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Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, Nirmal N, Suresh K, Ursache R, Mason GA, Gouran M, West DA, Borowsky AT, Shackel KA, Sinha N, Bailey-Serres J, Geldner N, Li S, Franke RB, Brady SM. A suberized exodermis is required for tomato drought tolerance. NATURE PLANTS 2024; 10:118-130. [PMID: 38168610 PMCID: PMC10808073 DOI: 10.1038/s41477-023-01567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/23/2023] [Indexed: 01/05/2024]
Abstract
Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Lidor Shaar-Moshe
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Concepción Manzano
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Prakash Timilsena
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Damien De Bellis
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Sharon Gray
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Julia Holbein
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - He Yang
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Sana Mohammad
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Niba Nirmal
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Kiran Suresh
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Robertas Ursache
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Mona Gouran
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Kenneth A Shackel
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Niko Geldner
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Rochus Benni Franke
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.
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Pessoa HP, Dariva FD, Copati MGF, de Paula RG, de Oliveira Dias F, Gomes CN. Uncovering tomato candidate genes associated with drought tolerance using Solanum pennellii introgression lines. PLoS One 2023; 18:e0287178. [PMID: 37319140 PMCID: PMC10270355 DOI: 10.1371/journal.pone.0287178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/29/2023] [Indexed: 06/17/2023] Open
Abstract
Tomato plants are sensitive to drought stress throughout their growth cycle. To be considered drought-tolerant, a cultivar should display tolerance at all developmental stages. This study aimed to evaluate whether Solanum pennellii introgression lines (ILs) previously selected as drought-tolerant during germination/seedling growth maintained this tolerance in the vegetative/reproductive stage. We then investigated these ILs to uncover candidate genes. The plants were subjected to two different environmental conditions: well-watered and drought-stressed (water withheld for ≤ 20 d after flowering). Phenotyping for morphological, physiological, fruit quality, and yield-related traits was performed, and the data was analyzed using a mixed-model approach. Using a multi-trait index that relies on factor analysis and genotype-ideotype distance (FAI-BLUP index), the genotypes were ordered based on how far they were from the drought-tolerant ideotype. Afterward, the tomato IL population map furnished by the SOL Genomics Network was utilized to identify introgressed segments of significance for the identification of candidate genes. Significant genotypic differences were found in the yield, water content, mean weight, length, and width of the fruit, the percentage of fruits displaying blossom-end rot, and titratable acidity. The drought-tolerance ideotype was built considering the maximum values for the fruit water content, number of fruits, mean fruit weight, and yield, minimum values for blossom-end rot, and mean values for titratable acidity. IL 1-4-18, IL 7-4-1, IL 7-1, IL 7-5-5, and IL 1-2 were ranked above M-82 and therefore considered drought-tolerant during the vegetative/reproductive stage. IL 1-4-18 and IL1-2 sustained drought tolerance displayed during germination/seedling growth into the vegetative/reproductive stage. The following candidate genes associated with drought tolerance were identified: AHG2, At1g55840, PRXIIF, SAP5, REF4-RELATED 1, PRXQ, CFS1, LCD, CCD1, and SCS. Because they are already associated with genetic markers, they can be transferred to elite tomato cultivars through marker-assisted technology after validation.
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Affiliation(s)
- Herika Paula Pessoa
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | | | | | | | - Carlos Nick Gomes
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Haber Z, Wilhelmi MDMR, Fernández-Bayo JD, Harrold DR, Stapleton JJ, Toubiana D, VanderGheynst JS, Blumwald E, Simmons CW, Sade N, Achmon Y. The effect of circular soil biosolarization treatment on the physiology, metabolomics, and microbiome of tomato plants under certain abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1009956. [PMID: 36426148 PMCID: PMC9679285 DOI: 10.3389/fpls.2022.1009956] [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: 08/02/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Soil biosolarization (SBS) is an alternative technique for soil pest control to standard techniques such as soil fumigation and soil solarization (SS). By using both solar heating and fermentation of organic amendments, faster and more effective control of soilborne pathogens can be achieved. A circular economy may be created by using the residues of a given crop as organic amendments to biosolarize fields that produce that crop, which is termed circular soil biosolarization (CSBS). In this study, CSBS was employed by biosolarizing soil with amended tomato pomace (TP) residues and examining its impact on tomato cropping under conditions of abiotic stresses, specifically high salinity and nitrogen deficiency. The results showed that in the absence of abiotic stress, CSBS can benefit plant physiological performance, growth and yield relative to SS. Moreover, CSBS significantly mitigated the impacts of abiotic stress conditions. The results also showed that CSBS impacted the soil microbiome and plant metabolome. Mycoplana and Kaistobacter genera were found to be positively correlated with benefits to tomato plants health under abiotic stress conditions. Conversely, the relative abundance of the orders RB41, MND1, and the family Ellin6075 and were negatively correlated with tomato plants health. Moreover, several metabolites were significantly affected in plants grown in SS- and CSBS-treated soils under abiotic stress conditions. The metabolite xylonic acid isomer was found to be significantly negatively correlated with tomato plants health performance across all treatments. These findings improve understanding of the interactions between CSBS, soil ecology, and crop physiology under abiotic stress conditions.
