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Zemach I, Alseekh S, Tadmor-Levi R, Fisher J, Torgeman S, Trigerman S, Nauen J, Hayut SF, Mann V, Rochsar E, Finkers R, Wendenburg R, Osorio S, Bergmann S, Lunn JE, Semel Y, Hirschberg J, Fernie AR, Zamir D. Multi-year field trials provide a massive repository of trait data on a highly diverse population of tomato and uncover novel determinants of tomato productivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1136-1151. [PMID: 37150955 DOI: 10.1111/tpj.16268] [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: 12/01/2022] [Revised: 04/21/2023] [Accepted: 04/29/2023] [Indexed: 05/09/2023]
Abstract
Tomato (Solanum lycopersicum) is a prominent fruit with rich genetic resources for crop improvement. By using a phenotype-guided screen of over 7900 tomato accessions from around the world, we identified new associations for complex traits such as fruit weight and total soluble solids (Brix). Here, we present the phenotypic data from several years of trials. To illustrate the power of this dataset we use two case studies. First, evaluation of color revealed allelic variation in phytoene synthase 1 that resulted in differently colored or even bicolored fruit. Secondly, in view of the negative relationship between fruit weight and Brix, we pre-selected a subset of the collection that includes high and low Brix values in each category of fruit size. Genome-wide association analysis allowed us to detect novel loci associated with total soluble solid content and fruit weight. In addition, we developed eight F2 biparental intraspecific populations. Furthermore, by taking a phenotype-guided approach we were able to isolate individuals with high Brix values that were not compromised in terms of yield. In addition, the demonstration of novel results despite the high number of previous genome-wide association studies of these traits in tomato suggests that adoption of a phenotype-guided pre-selection of germplasm may represent a useful strategy for finding target genes for breeding.
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Affiliation(s)
- Itay Zemach
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Roni Tadmor-Levi
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Josef Fisher
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Torgeman
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Shay Trigerman
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Nauen
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Shdema Filler Hayut
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Varda Mann
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Edan Rochsar
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Richard Finkers
- Plant Breeding, Wageningen Plant Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sonia Osorio
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora", University of Malaga-Consejo Superior de Investigaciones Cientıficas, Malaga, Spain
| | - Susan Bergmann
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - John E Lunn
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Yaniv Semel
- Phenome Networks, 10 Plaut Street, Science Park, 76706, Rehovot, Israel
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Dani Zamir
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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Ahouvi Y, Haber Z, Zach YY, Rosental L, Toubiana D, Sharma D, Alseekh S, Tajima H, Fernie AR, Brotman Y, Blumwald E, Sade N. The Alteration of Tomato Chloroplast Vesiculation Positively Affects Whole-Plant Source-Sink Relations and Fruit Metabolism under Stress Conditions. PLANT & CELL PHYSIOLOGY 2023; 63:2008-2026. [PMID: 36161338 DOI: 10.1093/pcp/pcac133] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato chloroplast vesiculation (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/CAS9) knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the l-glutamine and l-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
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Affiliation(s)
- Yoav Ahouvi
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Yair Yehoshua Zach
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Leah Rosental
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - David Toubiana
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Saleh Alseekh
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Hiromi Tajima
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
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Wu X, Chen F, Zhao X, Pang C, Shi R, Liu C, Sun C, Zhang W, Wang X, Zhang J. QTL Mapping and GWAS Reveal the Genetic Mechanism Controlling Soluble Solids Content in Brassica napus Shoots. Foods 2021; 10:foods10102400. [PMID: 34681449 PMCID: PMC8535538 DOI: 10.3390/foods10102400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022] Open
Abstract
Oilseed-vegetable-dual-purpose (OVDP) rapeseed can effectively alleviate the land contradiction between crops and it supplements vegetable supplies in winter or spring. The soluble solids content (SSC) is an important index that is used to evaluate the quality and sugar content of fruits and vegetables. However, the genetic architecture underlying the SSC in Brassica napus shoots is still unclear. Here, quantitative trait loci (QTLs) for the SSC in B. napus shoots were investigated by performing linkage mapping using a recombinant inbred line population containing 189 lines. A germplasm set comprising 302 accessions was also used to conduct a genome-wide association study (GWAS). The QTL mapping revealed six QTLs located on chromosomes A01, A04, A08, and A09 in two experiments. Among them, two major QTLs, qSSC/21GY.A04-1 and qSSC/21NJ.A08-1, accounted for 12.92% and 10.18% of the phenotypic variance, respectively. In addition, eight single-nucleotide polymorphisms with phenotypic variances between 5.62% and 10.18% were identified by the GWAS method. However, no locus was simultaneously identified by QTL mapping and GWAS. We identified AH174 (7.55 °Brix and 7.9 °Brix), L166 (8.9 °Brix and 8.38 °Brix), and L380 (8.9 °Brix and 7.74 °Brix) accessions can be used as superior parents. These results provide valuable information that increases our understanding of the genetic control of SSC and will facilitate the breeding of high-SSC B. napus shoots.
