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Zhang L, Wang X, Dong K, Tan B, Zheng X, Ye X, Wang W, Cheng J, Feng J. Tandem transcription factors PpNAC1 and PpNAC5 synergistically activate the transcription of the PpPGF to regulate peach softening during fruit ripening. PLANT MOLECULAR BIOLOGY 2024; 114:46. [PMID: 38630415 DOI: 10.1007/s11103-024-01429-w] [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: 11/16/2023] [Accepted: 02/18/2024] [Indexed: 04/19/2024]
Abstract
Peach fruit rapidly soften after harvest, a significant challenge for producers and marketers as it results in rotting fruit and significantly reduces shelf life. In this study, we identified two tandem genes, PpNAC1 and PpNAC5, within the sr (slow ripening) locus. Phylogenetic analysis showed that NAC1 and NAC5 are highly conserved in dicots and that PpNAC1 is the orthologous gene of Non-ripening (NOR) in tomato. PpNAC1 and PpNAC5 were highly expressed in peach fruit, with their transcript levels up-regulated at the onset of ripening. Yeast two-hybrid and bimolecular fluorescence complementation assays showed PpNAC1 interacting with PpNAC5 and this interaction occurs with the tomato and apple orthologues. Transient gene silencing experiments showed that PpNAC1 and PpNAC5 positively regulate peach fruit softening. Yeast one-hybrid and dual luciferase assays and LUC bioluminescence imaging proved that PpNAC1 and PpNAC5 directly bind to the PpPGF promoter and activate its transcription. Co-expression of PpNAC1 and PpNAC5 showed higher levels of PpPGF activation than expression of PpNAC1 or PpNAC5 alone. In summary, our findings demonstrate that the tandem transcription factors PpNAC1 and PpNAC5 synergistically activate the transcription of PpPGF to regulate fruit softening during peach fruit ripening.
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Affiliation(s)
- Langlang Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaofei Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kang Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China.
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Navarro A, Giménez R, Val J, Moreno MÁ. The Impact of Rootstock on "Big Top" Nectarine Postharvest Concerning Chilling Injury, Biochemical and Molecular Parameters. PLANTS (BASEL, SWITZERLAND) 2024; 13:677. [PMID: 38475523 DOI: 10.3390/plants13050677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Peaches and nectarines have a short shelf life even when harvested at appropriate physiological maturity. Market life is increased by storage at low temperatures. However, chilling injury symptoms can appear, causing physiological disorders and limiting shipping potential. The rootstock effect on the post-harvest quality has hardly been explored. Thus, the principal aim of this work was to study the influence of seven different Prunus rootstocks on the "Big Top" nectarine cv, considering harvest and post-harvest quality parameters and their correlation with chilling injury disorders. Basic fruit quality traits, individual sugars and organic acids analyzed by HPLC and other biochemical compounds such as relative antioxidant capacity, total phenolics content, flavonoids, anthocyanins, vitamin C and related enzyme activities (PAL, POD, PPO) were considered. In addition, correlations with possible candidate genes for chilling injury (CI) tolerance were searched by qPCR. Although a low susceptibility to CI symptoms has been found in "Big Top", rootstocks "PADAC 9902-01", "PADAC 99-05" and "ReplantPAC" exhibited lower CI symptoms. A statistically significant influence of the evaluated rootstocks was found concerning the parameters of this study. Phenols and anthocyanins seem to be important parameters to be considered in the prevention of chilling injury disorders. Moreover, PAL1, PPO4, PG2 and LDOX genes relative expressions were positively associated with chilling injury susceptibility. This study opens new perspectives for understanding peach fruit adaptation and response to cold storage temperatures during the post-harvest period.
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Affiliation(s)
- Aimar Navarro
- Department of Pomology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), P.O. Box 13034, 50080 Zaragoza, Spain
- Department of Genetics and Plant Production, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), P.O. Box 13034, 50080 Zaragoza, Spain
| | - Rosa Giménez
- Department of Pomology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), P.O. Box 13034, 50080 Zaragoza, Spain
| | - Jesús Val
- Department of Plant Biology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), P.O. Box 13034, 50080 Zaragoza, Spain
| | - María Ángeles Moreno
- Department of Pomology, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), P.O. Box 13034, 50080 Zaragoza, Spain
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Srivastav M, Radadiya N, Ramachandra S, Jayaswal PK, Singh N, Singh S, Mahato AK, Tandon G, Gupta A, Devi R, Subrayagowda SH, Kumar G, Prakash P, Singh S, Sharma N, Nagaraja A, Kar A, Rudra SG, Sethi S, Jaiswal S, Iquebal MA, Singh R, Singh SK, Singh NK. High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids. FRONTIERS IN PLANT SCIENCE 2023; 14:1135285. [PMID: 37351213 PMCID: PMC10282835 DOI: 10.3389/fpls.2023.1135285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Introduction Mango (Mangifera indica L.), acclaimed as the 'king of fruits' in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood. Methods For mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array. Results and discussion Initially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.
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Affiliation(s)
- Manish Srivastav
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nidhi Radadiya
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sridhar Ramachandra
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Pawan Kumar Jayaswal
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Nisha Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Sangeeta Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Ajay Kumar Mahato
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Gitanjali Tandon
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankit Gupta
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Rajni Devi
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sreekanth Halli Subrayagowda
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Gulshan Kumar
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Pragya Prakash
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Singh
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nimisha Sharma
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - A. Nagaraja
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Abhijit Kar
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shalini Gaur Rudra
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shruti Sethi
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nagendra Kumar Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
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Abbas F, Zhou Y, O'Neill Rothenberg D, Alam I, Ke Y, Wang HC. Aroma Components in Horticultural Crops: Chemical Diversity and Usage of Metabolic Engineering for Industrial Applications. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091748. [PMID: 37176806 PMCID: PMC10180852 DOI: 10.3390/plants12091748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Plants produce an incredible variety of volatile organic compounds (VOCs) that assist the interactions with their environment, such as attracting pollinating insects and seed dispersers and defense against herbivores, pathogens, and parasites. Furthermore, VOCs have a significant economic impact on crop quality, as well as the beverage, food, perfume, cosmetics and pharmaceuticals industries. These VOCs are mainly classified as terpenoids, benzenoids/phenylpropanes, and fatty acid derivates. Fruits and vegetables are rich in minerals, vitamins, antioxidants, and dietary fiber, while aroma compounds play a major role in flavor and quality management of these horticultural commodities. Subtle shifts in aroma compounds can dramatically alter the flavor and texture of fruits and vegetables, altering their consumer appeal. Rapid innovations in -omics techniques have led to the isolation of genes encoding enzymes involved in the biosynthesis of several volatiles, which has aided to our comprehension of the regulatory molecular pathways involved in VOC production. The present review focuses on the significance of aroma volatiles to the flavor and aroma profile of horticultural crops and addresses the industrial applications of plant-derived volatile terpenoids, particularly in food and beverages, pharmaceuticals, cosmetics, and biofuel industries. Additionally, the methodological constraints and complexities that limit the transition from gene selection to host organisms and from laboratories to practical implementation are discussed, along with metabolic engineering's potential for enhancing terpenoids volatile production at the industrial level.