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Affiliation(s)
- Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Jesus D. Fernández-Bayo
- Department of Food Science and Technology, University of California, Davis, CA, United States
| | - Duff R. Harrold
- Department of Food Science and Technology, University of California, Davis, CA, United States
| | - James J. Stapleton
- Statewide Integrated Pest Management Program, University of California Kearney Agricultural Research and Extension Center, Parlier, CA, United States
| | - David Toubiana
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Jean S. VanderGheynst
- College of Engineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA, United States
| | - Christopher W. Simmons
- Department of Food Science and Technology, University of California, Davis, CA, United States
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yigal Achmon
- Biotechnology and Food Engineering, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, China
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, China
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Ectopic Expression of Arabidopsis thaliana zDof1.3 in Tomato ( Solanum lycopersicum L.) Is Associated with Improved Greenhouse Productivity and Enhanced Carbon and Nitrogen Use. Int J Mol Sci 2022; 23:ijms231911229. [PMID: 36232530 PMCID: PMC9570051 DOI: 10.3390/ijms231911229] [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: 08/21/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
A large collection of transgenic tomato lines, each ectopically expressing a different Arabidopsis thaliana transcription factor, was screened for variants with alterations in leaf starch. Such lines may be affected in carbon partitioning, and in allocation to the sinks. We focused on ‘L4080’, which harbored an A. thaliana zDof (DNA-binding one zinc finger) isoform 1.3 (AtzDof1.3) gene, and which had a 2−4-fold higher starch-to-sucrose ratio in source leaves over the diel (p < 0.05). Our aim was to determine whether there were associated effects on productivity. L4080 plants were altered in nitrogen (N) and carbon (C) metabolism. The N-to-C ratio was higher in six-week-old L4080, and when treated with 1/10 N, L4080 growth was less inhibited compared to the wild-type and this was accompanied by faster root elongation (p < 0.05). The six-week-old L4080 acquired 42% more dry matter at 720 ppm CO2, compared to ambient CO2 (p < 0.05), while the wild-type (WT) remained unchanged. GC-MS-TOF data showed that L4080 source leaves were enriched in amino acids compared to the WT, and at 49 DPA, fruit had 25% greater mass, higher sucrose, and increased yield (25%; p < 0.05) compared to the WT. An Affymetrix cDNA array analysis suggested that only 0.39% of the 9000 cDNAs were altered by 1.5-fold (p < 0.01) in L4080 source leaves. 14C-labeling of fruit disks identified potential differences in 14-DPA fruit metabolism suggesting that post-transcriptional regulation was important. We conclude that AtzDof1.3 and the germplasm derived therefrom, should be investigated for their ‘climate-change adaptive’ potential.
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Dafna A, Halperin I, Oren E, Isaacson T, Tzuri G, Meir A, Schaffer AA, Burger J, Tadmor Y, Buckler ES, Gur A. Underground heterosis for yield improvement in melon. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6205-6218. [PMID: 0 DOI: 10.1093/jxb/erab219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/13/2021] [Indexed: 05/15/2023]
Abstract
Abstract
Heterosis, the superiority of hybrids over their parents, is a major genetic force associated with plant fitness and crop yield enhancement. We investigated root-mediated yield heterosis in melons (Cucumis melo) by characterizing a common variety grafted onto 190 hybrid rootstocks, resulting from crossing 20 diverse inbreds in a diallel-mating scheme. Hybrid rootstocks improved yield by more than 40% compared with their parents, and the best hybrid yield outperformed the reference commercial variety by 65% under both optimal and minimal irrigation treatments. To characterize the genetics of underground heterosis we conducted whole genome re-sequencing of the 20 founder lines, and showed that parental genetic distance was no predictor for the level of heterosis. Through inference of the 190 hybrid genotypes from their parental genomes, followed by genome-wide association analysis, we mapped multiple quantitative trait loci for root-mediated yield. Yield enhancement of the four best-performing hybrid rootstocks was validated in multiple experiments with four different scion varieties. Our grafting approach is complementary to the common roots genetic approach that focuses mainly on variation in root system architecture, and is a step towards discovery of candidate genes involved in root function and yield enhancement.
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Affiliation(s)
- Asaf Dafna
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ilan Halperin
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Elad Oren
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tal Isaacson
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Galil Tzuri
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Ayala Meir
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, Rishon LeZiyyon 7507101, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Edward S Buckler
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Amit Gur
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
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Leibman-Markus M, Gupta R, Pizarro L, Gershony O, Rav-David D, Elad Y, Bar M. Gene Editing of the Decoy Receptor LeEIX1 Increases Host Receptivity to Trichoderma Bio-Control. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:678840. [PMID: 37744104 PMCID: PMC10512410 DOI: 10.3389/ffunb.2021.678840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/20/2021] [Indexed: 09/26/2023]
Abstract
Fungal and bacterial pathogens generate devastating diseases and cause significant tomato crop losses worldwide. Due to chemical pesticides harming the environment and human health, alternative disease control strategies, including microorganismal bio-control agents (BCAs), are increasingly sought-after in agriculture. Bio-control microorganisms such as Trichoderma spp. have been shown to activate induced systemic resistance (ISR) in the host. However, examples of highly active bio-control microorganisms in agricultural settings are still lacking, due primarily to inconsistency in bio-control efficacy, often leading to widespread disease prior to the required ISR induction in the host. As part of its plant colonization strategy, Trichoderma spp. can secrete various compounds and molecules, which can effect host priming/ISR. One of these molecules synthesized and secreted from several species of Trichoderma is the family 11 xylanase enzyme known as ethylene inducing xylanase, EIX. EIX acts as an ISR elicitor in specific plant species and varieties. The response to EIX in tobacco and tomato cultivars is controlled by a single dominant locus, termed LeEIX, which contains two receptors, LeEIX1 and LeEIX2, both belonging to a class of leucine-rich repeat cell-surface glycoproteins. Both receptors are able to bind EIX, however, while LeEIX2 mediates plant defense responses, LeEIX1 acts as a decoy receptor and attenuates EIX induced immune signaling of the LeEIX2 receptor. By mutating LeEIX1 using CRISPR/Cas9, here, we report an enhancement of receptivity to T. harzianum mediated ISR and disease bio-control in tomato.
