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Su J, Li M, Yang H, Shu H, Yu K, Cao H, Xu G, Wang M, Zhu Y, Zhu Y, Ma C, Shao J. Enrichment of grape berries and tomato fruit with health-promoting tartaric acid by expression of the Vitis vinifera transketolase VvTK2 gene. Int J Biol Macromol 2024; 257:128734. [PMID: 38086429 DOI: 10.1016/j.ijbiomac.2023.128734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/27/2024]
Abstract
Tartaric acid (TA) is a major non-fermentable plant soluble acid that abundantly occur in grapes and wines, imparting low pH and tart flavour to berries thereby regulating numerous quality attributes of wine, such as flavour, microbial stability, and aging potential. Evaluation of acidity in mature fruits of 21 wine grape (Vitis vinifera) varieties revealed significant variation between 'Beichun' and 'Gewürztraminer', which was correlated with TA content. RNA-seq analysis of fruits from the two cultivars at different developmental stages revealed that a transketolase gene, VvTK2, was significantly dominantly expressed in the high TA phenotype 'Beichun' variety. Subcellular localization assay showed that VvTK2 protein was located in the chloroplast. Virus-induced VvTK2 gene silencing significantly decreased the expression of 2-keto-L-gulonic acid reductase (Vv2-KGR) as well as L-idonate dehydrogenase (VvL-IdnDH3) and inhibited TA accumulation, while its transient over-expression in grape showed the opposite results. Heterologous VvTK2 over-expression in tomato demonstrated its obvious capacity to induce TA synthesis. Overall, these results highlights a novel role of VvTK2 in modulating TA biosynthesis, which could be an excellent strategy for future genetic improvement of grape flavour.
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Affiliation(s)
- Jing Su
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Menghan Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Huanqi Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Helin Shu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Kunmiao Yu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Huiling Cao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Gezhe Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Minghui Wang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yifan Zhu
- College of Plant protection, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yingan Zhu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Chunhua Ma
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
| | - Jianhui Shao
- College of Plant protection, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
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2
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Jiang X, Liu K, Peng H, Fang J, Zhang A, Han Y, Zhang X. Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch). BMC PLANT BIOLOGY 2023; 23:16. [PMID: 36617558 PMCID: PMC9827700 DOI: 10.1186/s12870-023-04037-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Organic acids are important components that determine the fruit flavor of peach (Prunus persica L. Batsch). However, the dynamics of organic acid diversity during fruit ripening and the key genes that modulate the organic acids metabolism remain largely unknown in this kind of fruit tree which yield ranks sixth in the world. RESULTS In this study, we used 3D transcriptome data containing three dimensions of information, namely time, phenotype and gene expression, from 5 different varieties of peach to construct gene co-expression networks throughout fruit ripening of peach. With the network inferred, the time-ordered network comparative analysis was performed to select high-acid specific gene co-expression network and then clarify the regulatory factors controlling organic acid accumulation. As a result, network modules related to organic acid synthesis and metabolism under high-acid and low-acid comparison conditions were identified for our following research. In addition, we obtained 20 candidate genes as regulatory factors related to organic acid metabolism in peach. CONCLUSIONS The study provides new insights into the dynamics of organic acid accumulation during fruit ripening, complements the results of classical co-expression network analysis and establishes a foundation for key genes discovery from time-series multiple species transcriptome data.
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Affiliation(s)
- Xiaohan Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kangchen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huixiang Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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3
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Wang Q, Cao K, Cheng L, Li Y, Guo J, Yang X, Wang J, Khan IA, Zhu G, Fang W, Chen C, Wang X, Wu J, Xu Q, Wang L. Multi-omics approaches identify a key gene, PpTST1, for organic acid accumulation in peach. HORTICULTURE RESEARCH 2022; 9:uhac026. [PMID: 35184194 PMCID: PMC9171119 DOI: 10.1093/hr/uhac026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Organic acid content in fruit is an important determinant of peach organoleptic quality, which undergoes considerable variations during development and maturation. However, its molecular mechanism remains largely unclear. In this study, an integrative approach of genome-wide association studies and comparative transcriptome analysis were applied to identify candidate genes involved in organic acid accumulation in peach. A key gene PpTST1, encoding tonoplast sugar transporter, was identified and the genotype of PpTST1 with a single-base transversion (G1584T) in the third exon which leads to a single amino acid substitution (Q528H) was associated with low level of organic acid content in peach. Overexpression of PpTST1His resulted in reduced organic acid content along with increased sugar content both in peach and tomato fruits, suggesting its dual function in sugar accumulation and organic acid content reduction. Two V-type proton ATPases interact with PpTST1 in yeast two-hybridization assay. In addition, the G1584T transversion appeared and gradually accumulated during domestication and improvement, which indicated that PpTST1 was under selection. The identification and characterization of PpTST1 would facilitate the improvement of peach fruit quality.