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Affiliation(s)
- Farhat Abbas
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yiwei Zhou
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China
| | - Dylan O'Neill Rothenberg
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Intikhab Alam
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yanguo Ke
- College of Economics and Management, College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, China
| | - Hui-Cong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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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.
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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
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Sohi HS, Gill MIS, Chhuneja P, Arora NK, Maan SS, Singh J. Construction of Genetic Linkage Map and Mapping QTL Specific to Leaf Anthocyanin Colouration in Mapping Population 'Allahabad Safeda' × 'Purple Guava (Local)' of Guava ( Psidium guajava L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:2014. [PMID: 35956491 PMCID: PMC9370526 DOI: 10.3390/plants11152014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
In the present investigation, F1 hybrids were developed in guava (Psidium guajava L.) by crossing high leaf-anthocyanin reflective-index (ARI1) content cultivars purple guava (local) 'PG', 'CISH G-1' and low leaf-ARI1 content cultivar Seedless 'SL' with Allahabad Safeda 'AS'. On the basis of phenotypic observations, high ARI1 content was observed in the cross 'AS' × 'PG' (0.214). Further, an SSR-markers-based genetic linkage map was developed from a mapping population of 238 F1 individuals derived from cross 'AS' × 'PG'. The linkage map comprised 11 linkage groups (LGs), spanning 1601.7 cM with an average marker interval distance of 29.61 cM between adjacent markers. Five anthocyanin-content related gene-specific markers from apple were tested for parental polymorphism in the genotypes 'AS' and 'PG'. Subsequently, a marker, viz., 'MdMYB10F1', revealed a strong association with leaf anthocyanin content in the guava mapping population. QTL (qARI-6-1) on LG6 explains much of the variation (PVE = 11.51% with LOD = 4.67) in levels of leaf anthocyanin colouration. This is the first report of amplification/utilization of apple anthocyanin-related genes in guava. The genotypic data generated from the genetic map can be further exploited in future for the enrichment of linkage maps and for identification of complex quantitative trait loci (QTLs) governing economically important fruit quality traits in guava.
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Affiliation(s)
- Harjot Singh Sohi
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Manav Indra Singh Gill
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India;
| | - Naresh Kumar Arora
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Sukhjinder Singh Maan
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
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Lian X, Zhang H, Jiang C, Gao F, Yan L, Zheng X, Cheng J, Wang W, Wang X, Ye X, Li J, Zhang L, Li Z, Tan B, Feng J. De novo chromosome-level genome of a semi-dwarf cultivar of Prunus persica identifies the aquaporin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size. PLANT BIOTECHNOLOGY JOURNAL 2022. [PMID: 34919780 PMCID: PMC9055816 DOI: 10.1111/pbi.v20.5 10.1111/pbi.13767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Peach (Prunus persica) is one of the most important fruit crops globally, but its cultivation can be hindered by large tree size. 'Zhongyoutao 14' (CN14) is a temperature-sensitive semi-dwarf (TSSD) cultivar which might be useful as breeding stock. The genome of CN14 was sequenced and assembled de novo using single-molecule real-time sequencing and chromosome conformation capture assembly. A high-quality genome was assembled and annotated, with 228.82 Mb mapped to eight chromosomes. Eighty-six re-sequenced F1 individuals and 334 previously re-sequenced accessions were used to identify candidate genes controlling TSSD and flower type and size. An aquaporin tonoplast intrinsic protein (PpTIP2) was a strong candidate gene for control of TSSD. Sequence variations in the upstream regulatory region of PpTIP2 correlated with different transcriptional activity at different temperatures. PpB3-1, a candidate gene for flower type (SH) and flower size, contributed to petal development and promoted petal enlargement. The locus of another 12 agronomic traits was identified through genome-wide association study. Most of these loci exhibited consistent and precise association signals, except for flesh texture and flesh adhesion. A 6015-bp insertion in exon 3 and a 26-bp insertion upstream of PpMYB25 were associated with fruit hairless. Along with a 70.5-Kb gap at the F-M locus in CN14, another two new alleles were identified in peach accessions. Our findings will not only promote genomic research and agronomic breeding in peach but also provide a foundation for the peach pan-genome.
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Affiliation(s)
- Xiaodong Lian
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Haipeng Zhang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Chao Jiang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Fan Gao
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Liu Yan
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Xianbo Zheng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Jun Cheng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Wei Wang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Xiaobei Wang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Xia Ye
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Jidong Li
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Langlang Zhang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Zhiqian Li
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Bin Tan
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Jiancan Feng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
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8
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Lian X, Zhang H, Jiang C, Gao F, Yan L, Zheng X, Cheng J, Wang W, Wang X, Ye X, Li J, Zhang L, Li Z, Tan B, Feng J. De novo chromosome-level genome of a semi-dwarf cultivar of Prunus persica identifies the aquaporin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:886-902. [PMID: 34919780 PMCID: PMC9055816 DOI: 10.1111/pbi.13767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 05/16/2023]
Abstract
Peach (Prunus persica) is one of the most important fruit crops globally, but its cultivation can be hindered by large tree size. 'Zhongyoutao 14' (CN14) is a temperature-sensitive semi-dwarf (TSSD) cultivar which might be useful as breeding stock. The genome of CN14 was sequenced and assembled de novo using single-molecule real-time sequencing and chromosome conformation capture assembly. A high-quality genome was assembled and annotated, with 228.82 Mb mapped to eight chromosomes. Eighty-six re-sequenced F1 individuals and 334 previously re-sequenced accessions were used to identify candidate genes controlling TSSD and flower type and size. An aquaporin tonoplast intrinsic protein (PpTIP2) was a strong candidate gene for control of TSSD. Sequence variations in the upstream regulatory region of PpTIP2 correlated with different transcriptional activity at different temperatures. PpB3-1, a candidate gene for flower type (SH) and flower size, contributed to petal development and promoted petal enlargement. The locus of another 12 agronomic traits was identified through genome-wide association study. Most of these loci exhibited consistent and precise association signals, except for flesh texture and flesh adhesion. A 6015-bp insertion in exon 3 and a 26-bp insertion upstream of PpMYB25 were associated with fruit hairless. Along with a 70.5-Kb gap at the F-M locus in CN14, another two new alleles were identified in peach accessions. Our findings will not only promote genomic research and agronomic breeding in peach but also provide a foundation for the peach pan-genome.
