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Jia L, Zhang X, Zhang Z, Luo W, Nambeesan SU, Li Q, Qiao X, Yang B, Wang L, Zhang S. PbrbZIP15 promotes sugar accumulation in pear via activating the transcription of the glucose isomerase gene PbrXylA1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1392-1412. [PMID: 38044792 DOI: 10.1111/tpj.16569] [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: 08/31/2023] [Revised: 11/01/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
The composition and abundance of soluble sugars in mature pear (Pyrus) fruit are important for its acceptance by consumers. However, our understanding of the genes responsible for soluble sugar accumulation remains limited. In this study, a S1-group member of bZIP gene family, PbrbZIP15, was characterized from pear genome through the combined analyses of metabolite and transcriptome data followed by experimental validation. PbrbZIP15, located in nucleus, was found to function in fructose, sucrose, and total soluble sugar accumulation in pear fruit and calli. After analyzing the expression profiles of sugar-metabolism-related genes and the distribution of cis-acting elements in their promoters, the glucose isomerase 1 gene (PbrXylA1), whose corresponding protein catalyzed the isomerization of glucose and fructose in vitro, was identified as a downstream target gene of PbrbZIP15. PbrbZIP15 could directly bind to the G-box element in PbrXylA1 promoter and activate its transcription, as evidenced by chromatin immunoprecipitation-quantitative PCR, yeast one-hybrid, electrophoretic mobility shift assay, and dual-luciferase assay. PbrXylA1, featuring a leucine-rich signal peptide in its N-terminal, was localized to the endoplasmic reticulum. It was validated to play a significant role in fructose, sucrose, and total soluble sugar accumulation in pear fruit and calli, which was associated with the upregulated fructose/glucose ratio. Further studies revealed a positive correlation between the sucrose content and the expression levels of several sucrose-biosynthesis-related genes (PbrFRK3/8, PbrSPS1/3/4/8, and PbrSPP1) in PbrbZIP15-/PbrXylA1-transgenic fruit/calli. In conclusion, our results suggest that PbrbZIP15-induced soluble sugar accumulation during pear development is at least partly attributed to the activation of PbrXylA1 transcription.
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Affiliation(s)
- Luting Jia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Weiqi Luo
- U.S. Horticultural Research Laboratory, ARS-USDA, Ft. Pierce, Florida, 34945, USA
- CIPM, NC State University, Raleigh, North Carolina, 27606, USA
| | | | - Qionghou Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xin Qiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Bing Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Libin Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shaoling Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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2
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Wu G, Tian N, She F, Cao A, Wu W, Zheng S, Yang N. Characteristics analysis of Early Responsive to Dehydration genes in Arabidopsis thaliana ( AtERD). PLANT SIGNALING & BEHAVIOR 2023; 18:2105021. [PMID: 35916255 PMCID: PMC10730211 DOI: 10.1080/15592324.2022.2105021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Early Responsive to Dehydration (ERD) genes are rapidly induced in response to various biotic and abiotic stresses, such as bacteria, drought, light, temperature and high salt in Arabidopsis thaliana. Sixteen ERD of Arabidopsis thaliana (AtERD) genes have been previously identified. The lengths of the coding region of the genes are 504-2838 bp. They encode 137-745 amino acids. In this study, the AtERD genes structure and promoter are analyzed through bioinformatics, and a overall function is summarized and a systematic signal pathway involving AtERD genes is mapped. AtERD9, AtERD11 and AtERD13 have the GST domain. AtERD10 and AtERD14 have the Dehyd domain. The promoters regions contain 32 light responsive elements, 23 ABA responsive elements, 5 drought responsive elements, 5 meristem expression related elements and 132 core promoter elements. The study provides a theoretical guidance for subsequent studies of AtERD genes.