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Affiliation(s)
- Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xuanwen Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jiao Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Irshad Ahmad Khan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jinlong Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Qiang Xu
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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4
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Branchereau C, Quero-García J, Zaracho-Echagüe NH, Lambelin L, Fouché M, Wenden B, Donkpegan A, Le Dantec L, Barreneche T, Alletru D, Parmentier J, Dirlewanger E. New insights into flowering date in Prunus: fine mapping of a major QTL in sweet cherry. HORTICULTURE RESEARCH 2022; 9:uhac042. [PMID: 35184200 PMCID: PMC9070640 DOI: 10.1093/hr/uhac042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Flowering date is an important trait in Prunus fruit species, especially for their adaptation in a global warming context. Numerous quantitative trait loci (QTLs) have been identified and a major one was previously located on LG4. The objectives of this study were to fine-map this QTL in sweet cherry, to identify robust candidate genes by using the new sweet cherry genome sequence of the cultivar 'Regina' and to define markers usable in marker-assisted selection (MAS). We performed QTL analyses on two populations derived from crosses using cultivars 'Regina' and 'Garnet' as parents. The first one (n = 117) was phenotyped over ten years, while the second one (n = 1386) was evaluated during three years. Kompetitive allele specific PCR (KASP) markers located within the QTL region on LG4 were developed and mapped within this region, consisting in the first fine mapping in sweet cherry. The QTL interval was narrowed from 380 kb to 68 kb and candidate genes were identified by using the genome sequence of 'Regina'. Their expression was analyzed from bud dormancy period to flowering in cultivars 'Regina' and 'Garnet'. Several genes, such as PavBOI-E3, PavSR45a and PavSAUR71, were differentially expressed in these two cultivars and could be then considered as promising candidate genes. Two KASP markers were validated using a population derived from a cross between cultivars 'Regina' and 'Lapins' and two collections, including landraces and modern cultivars. Thanks to the high synteny within the Prunus genus, these results give new insights into the control of flowering date in Prunus species and pave the way for the development of molecular breeding strategies.
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Affiliation(s)
- Camille Branchereau
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - José Quero-García
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Nathalia Helena Zaracho-Echagüe
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA, Centre de Recerca en Agrigenómica CSIC-IRTAUAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Laurine Lambelin
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Mathieu Fouché
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Bénédicte Wenden
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Armel Donkpegan
- SYSAAF-Centre INRAE Val de Loire, UMR BOA, 37380 Nouzilly France
| | - Loïck Le Dantec
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Teresa Barreneche
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - David Alletru
- INRAE, UE 0393, Unité Expérimentale Arboricole, F-33210 Toulenne, France
| | - Julien Parmentier
- INRAE, UE 0393, Unité Expérimentale Arboricole, F-33210 Toulenne, France
| | - Elisabeth Dirlewanger
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
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5
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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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6
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Tan Q, Li S, Zhang Y, Chen M, Wen B, Jiang S, Chen X, Fu X, Li D, Wu H, Wang Y, Xiao W, Li L. Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach. HORTICULTURE RESEARCH 2021; 8:213. [PMID: 34593767 PMCID: PMC8484544 DOI: 10.1038/s41438-021-00648-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/18/2021] [Accepted: 06/13/2021] [Indexed: 05/09/2023]
Abstract
Prunus species include many important perennial fruit crops, such as peach, plum, apricot, and related wild species. Here, we report de novo genome assemblies for five species, including the cultivated species peach (Prunus persica), plum (Prunus salicina), and apricot (Prunus armeniaca), and the wild peach species Tibetan peach (Prunus mira) and Chinese wild peach (Prunus davidiana). The genomes ranged from 240 to 276 Mb in size, with contig N50 values of 2.27-8.30 Mb and 25,333-27,826 protein-coding gene models. As the phylogenetic tree shows, plum diverged from its common ancestor with peach, wild peach species, and apricot ~7 million years ago (MYA). We analyzed whole-genome resequencing data of 417 peach accessions, called 3,749,618 high-quality SNPs, 577,154 small indels, 31,800 deletions, duplications, and inversions, and 32,338 insertions, and performed a structural variant-based genome-wide association study (GWAS) of key agricultural traits. From our GWAS data, we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor, where a large inversion event correlates with higher OVATE expression in flat-shaped accessions. Furthermore, a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions. We also identified a locus encoding microRNA172d, where insertion of a transposable element into its promoter was found in double-flower accessions. Thus, our efforts have suggested roles for OVATE, a NAC transcription factor, and microRNA172d in fruit shape, fruit development period, and floral morphology, respectively, that can be connected to traits in other crops, thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species. In general, these genomic resources will facilitate functional genomics, evolutionary research, and agronomic improvement of these five and other Prunus species. We believe that structural variant-based GWASs can also be used in other plants, animal species, and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.