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Affiliation(s)
| | | | | | | | | | | | - Maya Bar
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
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Popowski E, Thomson SJ, Knäbel M, Tahir J, Crowhurst RN, Davy M, Foster TM, Schaffer RJ, Tustin DS, Allan AC, McCallum J, Chagné D. Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing. G3-GENES GENOMES GENETICS 2021; 11:6261761. [PMID: 34009255 PMCID: PMC8495948 DOI: 10.1093/g3journal/jkab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
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Affiliation(s)
- Elizabeth Popowski
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | | | | | | | - Marcus Davy
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | - Robert J Schaffer
- Plant & Food Research, Motueka, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Andrew C Allan
- Plant & Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - David Chagné
- Plant & Food Research, Palmerston North, New Zealand
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Martina M, Tikunov Y, Portis E, Bovy AG. The Genetic Basis of Tomato Aroma. Genes (Basel) 2021; 12:genes12020226. [PMID: 33557308 PMCID: PMC7915847 DOI: 10.3390/genes12020226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
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Genetic Analysis of Root-to-Shoot Signaling and Rootstock-Mediated Tolerance to Water Deficit in Tomato. Genes (Basel) 2020; 12:genes12010010. [PMID: 33374834 PMCID: PMC7823420 DOI: 10.3390/genes12010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022] Open
Abstract
Developing drought-tolerant crops is an important strategy to mitigate climate change impacts. Modulating root system function provides opportunities to improve crop yield under biotic and abiotic stresses. With this aim, a commercial hybrid tomato variety was grafted on a genotyped population of 123 recombinant inbred lines (RILs) derived from Solanum pimpinellifolium, and compared with self- and non-grafted controls, under contrasting watering treatments (100% vs. 70% of crop evapotranspiration). Drought tolerance was genetically analyzed for vegetative and flowering traits, and root xylem sap phytohormone and nutrient composition. Under water deficit, around 25% of RILs conferred larger total shoot dry weight than controls. Reproductive and vegetative traits under water deficit were highly and positively correlated to the shoot water content. This association was genetically supported by linkage of quantitative trait loci (QTL) controlling these traits within four genomic regions. From a total of 83 significant QTLs, most were irrigation-regime specific. The gene contents of 8 out of 12 genomic regions containing 46 QTLs were found significantly enriched at certain GO terms and some candidate genes from diverse gene families were identified. Thus, grafting commercial varieties onto selected rootstocks derived from S. pimpinellifolium provides a viable strategy to enhance drought tolerance in tomato.
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10
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Calafiore R, Aliberti A, Ruggieri V, Olivieri F, Rigano MM, Barone A. Phenotypic and Molecular Selection of a Superior Solanum pennellii Introgression Sub-Line Suitable for Improving Quality Traits of Cultivated Tomatoes. FRONTIERS IN PLANT SCIENCE 2019; 10:190. [PMID: 30853967 PMCID: PMC6395448 DOI: 10.3389/fpls.2019.00190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/05/2019] [Indexed: 05/21/2023]
Abstract
The Solanum pennellii Introgression Line (IL) population can be exploited to identify favorable alleles that can improve yield and fruit quality traits in commercial tomato varieties. Over the past few years, we have selected ILs that exhibit increased content of antioxidant compounds in the fruit compared to the cultivar M82, which represents the genetic background in which the different wild regions of the S. pennellii ILs were included. Recently, we have identified seven sub-lines of the IL7-3 accumulating different amounts of antioxidants in the ripe fruit. Since the wild region carried on chromosome 7 induces a low fruit production in IL7-3, the first aim of the present work was to evaluate yield performances of the selected sub-lines in three experimental fields located in the South of Italy. Another aim was to confirm in the same lines the high levels of antioxidants and evaluate other fruit quality traits. On red ripe fruit, the levels of soluble solids content, firmness, and ascorbic acid (AsA) were highly variable among the sub-lines grown in three environmental conditions, evidencing a significant genotype by environment interaction for soluble solids and AsA content. Only one sub-line (coded R182) exhibited a significantly higher firmness, even though no differences were observed for this trait between the parental lines M82 and IL7-3. The same sub-line showed significantly higher AsA content compared to M82, thus resembling IL7-3. Even though IL7-3 always exhibited a significantly lower yield, all the sub-lines showed yield variability over the three trials. Interestingly, the sub-line R182, selected for its better performances in terms of fruit quality, in all the trials showed a production comparable to that of the control line M82. A group of species-specific molecular markers was tested on R182 and on the parental genotypes in order to better define the wild genomic regions carried by the elite line R182. In these regions three candidate genes that could increase the level of AsA in the fruit were identified. In the future, the line R182 could be used as pre-breeding material in order to obtain new varieties improved for nutritional traits.
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Affiliation(s)
| | | | | | | | | | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Rothan C, Diouf I, Causse M. Trait discovery and editing in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:73-90. [PMID: 30417464 DOI: 10.1111/tpj.14152] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.