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Affiliation(s)
- Xiaodong Lian
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Haipeng Zhang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Chao Jiang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Fan Gao
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Liu Yan
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Xianbo Zheng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Jun Cheng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Wei Wang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Xiaobei Wang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Xia Ye
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Jidong Li
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Langlang Zhang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Zhiqian Li
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Bin Tan
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
| | - Jiancan Feng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Fruit and Cucurbit BiologyZhengzhouChina
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9
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Molecular Insights of Fruit Quality Traits in Peaches, Prunus persica. PLANTS 2021; 10:plants10102191. [PMID: 34686000 PMCID: PMC8541108 DOI: 10.3390/plants10102191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023]
Abstract
Fleshy fruits are the most demanded fruits because of their organoleptic qualities and nutritional values. The genus Prunus is a rich source of diversified stone/drupe fruits such as almonds, apricots, plums, sweet cherries, peaches, and nectarines. The fruit-ripening process in Prunus involves coordinated biochemical and physiological changes resulting in changes in fruit texture, aroma gain, color change in the pericarp, sugar/organic acid balance, fruit growth, and weight gain. There are different varieties of peaches with unique palatable qualities and gaining knowledge in the genetics behind these quality traits helps in seedling selection for breeding programs. In addition, peaches have shorter post-harvest life due to excessive softening, resulting in fruit quality reduction and market loss. Many studies have been executed to understand the softening process at the molecular level to find the genetic basis. To summarize, this review focused on the molecular aspects of peach fruit quality attributes and their related genetics to understand the underlying mechanisms.
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Shi P, Xu Z, Zhang S, Wang X, Ma X, Zheng J, Xing L, Zhang D, Ma J, Han M, Zhao C. Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch]. BMC PLANT BIOLOGY 2020; 20:438. [PMID: 32967617 PMCID: PMC7510285 DOI: 10.1186/s12870-020-02557-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/19/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted. RESULTS A high-density single nucleotide polymorphism (SNP)-based peach linkage map was constructed using specific locus amplified fragment sequencing (SLAF-seq). This genetic map consisted of 7998 SLAF markers, spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers. A total of 40 QTLs and 885 annotated candidate genes were detected for 10 fruit-related traits, including fruit weight (FW), fruit diameter (FD), percentage of red skin colour (PSC), eating quality (EQ), fruit flavour (FV), red in flesh (RF), red around pit (RP), adherence to pit (AP), fruit development period (FDP) and fruit fibre content (FFC). Eighteen QTLs for soluble solid content (SSC) were identified along LGs 1, 4, 5, and 6 in 2015 and 2016, and 540 genes were annotated in QTL intervals. Thirty-two QTLs for fruit acidity content (FA) were detected on LG1, and 2, 4, 5, 6, and 1232 candidate genes were identified. The expression profiles of 2 candidate genes for SSC and 4 for FA were analysed in parents and their offspring. CONCLUSIONS We constructed a high-density genetic map in peach based on SLAF-seq, which may contribute to the identification of important agronomic trait loci. Ninety QTLs for 12 fruit-related traits were identified, most of which overlapped with previous reports, and some new QTLs were obtained. A large number of candidate genes for fruit-related traits were screened and identified. These results may improve our understanding of the genetic control of fruit quality traits and provide useful information in marker-assisted selection for fruit quality in peach breeding programmes.
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Affiliation(s)
- Pei Shi
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ze Xu
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shaoyu Zhang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xianju Wang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaofei Ma
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jicheng Zheng
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Libo Xing
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Dong Zhang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Juanjuan Ma
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Mingyu Han
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Caiping Zhao
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
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Pinosio S, Marroni F, Zuccolo A, Vitulo N, Mariette S, Sonnante G, Aravanopoulos FA, Ganopoulos I, Palasciano M, Vidotto M, Magris G, Iezzoni A, Vendramin GG, Morgante M. A draft genome of sweet cherry (Prunus avium L.) reveals genome-wide and local effects of domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1420-1432. [PMID: 32391598 DOI: 10.1111/tpj.14809] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/01/2020] [Indexed: 05/26/2023]
Abstract
Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety "Big Star*" and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome-wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.
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Affiliation(s)
- Sara Pinosio
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
| | - Fabio Marroni
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Nicola Vitulo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Stephanie Mariette
- BIOGECO, INRA, University of Bordeaux, route d'Arcachon 69, Cestas, 33612, France
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources (IBBR), National Research Council, via Amendola 165/A, Bari, 70126, Italy
| | - Filippos A Aravanopoulos
- Faculty of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Breeding, Aristotle University of Thessaloniki, Thessaloníki, 54124, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization-DEMETER, Thermi, 57001, Greece
| | - Marino Palasciano
- Dipartimento di Scienze del Suolo, Università degli Studi di Bari Aldo Moro, della Pianta e degli Alimenti, Piazza Umberto I, Bari, 70121, Italy
| | - Michele Vidotto
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824-1325, USA
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
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12
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Rawandoozi ZJ, Hartmann TP, Carpenedo S, Gasic K, da Silva Linge C, Cai L, Van de Weg E, Byrne DH. Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach. BMC Genomics 2020; 21:522. [PMID: 32727362 PMCID: PMC7392839 DOI: 10.1186/s12864-020-06927-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/20/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time. RESULTS Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles. CONCLUSIONS A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.
