1
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Koji T, Iwata H, Ishimori M, Takanashi H, Yamasaki Y, Tsujimoto H. Multispectral Phenotyping and Genetic Analyses of Spring Appearance in Greening Plant, Phedimus spp. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0063. [PMID: 37383728 PMCID: PMC10292581 DOI: 10.34133/plantphenomics.0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
The change in appearance during the seasonal transitions in ornamental greening plants is an important characteristic. In particular, the early onset of green leaf color is a desirable trait for a cultivar. In this study, we established a method for phenotyping leaf color change by multispectral imaging and performed genetic analysis based on the phenotypes to clarify the potential of the approach in breeding greening plants. We performed multispectral phenotyping and quantitative trait locus (QTL) analysis of an F1 population derived from 2 parental lines of Phedimus takesimensis, known to be a drought and heat-tolerant rooftop plant species. The imaging was conducted in April of 2019 and 2020 when dormancy breakage occurs and growth extension begins. Principal component analysis of 9 different wavelength values showed a high contribution from the first principal component (PC1), which captured variation in the visible light range. The high interannual correlation in PC1 and in the intensity of visible light indicated that the multispectral phenotyping captured genetic variation in the color of leaves. We also performed restriction site-associated DNA sequencing and obtained the first genetic linkage map of Phedimus spp. QTL analysis revealed 2 QTLs related to early dormancy breakage. Based on the genotypes of the markers underlying these 2 QTLs, the F1 phenotypes with early (late) dormancy break, green (red or brown) leaves, and a high (low) degree of vegetative growth were classified. The results suggest the potential of multispectral phenotyping in the genetic dissection of seasonal leaf color changes in greening plants.
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Affiliation(s)
- Taeko Koji
- The United Graduate School of Agricultural Sciences,
Tottori University, 4-101 Koyamacho minami, Tottori-shi, Tottori 680-8553, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori-shi, Tottori 680-0001, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori-shi, Tottori 680-0001, Japan
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2
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Abebe AM, Kim Y, Kim J, Kim SL, Baek J. Image-Based High-Throughput Phenotyping in Horticultural Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:2061. [PMID: 37653978 PMCID: PMC10222289 DOI: 10.3390/plants12102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 09/02/2023]
Abstract
Plant phenotyping is the primary task of any plant breeding program, and accurate measurement of plant traits is essential to select genotypes with better quality, high yield, and climate resilience. The majority of currently used phenotyping techniques are destructive and time-consuming. Recently, the development of various sensors and imaging platforms for rapid and efficient quantitative measurement of plant traits has become the mainstream approach in plant phenotyping studies. Here, we reviewed the trends of image-based high-throughput phenotyping methods applied to horticultural crops. High-throughput phenotyping is carried out using various types of imaging platforms developed for indoor or field conditions. We highlighted the applications of different imaging platforms in the horticulture sector with their advantages and limitations. Furthermore, the principles and applications of commonly used imaging techniques, visible light (RGB) imaging, thermal imaging, chlorophyll fluorescence, hyperspectral imaging, and tomographic imaging for high-throughput plant phenotyping, are discussed. High-throughput phenotyping has been widely used for phenotyping various horticultural traits, which can be morphological, physiological, biochemical, yield, biotic, and abiotic stress responses. Moreover, the ability of high-throughput phenotyping with the help of various optical sensors will lead to the discovery of new phenotypic traits which need to be explored in the future. We summarized the applications of image analysis for the quantitative evaluation of various traits with several examples of horticultural crops in the literature. Finally, we summarized the current trend of high-throughput phenotyping in horticultural crops and highlighted future perspectives.