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Affiliation(s)
- Christophe Rothan
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Isidore Diouf
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
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12
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Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet JP, Bitton F, Gricourt J, Poncet C, Gautier V, Jiménez-Gómez JM, Rigaill G, Causse M. Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:635-650. [PMID: 30079488 DOI: 10.1111/tpj.14057] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype-by-environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F1 hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele-specific expression (ASE) in the F1 hybrid to the allelic expression in both parental lines, respectively, 3005 genes in leaf and 2857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types of factors. A total of 328 genes in leaf and 113 in fruit exhibited significant ASE-by-watering regime interaction, among which ~80% presented trans-by-watering regime interaction, suggesting a response to water deficit mediated through a majority of trans-acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 recombinant inbred lines (RILs) and identified 163 expression quantitative trait loci (eQTLs) mostly confirming the divergences identified by ASE. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Renaud Duboscq
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Muriel Latreille
- INRA, UMR1334, Amélioration génétique et Adaptation des Plantes, Montpellier SupAgro-INRA-IRD-UMII, 2 Place Pierre Viala, Montpellier, 34060, France
| | - Sylvain Santoni
- INRA, UMR1334, Amélioration génétique et Adaptation des Plantes, Montpellier SupAgro-INRA-IRD-UMII, 2 Place Pierre Viala, Montpellier, 34060, France
| | - Matthieu Beukers
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Jean-Paul Bouchet
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Fréderique Bitton
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Justine Gricourt
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Charles Poncet
- INRA, UMR1095, Génétique Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Véronique Gautier
- INRA, UMR1095, Génétique Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - José M Jiménez-Gómez
- INRA, UMR1318, Institut Jean-Pierre Bourgin, AgroParisTech-INRA-CNRS, Route de Saint Cyr, Versailles, 78026, France
| | - Guillem Rigaill
- INRA, UMR8071, Laboratoire de Mathématiques et Modélisation d'Evry, Université d'Evry Val d'Essonne, ENSIIE-INRA-CNRS, Évry, 91037, France
| | - Mathilde Causse
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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13
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Chandnani R, Wang B, Draye X, Rainville LK, Auckland S, Zhuang Z, Lubbers EL, May OL, Chee PW, Paterson AH. Segregation distortion and genome-wide digenic interactions affect transmission of introgressed chromatin from wild cotton species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2219-2230. [PMID: 28801756 DOI: 10.1007/s00122-017-2952-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species. From an interspecific cross, Gossypium hirsutum × Gossypium mustelinum, we studied G. mustelinum (the most distant tetraploid relative of Upland cotton) allele retention in 35 BC3F1 plants and segregation patterns in BC3F2 populations totaling 3202 individuals, using 216 DNA marker loci. The average retention of donor alleles across BC3F1 plants was higher than expected and the average frequency of G. mustelinum alleles in BC3F2 segregating families was less than expected. Despite surprisingly high retention of G. mustelinum alleles in BC3F1, 46 genomic regions showed no introgression. Regions on chromosomes 3 and 15 lacking introgression were closely associated with possible small inversions previously reported. Nonlinear two-locus interactions are abundant among loci with single-locus segregation distortion, and among loci originating from one of the two subgenomes. Comparison of the present results with those of prior studies indicates different permeability of Upland cotton for donor chromatin from different allotetraploid relatives. Different contributions of subgenomes to two-locus interactions suggest different fates of subgenomes in the evolution of allotetraploid cottons. Transmission genetics of G. hirsutum × G. mustelinum crosses reveals allelic interactions, constraints on fixation and selection of donor alleles, and challenges with retention of introgressed chromatin for crop improvement.
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Affiliation(s)
- Rahul Chandnani
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Baohua Wang
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Xavier Draye
- Unité d'écophysiologie et amélioration végétale, Université Catholique de Louvain, Croix du Sud 1-10, 1348, Louvain-la-Neuve, Belgium
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Susan Auckland
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Zhimin Zhuang
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Edward L Lubbers
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
| | - O Lloyd May
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
- Monsanto Cotton Breeding, Tifton, GA, 31793, USA
| | - Peng W Chee
- NESPAL Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 31793, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA.
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Fernandez-Moreno JP, Levy-Samoha D, Malitsky S, Monforte AJ, Orzaez D, Aharoni A, Granell A. Uncovering tomato quantitative trait loci and candidate genes for fruit cuticular lipid composition using the Solanum pennellii introgression line population. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2703-2716. [PMID: 28475776 PMCID: PMC5853253 DOI: 10.1093/jxb/erx134] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/28/2017] [Indexed: 05/19/2023]
Abstract
The cuticle is a specialized cell wall layer that covers the outermost surface of the epidermal cells and has important implications for fruit permeability and pathogen susceptibility. In order to decipher the genetic control of tomato fruit cuticle composition, an introgression line (IL) population derived from a biparental cross between Solanum pennellii (LA0716) and the Solanum lycopersicum cultivar M82 was used to build a first map of associated quantitative trait loci (QTLs). A total of 24 cuticular waxes and 26 cutin monomers were determined. They showed changes associated with 18 genomic regions distributed in nine chromosomes affecting 19 ILs. Out of the five main fruit cuticular components described for the wild species S. pennellii, three of them were associated with IL3.4, IL12.1, and IL7.4.1, causing an increase in n-alkanes (≥C30), a decrease in amyrin content, and a decrease in cuticle thickness of ~50%, respectively. Moreover, we also found a QTL associated with increased levels of amyrins in IL3.4. In addition, we propose some candidate genes on the basis of their differential gene expression and single nucleotide polymorphism variability between the introgressed and the recurrent alleles, which will be the subjects of further investigation.