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Affiliation(s)
- Zena J. Rawandoozi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Timothy P. Hartmann
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Silvia Carpenedo
- Embrapa Clima Temperado, BR-392, km 78, Cx. Postal 403, Pelotas, Rio Grande do Sul 96010-971 Brazil
| | - Ksenija Gasic
- Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634 USA
| | - Cassia da Silva Linge
- Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634 USA
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Eric Van de Weg
- Department of Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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Carrasco-Valenzuela T, Muñoz-Espinoza C, Riveros A, Pedreschi R, Arús P, Campos-Vargas R, Meneses C. Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [ Prunus persica (L.) Batsch]. FRONTIERS IN PLANT SCIENCE 2019; 10:1581. [PMID: 31850046 PMCID: PMC6901599 DOI: 10.3389/fpls.2019.01581] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/12/2019] [Indexed: 05/22/2023]
Abstract
Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. 'Venus' selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed 'Response to auxin' as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers.
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Affiliation(s)
- Tomás Carrasco-Valenzuela
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Aníbal Riveros
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Romina Pedreschi
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota, Chile
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Reinaldo Campos-Vargas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
- *Correspondence: Claudio Meneses,
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Guo S, Iqbal S, Ma R, Song J, Yu M, Gao Z. High-density genetic map construction and quantitative trait loci analysis of the stony hard phenotype in peach based on restriction-site associated DNA sequencing. BMC Genomics 2018; 19:612. [PMID: 30107781 PMCID: PMC6092793 DOI: 10.1186/s12864-018-4952-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peach (Prunus persica) is an important fruit crop that generally softens rapidly after harvest resulting in a short shelf-life. By contrast, stony hard (SH) peach fruit does not soften and hardly produces ethylene. To explore the candidate genes responsible for the SH phenotype, a high-density genetic map was constructed by restriction-site associated DNA sequencing technology. RESULTS In the present study, the linkage map consisted of 1310 single nucleotide polymorphism markers, spanning 454.2 cM, with an average marker distance of 0.347 cM. The single nucleotide polymorphisms were able to anchor eight linkage groups to their corresponding chromosomes. Based on this high-density integrated peach linkage map and two years of fruit phenotyping, two potential quantitative trait loci for the SH trait were identified and positioned on the genetic map. Additionally, Prupe.6G150900.1, a key gene in abscisic acid (ABA) biosynthesis, displayed a differential expression profile identical to the ABA accumulation pattern: mRNA transcripts were maintained at a high level during storage of SH peaches but occurred at low levels in melting fruit. CONCLUSION Thus Prupe.6G150900.1 might play a crucial role in the SH phenotype of peach in which ABA negatively regulates ethylene production. Also, this high-density linkage map of peach will contribute to the mapping of important fruit traits and quantitative trait loci identification.
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Affiliation(s)
- Shaolei Guo
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruijuan Ma
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China
| | - Juan Song
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
- Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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15
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Srimathi U, Nagarajan V, Chandiramouli R. Adsorption studies of volatile organic compounds on germanene nanotube emitted from banana fruit for quality assessment – A density functional application. J Mol Graph Model 2018; 82:129-136. [DOI: 10.1016/j.jmgm.2018.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 02/01/2023]
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16
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Kuhn DN, Bally ISE, Dillon NL, Innes D, Groh AM, Rahaman J, Ophir R, Cohen Y, Sherman A. Genetic Map of Mango: A Tool for Mango Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:577. [PMID: 28473837 PMCID: PMC5397511 DOI: 10.3389/fpls.2017.00577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/30/2017] [Indexed: 05/27/2023]
Abstract
Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color.
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Affiliation(s)
- David N. Kuhn
- Subtropical Horticulture Research Station, United States Department of Agriculture—Agriculture Research ServiceMiami, FL, USA
| | - Ian S. E. Bally
- Department of Agriculture and Fisheries, Centre for Tropical Agriculture, Horticulture and Forestry ScienceBrisbane, QLD, Australia
| | - Natalie L. Dillon
- Department of Agriculture and Fisheries, Centre for Tropical Agriculture, Horticulture and Forestry ScienceBrisbane, QLD, Australia
| | - David Innes
- Department of Agriculture and Fisheries, Centre for Tropical Agriculture, Horticulture and Forestry ScienceBrisbane, QLD, Australia
| | - Amy M. Groh
- International Center for Tropical Botany, Florida International UniversityMiami, FL, USA
| | - Jordon Rahaman
- International Center for Tropical Botany, Florida International UniversityMiami, FL, USA
| | - Ron Ophir
- Department of Fruit Tree Sciences, Plant Sciences Institute, Agriculture Research OrganizationRishon Letzion, Israel
| | - Yuval Cohen
- Department of Fruit Tree Sciences, Plant Sciences Institute, Agriculture Research OrganizationRishon Letzion, Israel
| | - Amir Sherman
- Department of Fruit Tree Sciences, Plant Sciences Institute, Agriculture Research OrganizationRishon Letzion, Israel
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Correia S, Schouten R, Silva AP, Gonçalves B. Factors Affecting Quality and Health Promoting Compounds during Growth and Postharvest Life of Sweet Cherry ( Prunus avium L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2166. [PMID: 29312407 PMCID: PMC5742238 DOI: 10.3389/fpls.2017.02166] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Sweet cherries are attractive fruits due to their taste, color, nutritional value, and beneficial health effects. Sweet cherry is a highly perishable fruit and all quality attributes and the level of health promoting compounds are affected by growth conditions, picking, packing, transport, and storage. During production, the correct combination of scion × rootstock will produce fruits with higher firmness, weight, sugars, vitamins, and phenolic compounds that boost the fruit antioxidant activity. Orchard management, such as applying drip irrigation and summer pruning, will increase fruit sugar levels and total phenolic content, while application of growth regulators can result in improved storability, increased red coloring, increased fruit size, and reduced cracking. Salicylic acid, oxalic acid, acetylsalicylic acid, and methyl salicylate are promising growth regulators as they also increase total phenolics, anthocyanins, and induce higher activity of antioxidant enzymes. These growth regulators are now also applied as fruit coatings that improve shelf-life with higher antioxidant enzyme activities and total phenolics. Optimizing storage and transport conditions, such as hydro cooling with added CaCl2, chain temperature and relative humidity control, are crucial for slowing down decay of quality attributes and increasing the antioxidant capacity. Application of controlled atmosphere during storage is successful in delaying quality attributes, but lowers ascorbic acid levels. The combination of low temperature storage in combination with modified atmosphere packaging (MAP) is successful in reducing the incidence of fruit decay, while preserving taste attributes and stem color with a higher antioxidant capacity. A new trend in MAP is the use of biodegradable films such as micro-perforated polylactic acid film that combine significant retention of quality attributes, high consumer acceptability, and a reduced environmental footprint. Another trend is to replace MAP with fruit edible coatings. Edible coatings, such as various lipid composite coatings, have advantages in retaining quality attributes and increasing the antioxidant activity (chitosan) and are regarded as approved food additives, although studies regarding consumer acceptance are needed. The recent publication of the sweet cherry genome will likely increase the identification of more candidate genes involved in growing and maintaining health related compounds and quality attributes.