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Affiliation(s)
| | | | | | | | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
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3
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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4
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Zhang X, Yang W, Tahir MM, Chen X, Saudreau M, Zhang D, Costes E. Contributions of leaf distribution and leaf functions to photosynthesis and water-use efficiency from leaf to canopy in apple: A comparison of interstocks and cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1117051. [PMID: 37123856 PMCID: PMC10146243 DOI: 10.3389/fpls.2023.1117051] [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: 12/06/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Grafting has been widely used in horticulture to induce dwarfing and avoid stress-derived limitations on plant growth and yield by affecting plant architecture and leaf functions. However, the respective effects on plant photosynthesis and water use efficiency (WUE) of leaf distribution and functions that depend on both rootstock and scion have not been fully elucidated. This study aimed to (i) clarify the scion × interstock impacts on the variability of leaf photosynthetic traits and WUE, and (ii) decipher the respective effects of leaf distribution and functions on canopy photosynthesis and WUE (WUEc). Leaf gas exchange over light gradients and responses to light, CO2, temperature, and vapor pressure deficit were measured in two apple cultivars, 'Liquan Fuji' ('Fuji') and 'Regal Gala' ('Gala'), grafted onto rootstocks combined with interstocks: a vigorous (VV, 'Qinguan'), or a dwarf one (VD, M26). The 3D architecture-based RATP model was parameterized to estimate the canopy photosynthesis rate (Ac ), transpiration rate (E c), and WUEc. Then, virtual scenarios were used to compare the relative contributions of cultivar and interstock to canopy A c, E c, and WUE c. These scenarios changed the leaf distribution and functions of either cultivar or interstock. At the leaf scale, VD trees had significantly higher leaf nitrogen per area but a lower maximum carboxylation rate and dark respiration in both cultivars. In parallel with higher leaf stomatal conductance (gs ) and transpiration in VD 'Fuji' and similar gs in VD 'Gala', VD trees showed significantly lower leaf photosynthesis rate and WUE than VV trees. However, lower leaf photosynthetic capacities in VD trees were compensated at the canopy scale, with A c and WUE c for 'Fuji' significantly improved in VD trees under both sunny and cloudy conditions, and for 'Gala' significantly improved in VD trees under cloudy conditions compared with VV trees. Switching scenarios highlighted that 'Gala' leaf functions and distribution and VD leaf distributions enhanced A c and WUE c simultaneously, irrespective of weather conditions. Up-scaling leaf gas exchange to the canopy scale by utilizing 3D architecture-based modeling and reliable measurements of tree architecture and leaf functional traits provides insights to explore the influence of genetic materials and tree management practices.
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Affiliation(s)
- Xiaoyun Zhang
- College of Agriculture, The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization in Xinjiang Production and Construction Group, Shihezi University, Shihezi, Xinjiang, China
| | - Weiwei Yang
- College of Agriculture, The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization in Xinjiang Production and Construction Group, Shihezi University, Shihezi, Xinjiang, China
- *Correspondence: Weiwei Yang,
| | | | - Xilong Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Marc Saudreau
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, France
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Evelyne Costes
- UMR AGAP Institute, University of Montpellier, INRAE, Institut Agro, CIRAD, Equipe ‘Architecture et Floraison des Especes Fruiteres’, Montpellier, France
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Li X, Zhou S, Liu Z, Lu L, Dang H, Li H, Chu B, Chen P, Ma Z, Zhao S, Li Z, van Nocker S, Ma F, Guan Q. Fine-tuning of SUMOylation modulates drought tolerance of apple. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:903-919. [PMID: 34978131 PMCID: PMC9055824 DOI: 10.1111/pbi.13772] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
SUMOylation is involved in various aspects of plant biology, including drought stress. However, the relationship between SUMOylation and drought stress tolerance is complex; whether SUMOylation has a crosstalk with ubiquitination in response to drought stress remains largely unclear. In this study, we found that both increased and decreased SUMOylation led to increased survival of apple (Malus × domestica) under drought stress: both transgenic MdSUMO2A overexpressing (OE) plants and MdSUMO2 RNAi plants exhibited enhanced drought tolerance. We further confirmed that MdDREB2A is one of the MdSUMO2 targets. Both transgenic MdDREB2A OE and MdDREB2AK192R OE plants (which lacked the key site of SUMOylation by MdSUMO2A) were more drought tolerant than wild-type plants. However, MdDREB2AK192R OE plants had a much higher survival rate than MdDREB2A OE plants. We further showed SUMOylated MdDREB2A was conjugated with ubiquitin by MdRNF4 under drought stress, thereby triggering its protein degradation. In addition, MdRNF4 RNAi plants were more tolerant to drought stress. These results revealed the molecular mechanisms that underlie the relationship of SUMOylation with drought tolerance and provided evidence for the tight control of MdDREB2A accumulation under drought stress mediated by SUMOylation and ubiquitination.