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Affiliation(s)
- Josefina-Patricia Fernandez-Moreno
- Fruit Genomics and Biotechnology Laboratory, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, Av/ Ingeniero Fausto Elio s/n, CP, Valencia, Spain
| | - Dorit Levy-Samoha
- Department of Plant Sciences and the Environment, Weizmann Institute of Science, Ullmann Building of Life Sciences, Room, Rehovot, Israel
| | - Sergey Malitsky
- Department of Plant Sciences and the Environment, Weizmann Institute of Science, Ullmann Building of Life Sciences, Room, Rehovot, Israel
| | - Antonio J Monforte
- Genomics in Plant Breeding Laboratory, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, Av/ Ingeniero Fausto Elio s/n, CP, Valencia, Spain
| | - Diego Orzaez
- Fruit Genomics and Biotechnology Laboratory, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, Av/ Ingeniero Fausto Elio s/n, CP, Valencia, Spain
| | - Asaph Aharoni
- Department of Plant Sciences and the Environment, Weizmann Institute of Science, Ullmann Building of Life Sciences, Room, Rehovot, Israel
- Correspondence: and
| | - Antonio Granell
- Fruit Genomics and Biotechnology Laboratory, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, Av/ Ingeniero Fausto Elio s/n, CP, Valencia, Spain
- Correspondence: and
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Albert E, Segura V, Gricourt J, Bonnefoi J, Derivot L, Causse M. Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6413-6430. [PMID: 27856709 PMCID: PMC5181584 DOI: 10.1093/jxb/erw411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Vincent Segura
- INRA, UR0588, Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, Centre de Recherche Val de Loire, CS 40001, Orléans, 45075, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | | | | | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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16
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Ikeda H, Shibuya T, Imanishi S, Aso H, Nishiyama M, Kanayama Y. Dynamic Metabolic Regulation by a Chromosome Segment from a Wild Relative During Fruit Development in a Tomato Introgression Line, IL8-3. PLANT & CELL PHYSIOLOGY 2016; 57:1257-1270. [PMID: 27076398 DOI: 10.1093/pcp/pcw075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/03/2016] [Indexed: 06/05/2023]
Abstract
We performed comparative metabolome and transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. Marked differences between M82 and IL8-3 were found not only in ripe fruits but also at 20 days after flowering (DAF) in the hierarchical clustering analysis of the metabolome, whereas patterns were similar between the two genotypes at 10 and 30 DAF. Our metabolome analysis conclusively showed that 20 DAF is an important stage of fruit metabolism and that the Solanum pennellii introgressed region in IL8-3 plays a key role in metabolic changes at this stage. Carbohydrate and amino acid metabolism were found to be promoted in IL8-3 at 20 DAF and the ripening stage, respectively, whereas transcriptome analysis showed no marked differences between the two genotypes, indicating that dynamic metabolic regulation at 20 DAF and the ripening stage was controlled by relatively few genes. The transcript levels of the cell wall invertase (LIN6) and sucrose synthase (TOMSSF) genes in starch and sucrose metabolic pathway and that of the glutamate synthase (SlGOGAT) gene in the amino acid metabolic pathway in IL8-3 fruit were higher than those in M82, and SlGOGAT expression was enhanced under high-sugar conditions. The results suggest that the promotion of carbohydrate metabolism by LIN6 and TOMSSF in IL8-3 fruit at 20 DAF affects SlGOGAT expression and amino acid accumulation via higher sugar concentration at the late stage of fruit development.
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Affiliation(s)
- Hiroki Ikeda
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan Present address: (H. Ikeda), NARO Tohoku Agricultural Research Center, Morioka 020-0198, Japan
| | - Tomoki Shibuya
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Shunsuke Imanishi
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, 514-2392 Japan
| | - Hisashi Aso
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Manabu Nishiyama
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
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Caruso G, Gomez LD, Ferriello F, Andolfi A, Borgonuovo C, Evidente A, Simister R, McQueen-Mason SJ, Carputo D, Frusciante L, Ercolano MR. Exploring tomato Solanum pennellii introgression lines for residual biomass and enzymatic digestibility traits. BMC Genet 2016; 17:56. [PMID: 27044251 PMCID: PMC4820949 DOI: 10.1186/s12863-016-0362-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/17/2016] [Indexed: 01/09/2023] Open
Abstract
Background Residual biomass production for fuel conversion represents a unique opportunity to avoid concerns about compromising food supply by using dedicated feedstock crops. Developing tomato varieties suitable for both food consumption and fuel conversion requires the establishment of new selection methods. Results A tomato Solanum pennellii introgression population was assessed for fruit yield, biomass phenotypic diversity, and for saccharification potential. Introgression lines 2–5, 2–6, 6–3, 7–2, 10–2 and 12–4 showed the best combination of fruit and residual biomass production. Lignin, cellulose, hemicellulose content and saccharification rate showed a wide variation in the tested lines. Within hemicellulose, xylose value was high in IL 6–3, IL 7–2 and IL 6–2, whereas arabinose showed a low content in IL 10–2, IL 6–3 and IL 2–6. The latter line showed also the highest ethanol potential production. Alkali pre-treatment resulted in the highest values of saccharification in most of lines tested, suggesting that chemical pretreatment is an important factor for improving biomass processability. Interestingly, extreme genotypes for more than one single trait were found, allowing the identification of better genotypes. Cell wall related genes mapping in genomic regions involved into tomato biomass production and digestibility variation highlighted potential candidate genes. Molecular expression profile of few of them provided useful information about challenged pathways. Conclusions The screening of S. pennellii introgression population resulted very useful for delving into complex traits such as biomass production and digestibility. The extreme genotypes identified could be fruitfully employed for both genetic studies and breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0362-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- G Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - L D Gomez
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK.
| | - F Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - A Andolfi
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - C Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - A Evidente
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - R Simister
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK
| | - S J McQueen-Mason
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK
| | - D Carputo
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - L Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - M R Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy.