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Affiliation(s)
- Qiuping Tan
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Sen Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Yuzheng Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Min Chen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, People's Republic of China
| | - Binbin Wen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Shan Jiang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Xiude Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Xiling Fu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Dongmei Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Hongyu Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Yong Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Wei Xiao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China.
| | - Ling Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China.
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7
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Geng X, Xia Y, Chen H, Du K, Yang J, Kang X. High-Frequency Homologous Recombination Occurred Preferentially in Populus. Front Genet 2021; 12:703077. [PMID: 34490036 PMCID: PMC8417060 DOI: 10.3389/fgene.2021.703077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination (HR), the most significant event in meiosis, has important implications for genetic diversity and evolution in organisms. Heteroduplex DNA (hDNA), the product of HR, can be captured by artificially induced chromosome doubling during the development of the embryo sac to inhibit postmeiotic segregation, subsequently, and hDNAs are directly detected using codominant simple sequence repeat (SSR) markers. In the present study, two hybrid triploid populations derived from doubling the chromosomes of the embryo sac induced by high temperature in Populus tomentosa served as starting materials. Eighty-seven, 62, and 79 SSR markers on chromosomes 01, 04, and 19, respectively, that were heterozygous in the maternal parent and different from the paternal parent were screened to detect and characterize the hDNA in P. tomentosa. The results showed that the hDNA frequency patterns on chromosomes changed slightly when the number of SSR primers increased. The highest hDNA frequency occurred at the adjacent terminal on chromosomes, which was slightly higher than those at the terminals in the two genotypic individuals, and the hDNA frequency gradually decreased as the locus-centromere distance decreased. With the increase in the number of SSR markers employed for detection, the number of recombination events (REs) detected significantly increased. In regions with high methylation or long terminal repeat (LTR) retrotransposon enrichment, the frequency of hDNA was low, and high frequencies were observed in regions with low sequence complexity and high gene density. High-frequency recombination occurring at high gene density regions strongly affected the association between molecular markers and quantitative trait loci (QTLs), which was an important factor contributing to the difficulty encountered by MAS in achieving the expected breeding results.
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Affiliation(s)
- Xining Geng
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-Economic Woody Plant, Pingdingshan University, Pingdingshan, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Yufei Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Hao Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Jun Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
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8
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Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. Nat Commun 2021; 12:3604. [PMID: 34127667 PMCID: PMC8203738 DOI: 10.1038/s41467-021-23879-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.
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Wang L, Jiang X, Zhao L, Wang F, Liu Y, Zhou H, He H, Han Y. A candidate PpRPH gene of the D locus controlling fruit acidity in peach. PLANT MOLECULAR BIOLOGY 2021; 105:321-332. [PMID: 33128723 DOI: 10.1007/s11103-020-01089-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
A candidate gene, designate PpRPH, in the D locus was identified to control fruit acidity in peach. Fruit acidity has a strong impact on organoleptic quality of fruit. Peach fruit acidity is controlled by a large-effect D locus on chromosome 5. In this study, the D locus was mapped to a 509-kb interval, with two markers, 5dC720 and 5C1019, co-segregating with the non-acid/acid trait of peach fruit. Within this interval, a candidate gene encoding a putative small protein, designated PpRPH, showed a consistency between gene expression and fruit acidity, with up- and down-regulation in non-acidic and acidic fruits, respectively. Transient ectopic expression of PpRPH in tobacco leaves caused an increase of pH by approximately 40% compared to the control transformed with empty vector. Whereas, the concentrations of citrate and malate decreased significantly by 22% and 37%, respectively, with respect to the empty vector control. All these results suggest that PpRPH is a strong candidate gene of the D locus. These findings contribute to our overall understanding of the complex mechanism underlying fruit acidity in peach as well as that in other fruit crops.