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Affiliation(s)
- Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Shuangxi Zhou
- Department of Biological SciencesMacquarie UniversityNorth RydeNSWAustralia
| | - Zeyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Liyuan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Huan Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Huimin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Baohua Chu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Ziqing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Steve van Nocker
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingChina
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6
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Jiang J, Yang N, Li L, Qin G, Ren K, Wang H, Deng J, Ding D. Tetraploidy in Citrus wilsonii Enhances Drought Tolerance via Synergistic Regulation of Photosynthesis, Phosphorylation, and Hormonal Changes. FRONTIERS IN PLANT SCIENCE 2022; 13:875011. [PMID: 35574073 PMCID: PMC9096895 DOI: 10.3389/fpls.2022.875011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy varieties have been reported to exhibit higher stress tolerance relative to their diploid relatives, however, the underlying molecular and physiological mechanisms remain poorly understood. In this study, a batch of autotetraploid Citrus wilsonii were identified from a natural seedling population, and these tetraploid seedlings exhibited greater tolerance to drought stress than their diploids siblings. A global transcriptome analysis revealed that a large number of genes involved in photosynthesis response were enriched in tetraploids under drought stress, which was consistent with the changes in photosynthetic indices including Pn, gs, Tr, Ci, and chlorophyll contents. Compared with diploids, phosphorylation was also modified in the tetraploids after drought stress, as detected through tandem mass tag (TMT)-labeled proteomics. Additionally, tetraploids prioritized the regulation of plant hormone signal transduction at the transcriptional level after drought stress, which was also demonstrated by increased levels of IAA, ABA, and SA and reduced levels of GA3 and JA. Collectively, our results confirmed that the synergistic regulation of photosynthesis response, phosphorylation modification and plant hormone signaling resulted in drought tolerance of autotetraploid C. wilsonii germplasm.
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Affiliation(s)
- Jinglong Jiang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Ni Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Li Li
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Gongwei Qin
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Kexin Ren
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Haotian Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Jiarui Deng
- Chenggu Fruit Industry Technical Guidance Station, Chenggu, China
| | - Dekuan Ding
- Chenggu Fruit Industry Technical Guidance Station, Chenggu, China
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7
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Coupel‐Ledru A, Pallas B, Delalande M, Segura V, Guitton B, Muranty H, Durel C, Regnard J, Costes E. Tree architecture, light interception and water-use related traits are controlled by different genomic regions in an apple tree core collection. THE NEW PHYTOLOGIST 2022; 234:209-226. [PMID: 35023155 PMCID: PMC9305758 DOI: 10.1111/nph.17960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/19/2021] [Indexed: 05/17/2023]
Abstract
Tree architecture shows large genotypic variability, but how this affects water-deficit responses is poorly understood. To assess the possibility of reaching ideotypes with adequate combinations of architectural and functional traits in the face of climate change, we combined high-throughput field phenotyping and genome-wide association studies (GWAS) on an apple tree (Malus domestica) core-collection. We used terrestrial light detection and ranging (T-LiDAR) scanning and airborne multispectral and thermal imagery to monitor tree architecture, canopy shape, light interception, vegetation indices and transpiration on 241 apple cultivars submitted to progressive field soil drying. GWAS was performed with single nucleotide polymorphism (SNP)-by-SNP and multi-SNP methods. Large phenotypic and genetic variability was observed for all traits examined within the collection, especially canopy surface temperature in both well-watered and water deficit conditions, suggesting control of water loss was largely genotype-dependent. Robust genomic associations revealed independent genetic control for the architectural and functional traits. Screening associated genomic regions revealed candidate genes involved in relevant pathways for each trait. We show that multiple allelic combinations exist for all studied traits within this collection. This opens promising avenues to jointly optimize tree architecture, light interception and water use in breeding strategies. Genotypes carrying favourable alleles depending on environmental scenarios and production objectives could thus be targeted.
