25 WGCNA modules. Of these, modules 1 (r = -0.98, P = 2E-21) and 2 (r = -0.52, P = 0.004), which were suppressed in AGala, were correlated with fruit maturation date. Surprisingly, 77 of the 152 member genes in module 1 were harbored in a 2.8-Mb genomic region on chromosome 6 that was deleted and replaced by a 10.7-kb gypsy-like retrotransposon (Gy-36) from chromosome 7 in AGala. Among the 77 member genes, MdACT7 was the most suppressed (by 10.5-fold) in AGala due to a disruptive 2.5-kb insertion in coding sequence. Moreover, MdACT7 is the exclusive apple counterpart of Arabidopsis ACT7 known of essential roles in plant development, and the functional allele MdACT7, which was lost to the deletion in AGala, was associated with early fruit maturation in 268 apple accessions. Overexpressing alleles MdACT7 and Mdact7 in an Arabidopsis act7 line showed that MdACT7 largely rescued its stunted growth and delayed initial flowering while Mdact7 did not. Therefore, the 2.8-Mb hemizygous deletion is largely genetically causal for fruit maturation delay in AGala, and the total loss of MdACT7 might have contributed to the phenotype.
Collapse
Affiliation(s)
- Seunghyun Ban
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| | - Islam El-Sharkawy
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, USA
- US Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| |
Collapse
|
26
|
Lin X, Feng C, Lin T, Harris AJ, Li Y, Kang M. Jackfruit genome and population genomics provide insights into fruit evolution and domestication history in China. HORTICULTURE RESEARCH 2022; 9:uhac173. [PMID: 36204202 PMCID: PMC9533223 DOI: 10.1093/hr/uhac173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/25/2022] [Indexed: 05/28/2023]
Abstract
As the largest known tree-borne fruit in the world, jackfruit (Artocarpus heterophyllus) is an important cultivated crop in tropical regions of South and Southeast Asia. The species has been cultivated in China for more than 1000 years, but the history of its introduction to the country remains unclear. We assembled a high-quality chromosome-level genome of jackfruit into 985.63 Mb with scaffold N50 of 32.81 Mb. We analyzed whole-genome resequencing data of 295 landraces to investigate the domestication history in China and agronomic trait evolution of jackfruit. Population structure analysis revealed that jackfruits of China could be traced back to originate from Southeast Asia and South Asia independently. Selection signals between jackfruit and its edible congener, cempedak (Artocarpus integer), revealed several important candidate genes associated with fruit development and ripening. Moreover, analyses of selective sweeps and gene expression revealed that the AhePG1 gene may be the major factor in determining fruit texture. This study not only resolves the origins of jackfruit of China, but also provides valuable genomic resources for jackfruit breeding improvement and offers insights into fruit size evolution and fruit texture changes.
Collapse
Affiliation(s)
| | | | - Tao Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | | | | |
Collapse
|
27
|
Liu W, Chen Z, Jiang S, Wang Y, Fang H, Zhang Z, Chen X, Wang N. Research Progress on Genetic Basis of Fruit Quality Traits in Apple ( Malus × domestica). FRONTIERS IN PLANT SCIENCE 2022; 13:918202. [PMID: 35909724 PMCID: PMC9330611 DOI: 10.3389/fpls.2022.918202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/23/2022] [Indexed: 06/01/2023]
Abstract
Identifying the genetic variation characteristics of phenotypic traits is important for fruit tree breeding. During the long-term evolution of fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity. Apple (Malus × domestica Borkh.) shows strong ecological adaptability and is widely cultivated, and is among the most economically important fruit crops worldwide. However, the high level of heterozygosity and large genome of apple, in combination with its perennial life history and long juvenile phase, complicate investigation of the genetic basis of fruit quality traits. With continuing augmentation in the apple genomic resources available, in recent years important progress has been achieved in research on the genetic variation of fruit quality traits. This review focuses on summarizing recent genetic studies on apple fruit quality traits, including appearance, flavor, nutritional, ripening, and storage qualities. In addition, we discuss the mapping of quantitative trait loci, screening of molecular markers, and mining of major genes associated with fruit quality traits. The overall aim of this review is to provide valuable insights into the mechanisms of genetic variation and molecular breeding of important fruit quality traits in apple.
Collapse
Affiliation(s)
- Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Zijing Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Shenghui Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yicheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hongcheng Fang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Zongying Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| |
Collapse
|
28
|
Yang Q, Yang X, Wang L, Zheng B, Cai Y, Ogutu CO, Zhao L, Peng Q, Liao L, Zhao Y, Zhou H, Han Y. Two R2R3-MYB genes cooperatively control trichome development and cuticular wax biosynthesis in Prunus persica. THE NEW PHYTOLOGIST 2022; 234:179-196. [PMID: 35023174 DOI: 10.1111/nph.17965] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The fruit surface has an enormous impact on the external appearance and postharvest shelf-life of fruit. Here, we report two functionally redundant genes, PpMYB25 and PpMYB26, involved in regulation of fruit skin texture in peach. PpMYB25 can activate transcription of PpMYB26 and they both induce trichome development and cuticular wax accumulation, resulting in peach fruit with a fuzzy and dull appearance. By contrast, nonfunctional mutation of PpMYB25 caused by an insertional retrotransposon in the last exon in nectarine fails to activate transcription of PpMYB26, resulting in nectarine fruit with a smooth and shiny appearance due to loss of trichome initiation and decreased cuticular wax accumulation. Secondary cell wall biosynthesis in peach fruit pubescence is controlled by a transcriptional regulatory network, including the master regulator PpNAC43 and its downstream MYB transcription factors such as PpMYB42, PpMYB46 and PpMYB83. Our results show that PpMYB25 and PpMYB26 coordinately regulate fruit pubescence and cuticular wax accumulation and their simultaneous perturbation results in the origin of nectarine, which is botanically classified as a subspecies of peach.