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18
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Albert E, Gricourt J, Bertin N, Bonnefoi J, Pateyron S, Tamby JP, Bitton F, Causse M. Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:395-418. [PMID: 26582510 DOI: 10.1007/s00122-015-2635-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/04/2015] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. ABSTRACT As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato (Solanum lycopersicum L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Nadia Bertin
- INRA, UR 1115, Plante et Système de cultures Horticoles, 228 Route de l'aérodrome, Centre de Recherche PACA, Domaine Saint Paul, CS40509, 84914, Avignon Cedex 9, France
| | | | - Stéphanie Pateyron
- INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Jean-Philippe Tamby
- INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Frédérique Bitton
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France.
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19
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Grandillo S, Cammareri M. Molecular Mapping of Quantitative Trait Loci in Tomato. COMPENDIUM OF PLANT GENOMES 2016. [DOI: 10.1007/978-3-662-53389-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Chitwood DH, Topp CN. Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:54-60. [PMID: 25658908 DOI: 10.1016/j.pbi.2015.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 05/22/2023]
Abstract
The plant phenotype is infinite. Plants vary morphologically and molecularly over developmental time, in response to the environment, and genetically. Exhaustive phenotyping remains not only out of reach, but is also the limiting factor to interpreting the wealth of genetic information currently available. Although phenotyping methods are always improving, an impasse remains: even if we could measure the entirety of phenotype, how would we interpret it? We propose the concept of cryptotype to describe latent, multivariate phenotypes that maximize the separation of a priori classes. Whether the infinite points comprising a leaf outline or shape descriptors defining root architecture, statistical methods to discern the quantitative essence of an organism will be required as we approach measuring the totality of phenotype.
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21
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Gur A, Zamir D. Mendelizing all Components of a Pyramid of Three Yield QTL in Tomato. FRONTIERS IN PLANT SCIENCE 2015; 6:1096. [PMID: 26697048 PMCID: PMC4678209 DOI: 10.3389/fpls.2015.01096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/22/2015] [Indexed: 05/03/2023]
Abstract
Molecular markers allowed breeders to mendelize quantitative trait loci (QTL) providing another demonstration that quantitative traits are governed by the same principles as single qualitative genes. This research extends the QTL analysis to two and three QTL and tests our ability to mendelize an oligogenic trait. In tomato, agricultural yield is determined by the weight of the fruits harvested per unit area and the total soluble solids (% Brix)-sugars and acids. The current study explores the segregation of multiple independent yield-related QTL that were identified and mapped using introgression lines (IL) of Solanum pennellii in cultivated processing tomato (S. lycopersicum). We screened 45 different double and triple IL-QTL combinations for agricultural yield, to identify QTL pyramids that behaved in an additive manner and were suitable substrate for mendelizing an oligogenic trait. A pyramid of three independent QTL that significantly improved Brix(∗)Yield (BXY - the soluble solids output per unit area) compared to M82 was selected. In the progenies of the tri-hybrid we bred using markers a nearly isogenic 'immortalized F2.' While the common mode of QTL-QTL interactions across the 45 IL-QTLs combinations was less than additive, the three QTLs in the selected triple-stack performed in an additive manner which made it an exceptional material for breeding. This study demonstrates that using the phenotypic effect of all 27 possible QTL-alleles combinations it is possible to make reliable predictions about the genotypes that will maximize the yield.
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22
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Rigano MM, Raiola A, Tenore GC, Monti DM, Del Giudice R, Frusciante L, Barone A. Quantitative Trait Loci Pyramiding Can Improve the Nutritional Potential of Tomato ( Solanum lycopersicum) Fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11519-27. [PMID: 25369113 DOI: 10.1021/jf502573n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Maria Manuela Rigano
- Department
of Agricultural Sciences, University of Naples Federico II, Via
Università 100, 80055 Portici (Naples), Italy
| | - Assunta Raiola
- Department
of Agricultural Sciences, University of Naples Federico II, Via
Università 100, 80055 Portici (Naples), Italy
| | - Gian Carlo Tenore
- Department
of Pharmacy, University of Naples Federico II, Via D. Montesano
49, 80131 Naples, Italy
| | - Daria Maria Monti
- Department
of Chemical Sciences, University of Naples Federico II, Complesso Universitario M.S.Angelo, via Cinthia 4, 80126, Naples, Italy
| | - Rita Del Giudice
- Department
of Chemical Sciences, University of Naples Federico II, Complesso Universitario M.S.Angelo, via Cinthia 4, 80126, Naples, Italy
| | - Luigi Frusciante
- Department
of Agricultural Sciences, University of Naples Federico II, Via
Università 100, 80055 Portici (Naples), Italy
| | - Amalia Barone
- Department
of Agricultural Sciences, University of Naples Federico II, Via
Università 100, 80055 Portici (Naples), Italy
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23
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Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014. [PMID: 25064008 DOI: 10.1038/ng3046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
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Affiliation(s)
- Anthony Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Federico Scossa
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l'Orticoltura, Pontecagnano, Italy
| | - Marie E Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Florian Maumus
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Takayuki Tohge
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hadi Quesneville
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Eric A Fich
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Mariana Conte
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Heike Keller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Korbinian Schneeberger
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rainer Schwacke
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Itai Ofner
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Sonia Osorio
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
| | - Saulo Alves Aflitos
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Elio Schijlen
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - José M Jiménez-Goméz
- 1] Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany. [2] INRA, UMR 1318, Institut Jean-Pierre Bourgin, Versailles, France
| | - Malgorzata Ryngajllo
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Seisuke Kimura