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Affiliation(s)
- Aude Coupel‐Ledru
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Benoît Pallas
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Magalie Delalande
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Vincent Segura
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Baptiste Guitton
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Hélène Muranty
- IRHSSFR QuaSaVUniversité d’Angers, Institut Agro, INRAE49000AngersFrance
| | - Charles‐Eric Durel
- IRHSSFR QuaSaVUniversité d’Angers, Institut Agro, INRAE49000AngersFrance
| | - Jean‐Luc Regnard
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Evelyne Costes
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
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8
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Xie Y, Bao C, Chen P, Cao F, Liu X, Geng D, Li Z, Li X, Hou N, Zhi F, Niu C, Zhou S, Zhan X, Ma F, Guan Q. Abscisic acid homeostasis is mediated by feedback regulation of MdMYB88 and MdMYB124. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:592-607. [PMID: 32995885 DOI: 10.1093/jxb/eraa449] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The phytohormone abscisic acid (ABA) is involved in various plant processes. In response to drought stress, plants quickly accumulate ABA, but the regulatory mechanism of ABA accumulation is largely unknown, especially in woody plants. In this study, we report that MdMYB88 and MdMYB124 are myeloblastosis (MYB) transcription factors critical for ABA accumulation in apple trees (Malus x domestica) following drought, and this regulation is negatively controlled by ABA. MdMYB88 and MdMYB124 positively regulate leaf water transpiration, photosynthetic capacity, and stress endurance in apple trees under drought conditions. MdMYB88 and MdMYB124 regulate the expression of biosynthetic and catabolic genes of ABA, as well as drought- and ABA- responsive genes. MdMYB88 associates with promoter regions of the ABA biosynthetic gene 9-cis-epoxycarotenoid dioxygenase 3 (NCED3). Finally, expression of MdMYB88 and MdMYB124 is repressed by ABA. Our results identify a feedback regulation of MdMYB88 and MdMYB124 in modulating ABA homeostasis in apple trees.
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Affiliation(s)
- Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Institute for Advanced Studies, Wuhan University, Wuhan, P.R. China
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xiaofang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Fang Zhi
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Shuangxi Zhou
- The New Zealand Institute for Plant and Food Research Ltd., Hawke's Bay, New Zealand
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
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9
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Coupel-Ledru A, Pallas B, Delalande M, Boudon F, Carrié E, Martinez S, Regnard JL, Costes E. Multi-scale high-throughput phenotyping of apple architectural and functional traits in orchard reveals genotypic variability under contrasted watering regimes. HORTICULTURE RESEARCH 2019; 6:52. [PMID: 31044079 PMCID: PMC6491481 DOI: 10.1038/s41438-019-0137-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 05/06/2023]
Abstract
Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees, phenotyping large populations in the field remains challenging. In this study, we used high-throughput phenotyping methods on an apple tree core-collection (1000 individuals) grown under contrasted watering regimes. First, architectural phenotyping was achieved using T-LiDAR scans for estimating convex and alpha hull volumes and the silhouette to total leaf area ratio (STAR). Second, a semi-empirical index (I PL) was computed from chlorophyll fluorescence measurements, as a proxy for leaf photosynthesis. Last, thermal infrared and multispectral airborne imaging was used for computing canopy temperature variations, water deficit, and vegetation indices. All traits estimated by these methods were compared to low-throughput in planta measurements. Vegetation indices and alpha hull volumes were significantly correlated with tree leaf area and trunk cross sectional area, while I PL values showed strong correlations with photosynthesis measurements collected on an independent leaf dataset. By contrast, correlations between stomatal conductance and canopy temperature estimated from airborne images were lower, emphasizing discrepancies across measurement scales. High heritability values were obtained for almost all the traits except leaf photosynthesis, likely due to large intra-tree variation. Genotypic means were used in a clustering procedure that defined six classes of architectural and functional combinations. Differences between groups showed several combinations between architectural and functional traits, suggesting independent genetic controls. This study demonstrates the feasibility and relevance of combining multi-scale high-throughput methods and paves the way to explore the genetic bases of architectural and functional variations in woody crops in field conditions.