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Affiliation(s)
- Sofia Correia
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- *Correspondence: Sofia Correia
| | - Rob Schouten
- Horticulture and Product Physiology, Wageningen University, Wageningen, Netherlands
| | - Ana P. Silva
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Berta Gonçalves
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
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18
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Pons C, Martí C, Forment J, Crisosto CH, Dandekar AM, Granell A. A genetic genomics-expression approach reveals components of the molecular mechanisms beyond the cell wall that underlie peach fruit woolliness due to cold storage. PLANT MOLECULAR BIOLOGY 2016; 92:483-503. [PMID: 27714490 DOI: 10.1007/s11103-016-0526-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 08/06/2016] [Indexed: 05/14/2023]
Abstract
Peach fruits subjected to prolonged cold storage (CS) to delay decay and over-ripening often develop a form of chilling injury (CI) called mealiness/woolliness (WLT), a flesh textural disorder characterized by lack of juiciness. Transcript profiles were analyzed after different lengths of CS and subsequent shelf life ripening (SLR) in pools of fruits from siblings of the Pop-DG population with contrasting sensitivity to develop WLT. This was followed by quantitative PCR on pools and individual lines of the Pop-DG population to validate and extend the microarray results. Relative tolerance to WLT development during SLR was related to the fruit's ability to recover from cold and the reactivation of normal ripening, processes that are probably regulated by transcription factors involved in stress protection, stress recovery and induction of ripening. Furthermore, our results showed that altered ripening in WLT fruits during shelf life is probably due, in part, to cold-induced desynchronization of the ripening program involving ethylene and auxin hormonal regulation of metabolism and cell wall. In addition, we found strong correlation between expression of RNA translation and protein assembly genes and the visual injury symptoms.
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Affiliation(s)
- Clara Pons
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain.
| | - Cristina Martí
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
| | - Carlos H Crisosto
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
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Desnoues E, Baldazzi V, Génard M, Mauroux JB, Lambert P, Confolent C, Quilot-Turion B. Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3419-31. [PMID: 27117339 PMCID: PMC4892732 DOI: 10.1093/jxb/erw169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity.
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Affiliation(s)
- Elsa Desnoues
- Génétique et Amélioration des Fruits et Légumes, INRA, 84000 Avignon, France Plantes et Systèmes de Culture Horticoles, INRA, 84000 Avignon, France
| | | | - Michel Génard
- Plantes et Systèmes de Culture Horticoles, INRA, 84000 Avignon, France
| | | | - Patrick Lambert
- Génétique et Amélioration des Fruits et Légumes, INRA, 84000 Avignon, France
| | - Carole Confolent
- Génétique et Amélioration des Fruits et Légumes, INRA, 84000 Avignon, France
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20
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Gu C, Wang L, Wang W, Zhou H, Ma B, Zheng H, Fang T, Ogutu C, Vimolmangkang S, Han Y. Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1993-2005. [PMID: 26850878 PMCID: PMC4783375 DOI: 10.1093/jxb/erw021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting flesh and stone adhesion. The F-M locus has three allelic copy number variants of endoPG, H1 (PpendoPGF and PpendoPGM), H2 (PpendoPGM), and H3 (null). The H2 haplotype represents the ancestral one while the H1 and H3 haplotypes are two variants due to duplication and deletion of PpendoPGM, respectively. Accessions with H1H1, H1H2, or H1H3 genotypes show the freestone or semi-freestone and melting flesh phenotype, while both H2H2 and H2H3 accessions have the clingstone and melting flesh phenotype. The H3H3 accessions have the clingstone and non-melting flesh phenotype. Our study not only demonstrates a driving role of gene copy number variations in flesh texture diversification in fruit trees, but also provides a useful diagnostic tool for early seedling selection in peach breeding programmes.
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Affiliation(s)
- Chao Gu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Hongyu Zheng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Sornkanok Vimolmangkang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-African Joint Research Center, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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21
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Bustamante CA, Monti LL, Gabilondo J, Scossa F, Valentini G, Budde CO, Lara MV, Fernie AR, Drincovich MF. Differential Metabolic Rearrangements after Cold Storage Are Correlated with Chilling Injury Resistance of Peach Fruits. FRONTIERS IN PLANT SCIENCE 2016; 7:1478. [PMID: 27746802 PMCID: PMC5044465 DOI: 10.3389/fpls.2016.01478] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/16/2016] [Indexed: 05/18/2023]
Abstract
Reconfiguration of the metabolome is a key component involved in the acclimation to cold in plants; however, few studies have been devoted to the analysis of the overall metabolite changes after cold storage of fruits prior to consumption. Here, metabolite profiling of six peach varieties with differential susceptibility to develop mealiness, a chilling-injury (CI) symptom, was performed. According to metabolic content at harvest; after cold treatment; and after ripening, either following cold treatment or not; peach fruits clustered in distinct groups, depending on harvest-time, cold treatment, and ripening state. Both common and distinct metabolic responses among the six varieties were found; common changes including dramatic galactinol and raffinose rise; GABA, Asp, and Phe increase; and 2-oxo-glutarate and succinate decrease. Raffinose content after long cold treatment quantitatively correlated to the degree of mealiness resistance of the different peach varieties; and thus, raffinose emerges as a candidate biomarker of this CI disorder. Xylose increase after cold treatment was found only in the susceptible genotypes, indicating a particular cell wall reconfiguration of these varieties while being cold-stored. Overall, results indicate that peach fruit differential metabolic rearrangements due to cold treatment, rather than differential metabolic priming before cold, are better related with CI resistance. The plasticity of peach fruit metabolism renders it possible to induce a diverse metabolite array after cold, which is successful, in some genotypes, to avoid CI.