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Daniel Koenig
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Lauren R Headland
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Roeland C H J van Ham
- 1] Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands. [2]
| | - René Klein Lankhorst
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Linyong Mao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Alexander Vogel
- Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Borjana Arsova
- Entwicklungs und Molekularbiologie der Pflanzen, Heinrich Heine Universität, Düsseldorf, Germany
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Zhangjun Fei
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [3] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Dani Zamir
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Fernando Carrari
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - James J Giovannoni
- 1] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [2] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Björn Usadel
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany. [3] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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24
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The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014; 46:1034-8. [PMID: 25064008 PMCID: PMC7036041 DOI: 10.1038/ng.3046] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/30/2014] [Indexed: 11/12/2022]
Abstract
Björn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response. Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
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25
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Long W, Li Y, Zhou W, Ling HQ, Zheng S. Sequence-based SSR marker development and their application in defining the Introgressions of LA0716 (Solanum pennellii) in the background of cv. M82 (Solanum lycopersicum). PLoS One 2013; 8:e81091. [PMID: 24339899 PMCID: PMC3855227 DOI: 10.1371/journal.pone.0081091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/18/2013] [Indexed: 12/02/2022] Open
Abstract
The introgression lines (ILs) from cv. M82 (Solanum lycopersicum) × LA0716 (S. pennellii) have been proven to be exceptionally useful for genetic analysis and gene cloning. The introgressions were originally defined by RFLP markers at their development. The objectives of this study are to develop polymorphic SSR markers, and to re-define the DNA introgression from LA0716 in the ILs. Tomato sequence data was scanned by software to generate SSR markers. In total, 829 SSRs, which could be robustly amplified by PCR, were developed. Among them, 658 SSRs were dinucleotide repeats, 162 were trinucleotide repeats, and nine were tetranucleotide repeats. The 829 SSRs together with 96 published RFLPs were integrated into the physical linkage map of S. lycopersicum. Introgressions of DNA fragments from LA0716 were re-defined among the 75 ILs using the newly developed SSRs. A specific introgression of DNA fragment from LA0716 was identified in 72 ILs as described previously by RFLP, whereas the specific DNA introgression described previously were not detected in the ILs LA4035, LA4059 and LA4091. The physical location of each investigated DNA introgression was finely determined by SSR mapping. Among the 72 ILs, eight ILs showed a shorter and three ILs (IL3-2, IL12-3 and IL12-3-1) revealed a longer DNA introgression than that framed by RFLPs. Furthermore, 54 previously undefined segments were found in 21 ILs, ranging from 1 to 11 DNA introgressions per IL. Generally, the newly developed SSRs provide additional markers for genetic studies of tomatoes, and the fine definition of DNA introgressions from LA0716 would facilitate the use of the ILs for genetic analysis and gene cloning.
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Affiliation(s)
- Wenbo Long
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ye Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (H-QL); (SZ)
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (H-QL); (SZ)
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26
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Chitwood DH, Sinha NR. A census of cells in time: quantitative genetics meets developmental biology. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:92-9. [PMID: 23218243 DOI: 10.1016/j.pbi.2012.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 11/06/2012] [Accepted: 11/08/2012] [Indexed: 05/09/2023]
Abstract
Quantitative genetics has become a popular method for determining the genetic basis of natural variation. Combined with genomic methods, it provides a tool for discerning the genetic basis of gene expression. So-called genetical genomics approaches yield a wealth of genomic information, but by necessity, because of cost and time, fail to resolve the differences between organs, tissues, and/or cell types. Similarly, quantitative approaches in development that might potentially address these issues are seldom applied to quantitative genetics. We discuss recent advances in cell type-specific isolation methods, the quantitative analysis of phenotype, and developmental modeling that are compatible with quantitative genetics and, with time, promise to bridge the gap between these two powerful disciplines yielding unprecedented biological insight.
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Affiliation(s)
- Daniel H Chitwood
- Department of Plant Biology, University of California at Davis, Davis, CA 95616, United States
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27
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Sacco A, Di Matteo A, Lombardi N, Trotta N, Punzo B, Mari A, Barone A. Quantitative trait loci pyramiding for fruit quality traits in tomato. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 31:217-222. [PMID: 23316114 PMCID: PMC3538004 DOI: 10.1007/s11032-012-9763-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/13/2012] [Indexed: 05/04/2023]
Abstract
Fruit quality is a major focus for most conventional and innovative tomato breeding strategies, with particular attention being paid to fruit antioxidant compounds. Tomatoes represent a major contribution to dietary nutrition worldwide and a reservoir of diverse antioxidant molecules. In a previous study, we identified two Solanum pennellii introgression lines (IL7-3 and IL12-4) harbouring quantitative trait loci (QTL) that increase the content of ascorbic acid (AsA), phenols and soluble solids (degrees Brix; °Bx) in tomato fruit. The purpose of the present work was to pyramid into cultivated varieties the selected QTL for enhanced antioxidant and °Bx content. To better understand the genetic architecture of each QTL, the two ILs were crossed to the recurrent parent M82 (ILH7-3 and ILH12-4) and between them (ILH7-3+12-4). F1 hybrids (ILH7-3+12-4) were then selfed up to obtain F3 progenies in order to stabilize the favourable traits at the homozygous condition. Species-specific molecular markers were identified for each introgressed region and allowed us to select four F2 genotypes carrying both introgressions at the homozygous condition. The F3 double homozygous plants displayed AsA, total phenols and °Bx content significantly higher than M82. Therefore, they may represent suitable genetic material for breeding schemes aiming to increase antioxidant content in tomato fruit.