Collapse
Affiliation(s)
- Qiurui Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Xianpeng Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lu Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yaming Cai
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lei Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Qian Peng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yun Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Hui Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230001, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| |
Collapse
|
29
|
Shen F, Bianco L, Wu B, Tian Z, Wang Y, Wu T, Xu X, Han Z, Velasco R, Fontana P, Zhang X. A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple. J Adv Res 2022; 42:149-162. [PMID: 36513410 PMCID: PMC9788957 DOI: 10.1016/j.jare.2022.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants. OBJECTIVES We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes. METHODS A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted. RESULTS By using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively. CONCLUSION The BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.
Collapse
Affiliation(s)
- Fei Shen
- College of Horticulture, China Agricultural University, Beijing 100193, China,Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, CREA, Conegliano, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Corresponding authors.
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| |
Collapse
|
30
|
Identification of the Complete Chloroplast Genome of Malus zhaojiaoensis Jiang and Its Comparison and Evolutionary Analysis with Other Malus Species. Genes (Basel) 2022; 13:genes13040560. [PMID: 35456366 PMCID: PMC9028542 DOI: 10.3390/genes13040560] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/19/2022] [Accepted: 03/19/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Malus is rich in species and many of its plastid genomes have been released. However, limited resources and few markers are not conducive to the comparison of differences among species and resource identification and evaluation. In this study, the complete chloroplast genome of Malus zhaojiaoensis was studied by NGS sequencing, with a total length of 159998 bp. It consists of four regions, LSC (88,070 bp), IRB (26,359 bp), SSC (19,210 bp) and IRA (26,359 bp). M. zhaojiaoensis cp genome contained a total of 111 genes made up of three classes: 78 coding sequences, 29 tRNA genes, and four rRNA genes. In addition, a total of 91 SSRs and 43 INEs were found in the M. zhaojiaoensis cp genome, which was slightly different from M. baccata and M. hupehensis in number. The analysis of codon usage and RNA editing showed that high-frequency codons tended to end at A/U bases and RNA editing mainly occurred at the second codon. Comparative genome analysis suggested that the cp genomes of eight Malus species had higher overall similarity, but there were more variation hotspots (rps16_trnK-UUU, trnG-UCC_atpA, atpH_atpF, trnT-GGU_psbD, etc.) in the LSC region. By building evolutionary trees, it can be clearly observed that M. zhaojiaoensis formed a large group with eight species of Malus, but was relatively independent in differentiation. In conclusion, this study provides high-quality chloroplast genome resources of M. zhaojiaoensis and discusses the genetic variation characteristics of Malus genus. The findings of this study will provide a good reference for plastid genome assembly and interspecific comparison in the future.
Collapse
|
31
|
Zhang Z, Shi Q, Wang B, Ma A, Wang Y, Xue Q, Shen B, Hamaila H, Tang T, Qi X, Fernie AR, Luo J, Li X. Jujube metabolome selection determined the edible properties acquired during domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1116-1133. [PMID: 34862996 DOI: 10.1111/tpj.15617] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/11/2021] [Accepted: 11/27/2021] [Indexed: 05/26/2023]
Abstract
Plants supply both food and medicinal compounds, which are ascribed to diverse metabolites produced by plants. However, studies on domestication-driven changes in the metabolome and genetic basis of bioactive molecules in perennial fruit trees are generally lacking. Here, we conducted multidimensional analyses revealing a singular domestication event involving the genomic and metabolomic selection of jujube trees (Ziziphus jujuba Mill.). The genomic selection for domesticated genes was highly enriched in metabolic pathways, including carbohydrates and specialized metabolism. Domesticated metabolome profiling indicated that 187 metabolites exhibited significant divergence as a result of directional selection. Malic acid was directly selected during domestication, and the simultaneous selection of specialized metabolites, including triterpenes, consequently lead to edible properties. Cyclopeptide alkaloids (CPAs) were specifically targeted for the divergence between dry and fresh cultivars. We identified 1080 significantly associated loci for 986 metabolites. Among them, 15 triterpenes were directly selected at six major loci, allowing the identification of a homologous cluster containing seven 2,3-oxidosqualene cyclases (OSCs). An OSC gene was found to contribute to the reduction in the content of triterpenes during domestication. The complete pathway for synthesizing ursolic acid was dissected by integration of the metabolome and transcriptome. Additionally, an N-methyltransferase involved in the biosynthesis of CPA and responsible for inter-cultivar content variation was identified. The present study promotes our understanding of the selection process of the global metabolome subsequent to fruit tree domestication and facilitates the genetic manipulation of specialized metabolites to enhance their edible traits.