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Affiliation(s)
- Claudia A. Bustamante
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
| | - Laura L. Monti
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
| | - Julieta Gabilondo
- Estación Experimental San Pedro, Instituto Nacional de Tecnología AgropecuariaSan Pedro, Argentina
| | - Federico Scossa
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la FrutticolturaRome, Italy
| | - Gabriel Valentini
- Estación Experimental San Pedro, Instituto Nacional de Tecnología AgropecuariaSan Pedro, Argentina
| | - Claudio O. Budde
- Estación Experimental San Pedro, Instituto Nacional de Tecnología AgropecuariaSan Pedro, Argentina
| | - María V. Lara
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - María F. Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
- *Correspondence: María F. Drincovich
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22
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Li L, Luo Z, Huang X, Zhang L, Zhao P, Ma H, Li X, Ban Z, Liu X. Label-free quantitative proteomics to investigate strawberry fruit proteome changes under controlled atmosphere and low temperature storage. J Proteomics 2015; 120:44-57. [PMID: 25753123 DOI: 10.1016/j.jprot.2015.02.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED To elucidate the mechanisms contributing to fruit responses to senescence and stressful environmental stimuli under low temperature (LT) and controlled atmosphere (CA) storage, a label-free quantitative proteomic investigation was conducted in strawberry (Fragaria ananassa, Duch. cv. 'Akihime'). Postharvest physiological quality traits including firmness, total soluble solids, total acidity, ascorbic acid and volatile production were characterized following storage under different conditions. The observed post-storage protein expression profiles may be associated with delayed senescence features in strawberry. A total of 454 proteins were identified in differentially treated strawberry fruits. Quantitative analysis, using normalized spectral counts, revealed 73 proteins common to all treatments, which formed three clusters in a hierarchical clustering analysis. The proteins spanned a range of functions in various metabolic pathways and networks involved in carbohydrate and energy metabolism, volatile biosynthesis, phenylpropanoid activity, stress response and protein synthesis, degradation and folding. After CA and LT storage, 16 (13) and 11 (17) proteins, respectively, were significantly increased (decreased) in abundance, while expression profile of 12 proteins was significantly changed by both CA and LT. To summarize, the differential variability of abundance in strawberry proteome, working in a cooperative manner, provided an overview of the biological processes that occurred during CA and LT storage. BIOLOGICAL SIGNIFICANCE Controlled atmosphere storage at an optimal temperature is regarded to be an effective postharvest technology to delay fruit senescence and maintain fruit quality during shelf life. Nonetheless, little information on fruit proteomic changes under controlled atmosphere and/or low temperature storage is available. The significance of this paper is that it is the first study employing a label-free approach in the investigation of strawberry fruit response to controlled atmosphere and cold storage. Changes in postharvest physiological quality traits including volatile production, firmness, ascorbic acid, soluble solids and total acidity were also characterized. Significant biological changes associated with senescence were revealed and differentially abundant proteins under various storage conditions were identified. Proteomic profiles were linked to physiological aspects of strawberry fruit senescence in order to provide new insights into possible regulation mechanisms. Findings from this study not only provide proteomic information on fruit regulation, but also pave the way for further quantitative studies at the transcriptomic and metabolomic levels.
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Affiliation(s)
- Li Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zisheng Luo
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Xinhong Huang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Lu Zhang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Pengyu Zhao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Hongyuan Ma
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xihong Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Zhaojun Ban
- Jinan Fruit Research Institute, All China Federation of Supply and Marketing Cooperatives, Jinan, Shandong 250014, PR China; College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, PR China
| | - Xia Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, PR China
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23
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Taiti C, Costa C, Menesatti P, Caparrotta S, Bazihizina N, Azzarello E, Petrucci WA, Masi E, Giordani E. Use of volatile organic compounds and physicochemical parameters for monitoring the post-harvest ripening of imported tropical fruits. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2438-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Electronic-nose applications for fruit identification, ripeness and quality grading. SENSORS 2015; 15:899-931. [PMID: 25569761 PMCID: PMC4327056 DOI: 10.3390/s150100899] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/25/2014] [Indexed: 11/17/2022]
Abstract
Fruits produce a wide range of volatile organic compounds that impart their characteristically distinct aromas and contribute to unique flavor characteristics. Fruit aroma and flavor characteristics are of key importance in determining consumer acceptance in commercial fruit markets based on individual preference. Fruit producers, suppliers and retailers traditionally utilize and rely on human testers or panels to evaluate fruit quality and aroma characters for assessing fruit salability in fresh markets. We explore the current and potential utilization of electronic-nose devices (with specialized sensor arrays), instruments that are very effective in discriminating complex mixtures of fruit volatiles, as new effective tools for more efficient fruit aroma analyses to replace conventional expensive methods used in fruit aroma assessments. We review the chemical nature of fruit volatiles during all stages of the agro-fruit production process, describe some of the more important applications that electronic nose (e-nose) technologies have provided for fruit aroma characterizations, and summarize recent research providing e-nose data on the effectiveness of these specialized gas-sensing instruments for fruit identifications, cultivar discriminations, ripeness assessments and fruit grading for assuring fruit quality in commercial markets.
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Micheletti D, Dettori MT, Micali S, Aramini V, Pacheco I, Da Silva Linge C, Foschi S, Banchi E, Barreneche T, Quilot-Turion B, Lambert P, Pascal T, Iglesias I, Carbó J, Wang LR, Ma RJ, Li XW, Gao ZS, Nazzicari N, Troggio M, Bassi D, Rossini L, Verde I, Laurens F, Arús P, Aranzana MJ. Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm. PLoS One 2015; 10:e0136803. [PMID: 26352671 PMCID: PMC4564248 DOI: 10.1371/journal.pone.0136803] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 08/07/2015] [Indexed: 12/24/2022] Open
Abstract
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.