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Affiliation(s)
- Guofan Wu
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Nongfu Tian
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Fawen She
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Aohua Cao
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Wangze Wu
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Sheng Zheng
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Ning Yang
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
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Wang H, Xu K, Li X, Blanco-Ulate B, Yang Q, Yao G, Wei Y, Wu J, Sheng B, Chang Y, Jiang CZ, Lin J. A pear S1-bZIP transcription factor PpbZIP44 modulates carbohydrate metabolism, amino acid, and flavonoid accumulation in fruits. HORTICULTURE RESEARCH 2023; 10:uhad140. [PMID: 37575657 PMCID: PMC10421730 DOI: 10.1093/hr/uhad140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
Fruit quality is defined by attributes that give value to a commodity. Flavor, texture, nutrition, and shelf life are key quality traits that ensure market value and consumer acceptance. In pear fruit, soluble sugars, organic acids, amino acids, and total flavonoids contribute to flavor and overall quality. Transcription factors (TFs) regulate the accumulation of these metabolites during development or in response to the environment. Here, we report a novel TF, PpbZIP44, as a positive regulator of primary and secondary metabolism in pear fruit. Analysis of the transient overexpression or RNAi-transformed pear fruits and stable transgenic tomato fruits under the control of the fruit-specific E8 promoter demonstrated that PpZIP44 substantially affected the contents of soluble sugar, organic acids, amino acids, and flavonoids. In E8::PpbZIP44 tomato fruit, genes involved in carbohydrate metabolism, amino acid, and flavonoids biosynthesis were significantly induced. Furthermore, in PpbZIP44 overexpression or antisense pear fruits, the expression of genes in the related pathways was significantly impacted. PpbZIP44 directly interacted with the promoter of PpSDH9 and PpProDH1 to induce their expression, thereby depleting sorbitol and proline, decreasing citrate and malate, and enhancing fructose contents. PpbZIP44 also directly bound to the PpADT and PpF3H promoters, which led to the carbon flux toward phenylalanine metabolites and enhanced phenylalanine and flavonoid contents. These findings demonstrate that PpbZIP44 mediates multimetabolism reprogramming by regulating the gene expression related to fruit quality compounds.
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Affiliation(s)
- Hong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Kexin Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xiaogang Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Bárbara Blanco-Ulate
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Qingsong Yang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yiduo Wei
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Jun Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
| | - Baolong Sheng
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Youhong Chang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, California, 95616, USA
| | - Jing Lin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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4
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Nishio S, Moriya S, Kunihisa M, Takeuchi Y, Imai A, Takada N. Rapid and easy construction of a simplified amplicon sequencing (simplified AmpSeq) library for marker-assisted selection. Sci Rep 2023; 13:10575. [PMID: 37386134 PMCID: PMC10310812 DOI: 10.1038/s41598-023-37522-1] [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: 05/10/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023] Open
Abstract
Marker-assisted selection (MAS) is fundamental for plant breeding programs, as it can identify desirable seedlings at a young stage and reduce the cost, time and space needed for plant maintenance, especially for perennial crops. To facilitate the process of genotyping, which is time consuming and laborious, we developed a simplified amplicon sequencing (simplified AmpSeq) library construction method for next-generation sequencing that can be applied to MAS in breeding programs. The method is based on one-step PCR with a mixture of two primer sets: the first consisting of tailed target primers, the second of primers that contain flow-cell binding sites, indexes and tail sequences complementary to those in the first set. To demonstrate the process of MAS using s implified AmpSeq, we created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.). Simplified AmpSeq has the advantages of high repeatability, ability to estimate allele number in polyploid species and semi-automatic evaluation using target allele frequencies. Because this method provides high flexibility for designing primer sets and targeting any variant, it will be useful for plant breeding programs.
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Affiliation(s)
- Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan.
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, Morioka, Iwate, 020-0123, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Yukie Takeuchi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Atsushi Imai
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Norio Takada
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
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Zhou Z, Zhang L, Shu J, Wang M, Li H, Shu H, Wang X, Sun Q, Zhang S. Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple. PLANTS (BASEL, SWITZERLAND) 2022; 11:1408. [PMID: 35684181 PMCID: PMC9182997 DOI: 10.3390/plants11111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.