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Affiliation(s)
- Lu Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiaohan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Li Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Furong Wang
- Institute of Fruit Tree and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430209, China
| | - Yudi Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Hui Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Huaping He
- Institute of Fruit Tree and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430209, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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García-Gómez BE, Salazar JA, Nicolás-Almansa M, Razi M, Rubio M, Ruiz D, Martínez-Gómez P. Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective. Int J Mol Sci 2020; 22:E333. [PMID: 33396946 PMCID: PMC7794732 DOI: 10.3390/ijms22010333] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/21/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023] Open
Abstract
In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands of genes to modify many biochemical and physiological signal cascades such as carbohydrate and organic acid metabolism, cell wall restructuring, ethylene production, stress response, and organoleptic compound formation. In Prunus species (including peaches, apricots, plums, and cherries), fruit ripening leads to the breakdown of complex carbohydrates into sugars, fruit firmness reductions (softening by cell wall degradation and cuticle properties alteration), color changes (loss of green color by chlorophylls degradation and increase in non-photosynthetic pigments like anthocyanins and carotenoids), acidity decreases, and aroma increases (the production and release of organic volatile compounds). Actually, the level of information of molecular events at the transcriptional, biochemical, hormonal, and metabolite levels underlying ripening in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from unripe to ripe fruits. The objective of this review was to analyze of the molecular bases of fruit quality in Prunus species through an integrated metabolic, genomic, transcriptomic, and epigenetic approach to better understand the molecular switch involved in the ripening process with important consequences from a breeding point of view.
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Affiliation(s)
- Beatriz E. García-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - Juan A. Salazar
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - María Nicolás-Almansa
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - Mitra Razi
- Department of Horticulture, Faculty of Agriculture, University of Zajan, Zanjan 45371-38791, Iran;
| | - Manuel Rubio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - David Ruiz
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain; (B.E.G.-G.); (J.A.S.); (M.N.-A.); (M.R.); (D.R.)
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11
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Iezzoni AF, McFerson J, Luby J, Gasic K, Whitaker V, Bassil N, Yue C, Gallardo K, McCracken V, Coe M, Hardner C, Zurn JD, Hokanson S, van de Weg E, Jung S, Main D, da Silva Linge C, Vanderzande S, Davis TM, Mahoney LL, Finn C, Peace C. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. HORTICULTURE RESEARCH 2020; 7:177. [PMID: 33328430 PMCID: PMC7603521 DOI: 10.1038/s41438-020-00398-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 08/30/2020] [Indexed: 05/05/2023]
Abstract
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
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Affiliation(s)
- Amy F Iezzoni
- Michigan State University, East Lansing, MI, 48824, USA.