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Affiliation(s)
- Diego Micheletti
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maria Teresa Dettori
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Valeria Aramini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Igor Pacheco
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | | | | | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy
| | - Teresa Barreneche
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France
| | | | | | - Thierry Pascal
- INRA UR1052 GAFL, Domaine Saint Maurice, Montfavet, France
| | - Ignasi Iglesias
- IRTA, Estació Experimental de Lleida, Parc de Gardeny, Edifici Fruitcentre, Lleida, Spain
| | - Joaquim Carbó
- IRTA, Estacio Experimental Mas Badia, La Tallada d'Empordà, Girona, Spain
| | - Li-rong Wang
- Zhenzhou Fruit Research Institute, CAAS, Zhengzhou, China
| | - Rui-juan Ma
- Horticultural Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiong-wei Li
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhong-shan Gao
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | | | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy
| | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, DiSAA, Milan, Italy
- Parco Tecnologico Padano, Lodi, Italy
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - François Laurens
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- * E-mail:
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26
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Pons C, Martí C, Forment J, Crisosto CH, Dandekar AM, Granell A. A bulk segregant gene expression analysis of a peach population reveals components of the underlying mechanism of the fruit cold response. PLoS One 2014; 9:e90706. [PMID: 24598973 PMCID: PMC3944608 DOI: 10.1371/journal.pone.0090706] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/04/2014] [Indexed: 11/29/2022] Open
Abstract
Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding strategies to better cope with chilling injury.
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Affiliation(s)
- Clara Pons
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Cristina Martí
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Javier Forment
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Carlos H. Crisosto
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Antonio Granell
- Plant Genomics and Biotechnology lab, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
- * E-mail:
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Association genetics of chilling injury susceptibility in peach (Prunus persica (L.) Batsch) across multiple years. 3 Biotech 2013; 3:481-490. [PMID: 28324420 PMCID: PMC3824784 DOI: 10.1007/s13205-012-0109-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/13/2012] [Indexed: 11/22/2022] Open
Abstract
Peach and nectarine (Prunus persica L.) are highly perishable; they ripen and deteriorate quickly at ambient temperature. Storage at low temperature (0–5 °C) is a common strategy used to slow the ripening processes and to extend shelf life. However, if susceptible varieties are held too long at a low temperature, they will not ripen properly and will develop chilling injury (CI) symptoms like mealiness (M), flesh browning (FB), and flesh bleeding (FBL). Understanding the genetic control of these traits to produce CI resistant cultivars will greatly benefit producers, shippers and consumers. In this study, we evaluated a population of 51 individuals from Pop-DG across 4 years with CI traits observed in one or two time points to detect molecular marker association with selected 960 single-nucleotide polymorphisms (SNPs) from 1,536 SNPs chip. Genotypic and phenotypic data were analyzed by general linear model and mixed linear model to see comparative results from both analyses. Among 960 SNPs used, 22 SNPs were found associated with CI susceptibility traits like M, FB, and FBL. Many SNP markers were located in or close to previously reported quantitative trait loci mapped by linkage analysis.
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Di Guardo M, Tadiello A, Farneti B, Lorenz G, Masuero D, Vrhovsek U, Costa G, Velasco R, Costa F. A multidisciplinary approach providing new insight into fruit flesh browning physiology in apple (Malus x domestica Borkh.). PLoS One 2013; 8:e78004. [PMID: 24205065 PMCID: PMC3799748 DOI: 10.1371/journal.pone.0078004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/09/2013] [Indexed: 11/18/2022] Open
Abstract
In terms of the quality of minimally processed fruit, flesh browning is fundamentally important in the development of an aesthetically unpleasant appearance, with consequent off-flavours. The development of browning depends on the enzymatic action of the polyphenol oxidase (PPO). In the 'Golden Delicious' apple genome ten PPO genes were initially identified and located on three main chromosomes (2, 5 and 10). Of these genes, one element in particular, here called Md-PPO, located on chromosome 10, was further investigated and genetically mapped in two apple progenies ('Fuji x Pink Lady' and 'Golden Delicious x Braeburn'). Both linkage maps, made up of 481 and 608 markers respectively, were then employed to find QTL regions associated with fruit flesh browning, allowing the detection of 25 QTLs related to several browning parameters. These were distributed over six linkage groups with LOD values spanning from 3.08 to 4.99 and showed a rate of phenotypic variance from 26.1 to 38.6%. Anchoring of these intervals to the apple genome led to the identification of several genes involved in polyphenol synthesis and cell wall metabolism. Finally, the expression profile of two specific candidate genes, up and downstream of the polyphenolic pathway, namely phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), provided insight into flesh browning physiology. Md-PPO was further analyzed and two haplotypes were characterised and associated with fruit flesh browning in apple.
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Affiliation(s)
- Mario Di Guardo
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Alice Tadiello
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Brian Farneti
- Department of Fruit Trees & Woody Plant Science, University of Bologna, Bologna, Italy
| | - Giorgia Lorenz
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Domenico Masuero
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Urska Vrhovsek
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Guglielmo Costa
- Department of Fruit Trees & Woody Plant Science, University of Bologna, Bologna, Italy
| | - Riccardo Velasco
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Fabrizio Costa
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
- * E-mail:
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29
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El Hadi MAM, Zhang FJ, Wu FF, Zhou CH, Tao J. Advances in fruit aroma volatile research. Molecules 2013; 18:8200-29. [PMID: 23852166 PMCID: PMC6270112 DOI: 10.3390/molecules18078200] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/02/2013] [Accepted: 07/03/2013] [Indexed: 11/16/2022] Open
Abstract
Fruits produce a range of volatile compounds that make up their characteristic aromas and contribute to their flavor. Fruit volatile compounds are mainly comprised of esters, alcohols, aldehydes, ketones, lactones, terpenoids and apocarotenoids. Many factors affect volatile composition, including the genetic makeup, degree of maturity, environmental conditions, postharvest handling and storage. There are several pathways involved in volatile biosynthesis starting from lipids, amino acids, terpenoids and carotenoids. Once the basic skeletons are produced via these pathways, the diversity of volatiles is achieved via additional modification reactions such as acylation, methylation, oxidation/reduction and cyclic ring closure. In this paper, we review the composition of fruit aroma, the characteristic aroma compounds of several representative fruits, the factors affecting aroma volatile, and the biosynthetic pathways of volatile aroma compounds. We anticipate that this review would provide some critical information for profound research on fruit aroma components and their manipulation during development and storage.
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Affiliation(s)
- Muna Ahmed Mohamed El Hadi
- College of Horticulture and Plant Protection, Yangzhou University, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou 225009, China.