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Affiliation(s)
- Zhou Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Lei Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Mengyu Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Han Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Huairui Shu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Xiaoyun Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
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6
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Serra O, de Sousa RM, Guimarães JB, Matos J, Vicente P, de Sousa ML, Simões F. Genome-wide clonal variability in European pear "Rocha" using high-throughput sequencing. HORTICULTURE RESEARCH 2022; 9:uhac111. [PMID: 38486834 PMCID: PMC10939347 DOI: 10.1093/hr/uhac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/27/2022] [Indexed: 03/17/2024]
Abstract
Pears (Pyrus) are one of the most economically important fruits worldwide. The Pyrus genus is characterized by a high degree of genetic variability between species and interspecific hybrids, and several studies have been performed to assess this variability for both cultivated and wild accessions. These studies have mostly been limited by the resolving power of traditional molecular markers, although in the recent past the availability of reference genome sequences or SNP arrays for pear have enhanced the capability of high-resolution genomics studies. These tools can also be applied to better understand the intra-varietal (or clonal) variability in pear. Here we report the first high resolution genomics analysis of a pear clonal population using whole genome sequencing (WGS). Results showed unique signatures for the accumulation of mutations and transposable element insertions in each clone, which are likely related to their history of propagation and cultivation. The nucleotide diversity remained low in the clonal collection with the exception of few genomic windows, suggesting that balancing selection may be occurring. These windows included mainly genes related to plant fertility. Regions with higher mutational load were partially associated with transcription factors, probably reflecting the distinctive phenotypes in the collection. The annotation of variants also revealed the theoretical disruption of relevant genes in pear. Taken together, the results from this study show that pear clones accumulate mutations differently, and that those mutations can play a role on pear phenotypes, meaning that the study of pear clonal populations can be relevant in genetic studies, mainly when comparing with traditional association studies.
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Affiliation(s)
- Octávio Serra
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Banco Português de Germoplasma Vegetal (BPGV), Quinta de S. José, S. Pedro de Merelim 4700-859 Braga, Portugal
| | - Rui Maia de Sousa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
| | - Joana Bagoin Guimarães
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - José Matos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia Vicente
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
| | - Miguel Leão de Sousa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
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Minamikawa MF, Nonaka K, Hamada H, Shimizu T, Iwata H. Dissecting Breeders' Sense via Explainable Machine Learning Approach: Application to Fruit Peelability and Hardness in Citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:832749. [PMID: 35222489 PMCID: PMC8867066 DOI: 10.3389/fpls.2022.832749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
"Genomics-assisted breeding", which utilizes genomics-based methods, e.g., genome-wide association study (GWAS) and genomic selection (GS), has been attracting attention, especially in the field of fruit breeding. Low-cost genotyping technologies that support genome-assisted breeding have already been established. However, efficient collection of large amounts of high-quality phenotypic data is essential for the success of such breeding. Most of the fruit quality traits have been sensorily and visually evaluated by professional breeders. However, the fruit morphological features that serve as the basis for such sensory and visual judgments are unclear. This makes it difficult to collect efficient phenotypic data on fruit quality traits using image analysis. In this study, we developed a method to automatically measure the morphological features of citrus fruits by the image analysis of cross-sectional images of citrus fruits. We applied explainable machine learning methods and Bayesian networks to determine the relationship between fruit morphological features and two sensorily evaluated fruit quality traits: easiness of peeling (Peeling) and fruit hardness (FruH). In each of all the methods applied in this study, the degradation area of the central core of the fruit was significantly and directly associated with both Peeling and FruH, while the seed area was significantly and directly related to FruH alone. The degradation area of albedo and the area of flavedo were also significantly and directly related to Peeling and FruH, respectively, except in one or two methods. These results suggest that an approach that combines explainable machine learning methods, Bayesian networks, and image analysis can be effective in dissecting the experienced sense of a breeder. In breeding programs, collecting fruit images and efficiently measuring and documenting fruit morphological features that are related to fruit quality traits may increase the size of data for the analysis and improvement of the accuracy of GWAS and GS on the quality traits of the citrus fruits.
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Affiliation(s)
- Mai F. Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keisuke Nonaka
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shizuoka, Japan
| | - Hiroko Hamada
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shizuoka, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shizuoka, 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, Tokyo, Japan
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