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Affiliation(s)
- Adriana Sacco
- Department of Soil, Plant, Environmental and Animal Sciences, University of Naples Federico II, Portici, Italy
| | - Antonio Di Matteo
- Department of Soil, Plant, Environmental and Animal Sciences, University of Naples Federico II, Portici, Italy
| | - Nadia Lombardi
- Department of Soil, Plant, Environmental and Animal Sciences, University of Naples Federico II, Portici, Italy
| | - Nikita Trotta
- CRA-ORT, Italian Agricultural Research Council, Research Centre for Vegetable Crops, Pontecagnano, Italy
| | - Biancavaleria Punzo
- Department of Soil, Plant, Environmental and Animal Sciences, University of Naples Federico II, Portici, Italy
| | - Angela Mari
- CNR-ISA, Institute for Food Science, Avellino, Italy
- Present Address: Department of Pharmaceutical and Biomedical Sciences, University of Salerno, Salerno, Italy
| | - Amalia Barone
- Department of Soil, Plant, Environmental and Animal Sciences, University of Naples Federico II, Portici, Italy
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28
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Sun YD, Liang Y, Wu JM, Li YZ, Cui X, Qin L. Dynamic QTL analysis for fruit lycopene content and total soluble solid content in a Solanum lycopersicum x S. pimpinellifolium cross. GENETICS AND MOLECULAR RESEARCH 2012; 11:3696-710. [PMID: 22930431 DOI: 10.4238/2012.august.17.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruit lycopene content and total soluble solid content are important factors determining fruit quality of tomatoes; however, the dynamic quantitative trait loci (QTL) controlling lycopene and soluble solid content have not been well studied. We mapped the chromosomal regions controlling these traits in different periods in F(2:3) families derived from a cross between the domestic and wild tomato species Solanum lycopersicum and S. pimpinellifolium. Fifteen QTLs for lycopene and soluble solid content and other related traits analyzed at three different fruit ripening stages were detected with a composite interval mapping method. These QTLs explained 7-33% of the individual phenotypic variation. QTLs detected in the color-changing period were different from those detected in the other two periods. On chromosome 1, the soluble solid content QTL was located in the same region during the color-changing and full-ripe periods. On chromosome 4, the same QTL for lycopene content was found during the color-changing and full-ripe periods. The QTL for lycopene content on chromosome 4 co-located with the QTL for soluble solid content during the full-ripe period. Co-location of lycopene content QTL and soluble solid content QTLs may be due to pleiotropic effects of a single gene or a cluster of genes via physiological relationships among traits. On chromosome 9, the same two QTLs for lycopene content at two different fruit ripening periods may reflect genes controlling lycopene content that are always expressed in tomato fruit development.
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Affiliation(s)
- Y D Sun
- Key Laboratory of Horticulture Plant Germplasm and Genetic Improvement, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, Shaanxi, China
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29
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Thalapati S, Batchu AK, Neelamraju S, Ramanan R. Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice. Funct Integr Genomics 2012; 12:277-89. [PMID: 22367483 DOI: 10.1007/s10142-012-0265-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 01/27/2012] [Accepted: 02/07/2012] [Indexed: 12/11/2022]
Abstract
Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region including Os11Gsk and its flanking regions could be PCR amplified only from IL50-7, O. rufipogon, japonica varieties of rice-Nipponbare and Kitaake but not from the indica varieties, KMR3 and Taichung Native-1. Three sister lines of IL50-7 yielding higher than KMR3 showed presence of Os11Gsk, whereas the gene was absent in three other ILs from the same cross having lower yield than KMR3, indicating an association of the presence of Os11Gsk with high yield. Southern analysis showed additional bands in the genomic DNA of O. rufipogon and IL50-7 with Os11Gsk probe. Genomic sequence analysis of ten highly co-expressed differentially regulated genes revealed that two upregulated genes in IL50-7 were derived from O. rufipogon and most of the downregulated genes were either from KMR3 or common to KMR3, IL50-7, and O. rufipogon. Thus, we show that Os11Gsk is a wild rice-derived gene introduced in KMR3 background and increases yield either by regulating expression of functional genes sharing homology with it or by causing epigenetic modifications in the introgression line.
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Affiliation(s)
- Sudhakar Thalapati
- Biotechnology Unit, Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, India
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30
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Gur A, Osorio S, Fridman E, Fernie AR, Zamir D. hi2-1, a QTL which improves harvest index, earliness and alters metabolite accumulation of processing tomatoes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1587-99. [PMID: 20680612 PMCID: PMC2963733 DOI: 10.1007/s00122-010-1412-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 07/17/2010] [Indexed: 05/18/2023]
Abstract
Harvest index, defined as the ratio of reproductive yield to total plant biomass, and early ripening are traits with important agronomic value in processing tomatoes. The Solanum pennellii introgression-line (IL) population shows variation for harvest index and earliness. Most of the QTL mapped for these traits display negative agronomic effects; however, hi2-1 is a unique QTL displaying improved harvest index and earliness. This introgression was tested over several years and under different genetic backgrounds. Thirty-one nearly isogenic sub-lines segregating for the 18 cM TG33-TG276 interval were used for fine mapping of this multi-phenotypic QTL. Based on this analysis the phenotypic effects for plant weight, Brix, total yield and earliness were co-mapped to the same region. In a different mapping experiment these sub-lines were tested as heterozygotes in order to map the harvest index QTL which were only expressed in the heterozygous state. These QTL mapped to the same candidate region, suggesting that hi2-1 is either a single gene with pleiotropic effects or represents linked genes independently affecting these traits. Metabolite profiling of the fruit pericarp revealed that a number of metabolic QTL co-segregate with the harvest index trait including those for important transport assimilates such as sugars and amino acids. Analysis of the flowering pattern of these lines revealed induced flowering at IL2-1 plants, suggest that hi2-1 may also affect harvest index and early ripening by changing plant architecture and flowering rate.
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Affiliation(s)
- Amit Gur
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100 Israel
| | - Sonia Osorio
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Eyal Fridman
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100 Israel
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dani Zamir
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100 Israel
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