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Yun Z, Jin S, Ding Y, Wang Z, Gao H, Pan Z, Xu J, Cheng Y, Deng X. Comparative transcriptomics and proteomics analysis of citrus fruit, to improve understanding of the effect of low temperature on maintaining fruit quality during lengthy post-harvest storage. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2873-93. [PMID: 22323274 PMCID: PMC3350911 DOI: 10.1093/jxb/err390] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/03/2011] [Accepted: 11/07/2011] [Indexed: 05/18/2023]
Abstract
Fruit quality is a very complex trait that is affected by both genetic and non-genetic factors. Generally, low temperature (LT) is used to delay fruit senescence and maintain fruit quality during post-harvest storage but the molecular mechanisms involved are poorly understood. Hirado Buntan Pummelo (HBP; Citrus grandis × C. paradis) fruit were chosen to explore the mechanisms that maintain citrus fruit quality during lengthy LT storage using transcriptome and proteome studies based on digital gene expression (DGE) profiling and two-dimensional gel electrophoresis (2-DE), respectively. Results showed that LT up-regulated stress-responsive genes, arrested signal transduction, and inhibited primary metabolism, secondary metabolism and the transportation of metabolites. Calcineurin B-like protein (CBL)-CBL-interacting protein kinase complexes might be involved in the signal transduction of LT stress, and fruit quality is likely to be regulated by sugar-mediated auxin and abscisic acid (ABA) signalling. Furthermore, ABA was specific to the regulation of citrus fruit senescence and was not involved in the LT stress response. In addition, the accumulation of limonin, nomilin, methanol, and aldehyde, together with the up-regulated heat shock proteins, COR15, and cold response-related genes, provided a comprehensive proteomics and transcriptomics view on the coordination of fruit LT stress responses.
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Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 2012; 7:e35668. [PMID: 22536421 PMCID: PMC3334984 DOI: 10.1371/journal.pone.0035668] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/19/2012] [Indexed: 01/14/2023] Open
Abstract
Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.
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Affiliation(s)
- Ignazio Verde
- Fruit Tree Research Center, Rome, Italy
- * E-mail: (IV); (CP)
| | - Nahla Bassil
- United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | | | - Barbara Gilmore
- United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | | | - Ksenija Gasic
- School of Agricultural, Forest and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Diego Micheletti
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Umesh R. Rosyara
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | | | | | - Dorrie Main
- Department of Horticulture & Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | | | - Andrea L. Blas
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Todd C. Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Douglas W. Bryant
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Intuitive Genomics, Inc., St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Michela Troggio
- The Istituto Agrario di San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Italy
| | - Bryon Sosinski
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Cameron Peace
- Department of Horticulture & Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail: (IV); (CP)
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32
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Nilo P. R, Campos-Vargas R, Orellana A. Assessment of Prunus persica fruit softening using a proteomics approach. J Proteomics 2012; 75:1618-38. [DOI: 10.1016/j.jprot.2011.11.037] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 12/23/2022]
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Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla JF, Amaya I. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011. [PMID: 21667037 DOI: 10.1007/s00122-011-1624-1626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.
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Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla JF, Amaya I. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:755-78. [PMID: 21667037 DOI: 10.1007/s00122-011-1624-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/14/2011] [Indexed: 05/04/2023]
Abstract
Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.
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35
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New approaches to Prunus transcriptome analysis. Genetica 2011; 139:755-69. [PMID: 21584650 DOI: 10.1007/s10709-011-9580-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 04/26/2011] [Indexed: 12/11/2022]
Abstract
The recent sequencing of the complete genome of the peach offers new opportunities for further transcriptomic studies in Prunus species in the called post-genomics era. First works on transcriptome analysis in Prunus species started in the early 2000s with the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. Later, new strategies of massive analysis (high throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single experiment. One of these systems is massive transcriptome analysis using cDNA biochips (microarrays) to analyze thousands of genes by hybridization of mRNA labelled with fluorescence. However, the recent emergence of a massive sequencing methodology ("deep-sequencing") of the transcriptome (RNA-Seq), based on lowering the costs of DNA (in this cases complementary, cDNA) sequencing, could be more suitable than the application of microarrays. Recent papers have described the tremendous power of this technology, both in terms of profiling coverage and quantitative accuracy in transcriptomic studies. Now this technology is being applied to plant species, including Prunus. In this work, we analyze the potential in using this RNA-Seq technology in the study of Prunus transcriptomes and the development of genomic tools. In addition, the strengths and limitations of RNA-Seq relative to microarray profiling have been discussed.
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Aranzana MJ, Abbassi EK, Howad W, Arús P. Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genet 2010; 11:69. [PMID: 20646280 PMCID: PMC2915947 DOI: 10.1186/1471-2156-11-69] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Accepted: 07/20/2010] [Indexed: 12/16/2022] Open
Abstract
Background Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim was an in-depth study of the extent, distribution and structure of peach genetic variation in North American and European commercial varieties as well as old Spanish varieties and several founders used in the early USA peach breeding programmes. For this we genotyped 224 peach cultivars using 50 SSRs evenly distributed along the 8 linkage groups of the Prunus reference map. Results Genetic distance analysis based on SSRs divided the peach cultivars in three main groups based mainly on their fruit characteristics: melting flesh peaches, melting flesh nectarines and non-melting varieties. Whereas non-melting flesh peaches had a higher number of alleles than melting peaches and nectarines, they were more homozygous. With some exceptions ('Admiral Dewey', 'Early Crawford' and 'Chinese Cling'), the founder US cultivars clustered together with the commercial melting peaches, indicating that their germplasm is well represented in modern cultivars. Population structure analysis showed a similar subdivision of the sample into subpopulations. Linkage disequilibrium (LD) analysis in three unstructured, or barely structured, subpopulations revealed a high level of LD conservation in peach extending up to 13-15 cM. Conclusions Using a much larger set of SSRs, our results confirm previous observations on peach variability and population structure and provide additional tools for breeding and breeders' rights enforcement. SSR data are also used for the estimation of marker mutation rates and allow pedigree inferences, particularly with founder genotypes of the currently grown cultivars, which are useful to understand the evolution of peach as a crop. Results on LD conservation can be explained by the self-pollinating nature of peach cultivated germplasm and by a bottleneck that occurred at the beginning of modern breeding practices. High LD suggests that the development of whole-genome scanning approaches is suitable for genetic studies of agronomically important traits in peach.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils, Barcelona, Spain
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