| | - Jim McFerson
- Washington State University, Wenatchee, WA, 98801, USA
| | - James Luby
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | - Chengyan Yue
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | - Michael Coe
- Cedar Lake Research Group, Portland, OR, 97215, USA
| | | | | | | | - Eric van de Weg
- Wageningen University and Research, 6700 AA, Wageningen, The Netherlands
| | - Sook Jung
- Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Washington State University, Pullman, WA, 99164, USA
| | | | | | | | | | | | - Cameron Peace
- Washington State University, Pullman, WA, 99164, USA
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12
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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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Calle A, Wünsch A. Multiple-population QTL mapping of maturity and fruit-quality traits reveals LG4 region as a breeding target in sweet cherry ( Prunus avium L.). HORTICULTURE RESEARCH 2020; 7:127. [PMID: 32821410 PMCID: PMC7395078 DOI: 10.1038/s41438-020-00349-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/08/2020] [Accepted: 06/13/2020] [Indexed: 05/29/2023]
Abstract
Sweet cherry maturity date and fruit quality are relevant traits for its marketability, transport, and consumer acceptance. In this work, sweet cherry fruit development time, maturity date, and commercial fruit-quality traits (size, weight, firmness, soluble solid content, and titratable acidity) were investigated to improve the knowledge of their genetic control, and to identify alleles of breeding interest. Six sweet cherry populations segregating for these traits were used for QTL analyses. These populations descend from cross- and self-pollinations of local Spanish sweet cherries 'Ambrunés' and 'Cristobalina', and breed cultivars ('Brooks', 'Lambert', or 'Vic'). The six populations (n = 411), previously genotyped with RosBREED Cherry 6 K SNP array, were phenotyped for 2 years. QTL analyses were conducted using a multifamily approach implemented by FlexQTL™. Fruit development time, soluble solid content, and titratable acidity QTLs are first reported in sweet cherry in this work. Significant QTLs were detected for all the traits. Eighteen were more stable as they were detected for 2 years. Of these, nine are first reported in this work. The major QTLs for fruit development time, maturity date, firmness, and soluble solid content were identified on the same narrow region of linkage group 4. These traits also showed significant positive correlation (long fruit development time associated with late maturity, high firmness, and high SSC). NAC transcription factor genes identified on this LG4 region may be candidate genes for the regulation of these traits in sweet cherry, as previously described in syntenic regions of other Rosaceae species. Haplotypes of breeding interest on this LG4 genomic region were identified and will be useful for sweet cherry breeding from this and related plant material.
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Affiliation(s)
- Alejandro Calle
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA). Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Ana Wünsch
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA). Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
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14
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Zheng B, Zhao L, Jiang X, Cherono S, Liu J, Ogutu C, Ntini C, Zhang X, Han Y. Assessment of organic acid accumulation and its related genes in peach. Food Chem 2020; 334:127567. [PMID: 32707362 DOI: 10.1016/j.foodchem.2020.127567] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022]
Abstract
Fruit acidity is an important determinant of peach organoleptic quality, but its regulatory mechanism remains elusive. Measurement of organic acids in ripe fruits of seventy-five peach cultivars revealed the predominant components malate and citrate, accompanied by quinate. Organic acid accumulation increased at early stages of fruit growth, but exhibited a more dramatic reduction in low-acid cultivar during later stages of fruit development compared to high-acid cultivars. Low-acid cultivars showed citrate degradation and less transport of malate into the vacuole due to up- and down-regulation of a GABA pathway gene GAD and a malate transporter gene ALMT9, respectively. The NAD-MDH1 gene might control the rate-limiting step in malate synthesis, while three genes, PDK, PK, and ADH, could affect citrate synthesis through the pyruvate-to-acetyl-CoA-to-citrate pathway. Altogether, these results suggested that malate accumulation is controlled at the level of metabolism and vacuolar storage, while metabolism is crucial for citrate accumulation in peach.
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Affiliation(s)
- Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Li Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xiaohan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China.
| | - Sylvia Cherono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - JingJing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China.
| | - Collins Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Charmaine Ntini
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xiujun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074 China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
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15
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Peng Q, Wang L, Ogutu C, Liu J, Liu L, Mollah MDA, Han Y. Functional Analysis Reveals the Regulatory Role of PpTST1 Encoding Tonoplast Sugar Transporter in Sugar Accumulation of Peach Fruit. Int J Mol Sci 2020; 21:E1112. [PMID: 32046163 PMCID: PMC7038102 DOI: 10.3390/ijms21031112] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 11/26/2022] Open
Abstract
Sugar content is related to fruit sweetness, and the complex mechanisms underlying fruit sugar accumulation still remain elusive. Here, we report a peach PpTST1 gene encoding tonoplast sugar transporter that is located in the quantitative trait loci (QTL) interval on Chr5 controlling fruit sucrose content. One derived Cleaved Amplified Polymorphic Sequence (dCAPS) marker was developed based on a nonsynonymous G/T variant in the third exon of PpTST1. Genotyping of peach cultivars with the dCAPS marker revealed a significant difference in fruit sugar content among genotypes. PpTST1 is located in the tonoplast, and substitution of glutamine by histidine caused by the G/T variation has no impact on subcellular location. The expression profile of PpTST1 exhibited a consistency with the sugar accumulation pattern, and its transient silencing significantly inhibited sugar accumulation in peach fruits. All of these results demonstrated the role of PpTST1 in regulating sugar accumulation in peach fruit. In addition, cis-elements for binding of MYB and WRKY transcript factors were found in the promoter sequence of PpTST1, suggesting a gene regulatory network of fruit sugar accumulation. Our results are not only helpful for understanding the mechanisms underlying fruit sugar accumulation, but will also be useful for the genetic improvement of fruit sweetness in peach breeding programs.