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Affiliation(s)
- Aude Coupel-Ledru
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
- Present Address: University of Bristol, School of Biological Sciences, Life Science Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Benoît Pallas
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
| | - Magalie Delalande
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
| | - Frédéric Boudon
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
- CIRAD, 34398 Montpellier Cedex 5, France
| | - Emma Carrié
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
| | - Sébastien Martinez
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
| | - Jean-Luc Regnard
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
| | - Evelyne Costes
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier Cedex 5, France
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10
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Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. HORTICULTURE RESEARCH 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
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Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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11
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Wang H, Zhao S, Mao K, Dong Q, Liang B, Li C, Wei Z, Li M, Ma F. Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress. BMC PLANT BIOLOGY 2018; 18:136. [PMID: 29940853 PMCID: PMC6019725 DOI: 10.1186/s12870-018-1308-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/10/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Improvement of water-use efficiency (WUE) can effectively reduce production losses caused by drought stress. A better understanding of the genetic determination of WUE in crops under drought stress has great potential value for developing cultivars adapted to arid regions. To identify the genetic loci associated with WUE and reveal genes responsible for the trait in apple, we aim to map the quantitative trait loci (QTLs) for carbon isotope composition, the proxy for WUE, applying two contrasting irrigating regimes over the two-year experiment and search for the candidate genes encompassed in the mapped QTLs. RESULTS We constructed a high-density genetic linkage map with 10,172 markers of apple, using single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RADseq) and a final segregating population of 350 seedlings from the cross of Honeycrisp and Qinguan. In total, 33 QTLs were identified for carbon isotope composition in apple under both well-watered and drought-stressed conditions. Three QTLs were stable over 2 years under drought stress on linkage groups LG8, LG15 and LG16, as validated by Kompetitive Allele-Specific PCR (KASP) assays. In those validated QTLs, 258 genes were screened according to their Gene Ontology functional annotations. Among them, 28 genes were identified, which exhibited significant responses to drought stress in 'Honeycrisp' and/or 'Qinguan'. These genes are involved in signaling, photosynthesis, response to stresses, carbohydrate metabolism, protein metabolism and modification, hormone metabolism and transport, transport, respiration, transcriptional regulation, and development regulation. They, especially those for photoprotection and relevant signal transduction, are potential candidate genes connected with WUE regulation in drought-stressed apple. CONCLUSIONS We detected three stable QTLs for carbon isotope composition in apple under drought stress over 2 years, and validated them by KASP assay. Twenty-eight candidate genes encompassed in these QTLs were identified. These stable genetic loci and series of genes provided here serve as a foundation for further studies on marker-assisted selection of high WUE and regulatory mechanism of WUE in apple exposed to drought conditions, respectively.
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Affiliation(s)
- Haibo Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Qinglong Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Bowen Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Zhiwei Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
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12
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Understanding Forest Health with Remote Sensing-Part II—A Review of Approaches and Data Models. REMOTE SENSING 2017. [DOI: 10.3390/rs9020129] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Durand JB, Allard A, Guitton B, van de Weg E, Bink MCAM, Costes E. Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping. FRONTIERS IN PLANT SCIENCE 2017; 8:858. [PMID: 28638387 PMCID: PMC5461300 DOI: 10.3389/fpls.2017.00858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/08/2017] [Indexed: 05/18/2023]
Abstract
Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γ g ) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γ g and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.
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Affiliation(s)
- Jean-Baptiste Durand
- Laboratoire Jean Kuntzmann, Inria Mistis, Université Grenoble AlpesGrenoble, France
- Virtual Plants Team, Inria and CIRAD, UMR AGAPMontpellier, France
| | - Alix Allard
- Equipe Architecture et Fonctionnement des Espèces Fruitières, UMR AGAP, Institut National de la Recherche AgronomiqueMontpellier, France
| | - Baptiste Guitton
- Equipe Architecture et Fonctionnement des Espèces Fruitières, UMR AGAP, Institut National de la Recherche AgronomiqueMontpellier, France
| | - Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
| | - Marco C. A. M. Bink
- Biometris, Wageningen University and ResearchWageningen, Netherlands
- Research & Technology Centre, Hendrix GeneticsBoxmeer, Netherlands
| | - Evelyne Costes
- Equipe Architecture et Fonctionnement des Espèces Fruitières, UMR AGAP, Institut National de la Recherche AgronomiqueMontpellier, France
- *Correspondence: Evelyne Costes
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14
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Beltramo C, Valentini N, Portis E, Torello Marinoni D, Boccacci P, Sandoval Prando MA, Botta R. Genetic mapping and QTL analysis in European hazelnut (Corylus avellana L.). MOLECULAR BREEDING 2016; 36:27. [PMID: 0 DOI: 10.1007/s11032-016-0450-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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15
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Pieruschka R, Lawson T. Phenotyping in Plants. Preface. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5385-7. [PMID: 26512383 PMCID: PMC4585426 DOI: 10.1093/jxb/erv395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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