Collapse
Affiliation(s)
- Zhong Zhang
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Qianqian Shi
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Aimin Ma
- Key Laboratory of Plant Molecular, Physiology Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongkang Wang
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taigu, 030815, China
| | - Qingtun Xue
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Bingqi Shen
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Halina Hamaila
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular, Physiology Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Xingang Li
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| |
Collapse
|
32
|
Wang Z, Ma B, Yang N, Jin L, Wang L, Ma S, Ruan YL, Ma F, Li M. Variation in the promoter of the sorbitol dehydrogenase gene MdSDH2 affects binding of the transcription factor MdABI3 and alters fructose content in apple fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1183-1198. [PMID: 34888978 DOI: 10.1111/tpj.15624] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/14/2021] [Accepted: 12/06/2021] [Indexed: 06/13/2023]
Abstract
Fructose (Fru) content is a key determinant of fruit sweetness and quality. An F1 hybrid population of the apple cultivars 'Honeycrisp' × 'Qinguan' was used to investigate the quantitative trait locus (QTL) regions and genes controlling Fru content in fruit. A stable QTL on linkage group (LG) 01 in 'Honeycrisp' was detected on the single nucleotide polymorphism (SNP) genetic linkage maps. In this region, a sorbitol dehydrogenase (SDH) gene, MdSDH2, was detected and showed promoter variations and differential expression patterns between 'Honeycrisp' and 'Qinguan' fruits as well as their hybrids. A SNP variant (A/G) in the MdSDH2 promoter region (SDH2p-491) affected the binding ability of the transcription factor MdABI3, which can affect the expression of MdSDH2. Promoter sequences with an A nucleotide at SDH2p-491 had stronger binding affinity for MdABI3 than those with a G. Among 27 domesticated apple cultivars and wild relatives, this SNP (A/G) was associated with Fru content. Our results indicate that MdSDH2 can alter Fru content as the major regulatory gene and that ABA signaling might be involved in Fru content accumulation in apple fruit.
Collapse
Affiliation(s)
- Zhengyang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Nanxiang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ling Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Songya Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yong-Ling Ruan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
33
|
Cazenave X, Petit B, Lateur M, Nybom H, Sedlak J, Tartarini S, Laurens F, Durel CE, Muranty H. Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple. G3 (BETHESDA, MD.) 2021; 12:6459174. [PMID: 34893831 PMCID: PMC9210277 DOI: 10.1093/g3journal/jkab420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e., genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation.
Collapse
Affiliation(s)
- Xabi Cazenave
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Bernard Petit
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Jiri Sedlak
- Výzkumný a Šlechtitelský ústav Ovocnářský Holovousy s.r.o, Holovousy, Czech Republic
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - François Laurens
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Charles-Eric Durel
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Hélène Muranty
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France,Corresponding author:
| |
Collapse
|
34
|
Chen P, Li Z, Zhang D, Shen W, Xie Y, Zhang J, Jiang L, Li X, Shen X, Geng D, Wang L, Niu C, Bao C, Yan M, Li H, Li C, Yan Y, Zou Y, Micheletti D, Koot E, Ma F, Guan Q. Insights into the effect of human civilization on Malus evolution and domestication. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2206-2220. [PMID: 34161653 PMCID: PMC8541786 DOI: 10.1111/pbi.13648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 05/09/2023]
Abstract
The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.
Collapse
Affiliation(s)
- Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Lijuan Jiang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Mingjia Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Haiyan Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yangjun Zou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | | | - Emily Koot
- The New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| |
Collapse
|
35
|
Huang XY, Wang CK, Zhao YW, Sun CH, Hu DG. Mechanisms and regulation of organic acid accumulation in plant vacuoles. HORTICULTURE RESEARCH 2021; 8:227. [PMID: 34697291 PMCID: PMC8546024 DOI: 10.1038/s41438-021-00702-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/09/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
In fleshy fruits, organic acids are the main source of fruit acidity and play an important role in regulating osmotic pressure, pH homeostasis, stress resistance, and fruit quality. The transport of organic acids from the cytosol to the vacuole and their storage are complex processes. A large number of transporters carry organic acids from the cytosol to the vacuole with the assistance of various proton pumps and enzymes. However, much remains to be explored regarding the vacuolar transport mechanism of organic acids as well as the substances involved and their association. In this review, recent advances in the vacuolar transport mechanism of organic acids in plants are summarized from the perspectives of transporters, channels, proton pumps, and upstream regulators to better understand the complex regulatory networks involved in fruit acid formation.
Collapse
Affiliation(s)
- Xiao-Yu Huang
- National Key Laboratory of Crop Biology; Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chu-Kun Wang
- National Key Laboratory of Crop Biology; Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yu-Wen Zhao
- National Key Laboratory of Crop Biology; Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Cui-Hui Sun
- National Key Laboratory of Crop Biology; Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology; Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| |
Collapse
|