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Affiliation(s)
- Qian Peng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Lu Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Collins Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jingjing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Li Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Md. Dulal Ali Mollah
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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16
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Cao K, Li Y, Deng CH, Gardiner SE, Zhu G, Fang W, Chen C, Wang X, Wang L. Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1954-1970. [PMID: 30950186 PMCID: PMC6737019 DOI: 10.1111/pbi.13112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 05/21/2023]
Abstract
Crop evolution is a long-term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome-wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue-specific expression patterns indicated that the up-regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up-regulated selection genes were identified in leaves and seeds than in the other organs. Genome-wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large-scale characterization of key agronomic traits in this crop species.
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Affiliation(s)
- Ke Cao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR)Palmerston North Research CentrePalmerston NorthNew Zealand
| | - Gengrui Zhu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. HORTICULTURE RESEARCH 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Yang S, Fresnedo-Ramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark M, Luby J, Manns DC, Sacks G, Mansfield AK, Londo J, Fennell A, Gadoury D, Reisch B, Cadle-Davidson L, Sun Q. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. HORTICULTURE RESEARCH 2016; 3:16002. [PMID: 27257505 PMCID: PMC4879517 DOI: 10.1038/hortres.2016.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 05/07/2023]
Abstract
Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.
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Affiliation(s)
- Shanshan Yang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Minghui Wang
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Linda Cote
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Schweitzer
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth M Takacs
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - James Luby
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - David C Manns
- Department of Food Science, Cornell University, Geneva, NY 14456, USA
| | - Gavin Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Jason Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anne Fennell
- Plant Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - David Gadoury
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
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Huang D, Zhao Y, Cao M, Qiao L, Zheng ZL. Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck). FRONTIERS IN PLANT SCIENCE 2016; 7:486. [PMID: 27092171 PMCID: PMC4824782 DOI: 10.3389/fpls.2016.00486] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/25/2016] [Indexed: 05/18/2023]
Abstract
Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.
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Affiliation(s)
- Dingquan Huang
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Yihong Zhao
- Division of Biostatistics, Department of Child Psychiatry, New York University Langone Medical Center, New YorkNY, USA
- *Correspondence: Yihong Zhao, ; Zhi-Liang Zheng,
| | - Minghao Cao
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Liang Qiao
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Zhi-Liang Zheng
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
- Department of Biological Sciences, Lehman College, City University of New York, BronxNY, USA
- *Correspondence: Yihong Zhao, ; Zhi-Liang Zheng,
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Houel C, Chatbanyong R, Doligez A, Rienth M, Foria S, Luchaire N, Roux C, Adivèze A, Lopez G, Farnos M, Pellegrino A, This P, Romieu C, Torregrosa L. Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip. BMC PLANT BIOLOGY 2015; 15:205. [PMID: 26283631 PMCID: PMC4539925 DOI: 10.1186/s12870-015-0588-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/06/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci). RESULTS Ten stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered. CONCLUSIONS This study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variation.
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Affiliation(s)
- Cléa Houel
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- INRA, UMR AGAP, F-34060, Montpellier, France.
| | - Ratthaphon Chatbanyong
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- INRA, UMR AGAP, F-34060, Montpellier, France.
| | | | - Markus Rienth
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- INRA, UMR AGAP, F-34060, Montpellier, France.
- Fondation Jean Poupelain, 30 rue Gâte Chien, F-16100, Javrezac, France.
- Changins, Haute Ecole de Viticulture et Oenologie, 1260, Nyon, Switzerland.
| | - Serena Foria
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, I-33100, Udine, Italy.
| | - Nathalie Luchaire
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
- Montpellier SupAgro, UMR LEPSE, F- 34060, Montpellier, France.
| | | | | | - Gilbert Lopez
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
| | - Marc Farnos
- INRA, UMR AGAP, F-34060, Montpellier, France.
| | - Anne Pellegrino
- Montpellier SupAgro, UMR LEPSE, F- 34060, Montpellier, France.
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Wang L, Zhao S, Gu C, Zhou Y, Zhou H, Ma J, Cheng J, Han Y. Deep RNA-Seq uncovers the peach transcriptome landscape. PLANT MOLECULAR BIOLOGY 2013; 83:365-77. [PMID: 23783411 DOI: 10.1007/s11103-013-0093-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/15/2013] [Indexed: 05/18/2023]
Abstract
Peach (Prunus persica) is one of the most important of deciduous fruit trees worldwide. To facilitate isolation of genes controlling important horticultural traits of peach, transcriptome sequencing was conducted in this study. A total of 133 million pair-end RNA-Seq reads were generated from leaf, flower, and fruit, and 90 % of reads were mapped to the peach draft genome. Sequence assembly revealed 1,162 transcription factors and 2,140 novel transcribed regions (NTRs). Of these 2,140 NTRs, 723 contain an open reading frame, while the rest 1,417 are non-coding RNAs. A total of 9,587 SNPs were identified across six peach genotypes, with an average density of one SNP per ~5.7 kb. The top of chromosome 2 has higher density of expressed SNPs than the rest of the peach genome. The average density of SSR is 312.5/Mb, with tri-nucleotide repeats being the most abundant. Most of the detected SSRs are AT-rich repeats and the most common di-nucleotide repeat is CT/TC. The predominant type of alternative splicing (AS) events in peach is exon-skipping isoforms, which account for 43 % of all the observed AS events. In addition, the most active transcribed regions in peach genome were also analyzed. Our study reveals for the first time the complexity of the peach transcriptome, and our results will be helpful for functional genomics research in peach.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China,
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22
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Zaman A, Ihsanullah I, Shah AA, Khattak TN, Gul S, Muhammadzai IU. Combined effect of gamma irradiation and hot water dipping on the selected nutrients and shelf life of peach. J Radioanal Nucl Chem 2013. [DOI: 10.1007/s10967-013-2656-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Zhang Q, Ma B, Li H, Chang Y, Han Y, Li J, Wei G, Zhao S, Khan MA, Zhou Y, Gu C, Zhang X, Han Z, Korban SS, Li S, Han Y. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple. BMC Genomics 2012; 13:537. [PMID: 23039990 PMCID: PMC3704940 DOI: 10.1186/1471-2164-13-537] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 10/04/2012] [Indexed: 11/10/2022] Open
Abstract
Background Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae.
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Affiliation(s)
- Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, People's Republic of China
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Bai Y, Dougherty L, Li M, Fazio G, Cheng L, Xu K. A natural mutation-led truncation in one of the two aluminum-activated malate transporter-like genes at the Ma locus is associated with low fruit acidity in apple. Mol Genet Genomics 2012; 287:663-78. [DOI: 10.1007/s00438-012-0707-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 07/03/2012] [Indexed: 12/21/2022]
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Bondada BR, Keller M. Not All Shrivels Are Created Equal—Morpho-Anatomical and Compositional Characteristics Differ among Different Shrivel Types That Develop during Ripening of Grape (<i>Vitis vinifera</i> L.) Berries. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ajps.2012.37105] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cachi AM, Wünsch A. Characterization and mapping of non-S gametophytic self-compatibility in sweet cherry (Prunus avium L.). JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1847-56. [PMID: 21127024 DOI: 10.1093/jxb/erq374] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Self-incompatibility in Prunus (Rosaceae) species, such as sweet cherry, is controlled by a multiallelic locus (S), in which two tightly linked genes, S-RNase and SFB (S haplotype-specific F-box), determine the specificity of the pollen and the style. Fertilization in these species occurs only if the S-specificities expressed in the pollen and the pistils are different. However, modifier genes have been proposed to be necessary for a full manifestation of the self-incompatibility response. 'Cristobalina' is a spontaneous self-compatible sweet cherry cultivar that originated in Eastern Spain. Previous studies with this genotype suggested that pollen modifier gene(s), not linked to the S-locus, may be the cause of self-incompatibility breakdown. In this work, an F(1) population from 'Cristobalina' that segregates for this trait was used to identify molecular markers linked to self-compatibility by bulked segregant analysis. One simple sequence repeat (SSR) locus (EMPaS02) was found to be linked to self-compatibility in this population at 3.2 cM. Two additional populations derived from 'Cristobalina' were used to confirm the linkage of this marker to self-compatibility. Since EMPaS02 has been mapped to the sweet cherry linkage group 3, other markers located on the same linkage group were analysed in these populations to confirm the location of the self-compatibility locus.
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Affiliation(s)
- A M Cachi
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
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Brandi F, Bar E, Mourgues F, Horváth G, Turcsi E, Giuliano G, Liverani A, Tartarini S, Lewinsohn E, Rosati C. Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism. BMC PLANT BIOLOGY 2011; 11:24. [PMID: 21269483 PMCID: PMC3045293 DOI: 10.1186/1471-2229-11-24] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 01/26/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Carotenoids are plant metabolites which are not only essential in photosynthesis but also important quality factors in determining the pigmentation and aroma of flowers and fruits. To investigate the regulation of carotenoid metabolism, as related to norisoprenoids and other volatile compounds in peach (Prunus persica L. Batsch.), and the role of carotenoid dioxygenases in determining differences in flesh color phenotype and volatile composition, the expression patterns of relevant carotenoid genes and metabolites were studied during fruit development along with volatile compound content. Two contrasted cultivars, the yellow-fleshed 'Redhaven' (RH) and its white-fleshed mutant 'Redhaven Bianca' (RHB) were examined. RESULTS The two genotypes displayed marked differences in the accumulation of carotenoid pigments in mesocarp tissues. Lower carotenoid levels and higher levels of norisoprenoid volatiles were observed in RHB, which might be explained by differential activity of carotenoid cleavage dioxygenase (CCD) enzymes. In fact, the ccd4 transcript levels were dramatically higher at late ripening stages in RHB with respect to RH. The two genotypes also showed differences in the expression patterns of several carotenoid and isoprenoid transcripts, compatible with a feed-back regulation of these transcripts. Abamine SG - an inhibitor of CCD enzymes - decreased the levels of both isoprenoid and non-isoprenoid volatiles in RHB fruits, indicating a complex regulation of volatile production. CONCLUSIONS Differential expression of ccd4 is likely to be the major determinant in the accumulation of carotenoids and carotenoid-derived volatiles in peach fruit flesh. More in general, dioxygenases appear to be key factors controlling volatile composition in peach fruit, since abamine SG-treated 'Redhaven Bianca' fruits had strongly reduced levels of norisoprenoids and other volatile classes. Comparative functional studies of peach carotenoid cleavage enzymes are required to fully elucidate their role in peach fruit pigmentation and aroma.
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Affiliation(s)
- Federica Brandi
- Consiglio per la Ricerca in Agricoltura, Unità di Ricerca per la Frutticoltura-Forlì (CRA-FRF), via la Canapona 1 bis, 47100 Forlì, Italy
| | - Einat Bar
- Dept. of Vegetable Crops, ARO Newe Ya'ar Research Center, P.O. Box 1021, 30095 Ramat Yishay, Israel
| | - Fabienne Mourgues
- National Agency for New technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Center, S.S. 106 km 419+500, 75026 Rotondella, Italy
| | - Györgyi Horváth
- University of Pécs, Medical School Department of Pharmacognosy, H-7624 Pécs, Rókus u. 2, Hungary
| | - Erika Turcsi
- University of Pécs, Medical School, Department of Biochemistry and Medical Chemistry, H-7624 Pécs, Szigeti út 12, Hungary
| | - Giovanni Giuliano
- ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Alessandro Liverani
- Consiglio per la Ricerca in Agricoltura, Unità di Ricerca per la Frutticoltura-Forlì (CRA-FRF), via la Canapona 1 bis, 47100 Forlì, Italy
| | - Stefano Tartarini
- Dipartimento Colture Arboree, Università di Bologna, via Fanin 42, 40127 Bologna, Italy
| | - Efraim Lewinsohn
- Dept. of Vegetable Crops, ARO Newe Ya'ar Research Center, P.O. Box 1021, 30095 Ramat Yishay, Israel
| | - Carlo Rosati
- National Agency for New technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Center, S.S. 106 km 419+500, 75026 Rotondella, Italy
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