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Affiliation(s)
- Xu Wu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (X.W.); (C.L.)
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
| | - Feng Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
| | - Xiaozhen Zhao
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengke Pang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Shi
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Changle Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (X.W.); (C.L.)
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
| | - Chengming Sun
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
| | - Wei Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (F.C.); (X.Z.); (C.P.); (R.S.); (C.S.); (W.Z.)
- Correspondence: (X.W.); (J.Z.)
| | - Jiefu Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (X.W.); (C.L.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (X.W.); (J.Z.)
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Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol 2021; 19:128. [PMID: 34448979 PMCID: PMC8397809 DOI: 10.1186/s43141-021-00231-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/17/2021] [Indexed: 11/28/2022]
Abstract
Background DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. Main body of the abstract In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. Short conclusion MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.
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Affiliation(s)
- Nazarul Hasan
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India.
| | - Sana Choudhary
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Neha Naaz
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Nidhi Sharma
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
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Scossa F, Alseekh S, Fernie AR. Integrating multi-omics data for crop improvement. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153352. [PMID: 33360148 DOI: 10.1016/j.jplph.2020.153352] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178, Rome, Italy.
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut ( Arachis hypogaea L.). Genes (Basel) 2020; 11:genes11121402. [PMID: 33255801 PMCID: PMC7761091 DOI: 10.3390/genes11121402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/24/2023] Open
Abstract
Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and a synthetic wild allotetraploid (Arachis ipaensis × Arachis duranensis)4x. In the AB-QTL population, a major QTL for pod and seed size was detected in a ~5 Mb interval in the proximal region of chromosome A07. In the CSSL population, the line 12CS_091, which carries the QTL region and that produces smaller pods and seeds than Fleur11, was identified. In this study, we used a two-step strategy to fine-map the seed size QTL region on chromosome A07. We developed new SSR and SNP markers, as well as near-isogenic lines (NILs) in the target QTL region. We first located the QTL in ~1 Mb region between two SSR markers, thanks to the genotyping of a large F2 population of 2172 individuals and a single marker analysis approach. We then used nine new SNP markers evenly distributed in the refined QTL region to genotype 490 F3 plants derived from 88 F2, and we selected 10 NILs. The phenotyping of the NILs and marker/trait association allowed us to narrowing down the QTL region to a 168.37 kb chromosome segment, between the SNPs Aradu_A07_1148327 and Aradu_A07_1316694. This region contains 22 predicted genes. Among these genes, Aradu.DN3DB and Aradu.RLZ61, which encode a transcriptional regulator STERILE APETALA-like (SAP) and an F-box SNEEZY (SNE), respectively, were of particular interest. The function of these genes in regulating the variation of fruit and seed size is discussed. This study will contribute to a better knowledge of genes that have been targeted during peanut domestication.
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Roohanitaziani R, de Maagd RA, Lammers M, Molthoff J, Meijer-Dekens F, van Kaauwen MPW, Finkers R, Tikunov Y, Visser RGF, Bovy AG. Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits. Genes (Basel) 2020; 11:genes11111278. [PMID: 33137951 PMCID: PMC7692805 DOI: 10.3390/genes11111278] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/21/2020] [Indexed: 02/04/2023] Open
Abstract
A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement.
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Affiliation(s)
- Raana Roohanitaziani
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
- Graduate School Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ruud A. de Maagd
- Bioscience, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands; (R.A.d.M.); (M.L.)
| | - Michiel Lammers
- Bioscience, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands; (R.A.d.M.); (M.L.)
| | - Jos Molthoff
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Fien Meijer-Dekens
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Martijn P. W. van Kaauwen
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
- Correspondence: ; Tel.: +31-317-480762
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Liu X, Yang W, Wang J, Yang M, Wei K, Liu X, Qiu Z, van Giang T, Wang X, Guo Y, Li J, Liu L, Shu J, Du Y, Huang Z. SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height. Front Genet 2020; 11:881. [PMID: 32849843 PMCID: PMC7427465 DOI: 10.3389/fgene.2020.00881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/17/2020] [Indexed: 11/24/2022] Open
Abstract
Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R2), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL-qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL-qtph1.1 could not be rescued by exogenous GA3 treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL-qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Wencai Yang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Jing Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengxia Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Wei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengkun Qiu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Tong van Giang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoxuan Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanmei Guo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junming Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinshuai Shu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongchen Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zejun Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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9
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Shen X, Zhao R, Liu L, Zhu C, Li M, Du H, Zhang Z. Identification of a candidate gene underlying qKRN5b for kernel row number in Zea mays L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3439-3448. [PMID: 31612262 DOI: 10.1007/s00122-019-03436-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
A quantitative trait locus for kernel row number, qKRN5, was dissected into two tightly linked loci, qKRN5a and qKRN5b. Fine mapping, comparative analysis of nucleotide sequences and gene expression established the endonuclease/exonuclease/phosphatase family protein-encoding gene Zm00001d013603 as a causal gene of qKRN5b. Maize grain yield is determined by agronomically important traits that are controlled by interactions among and between genes and environmental factors. Considerable efforts have been made to identify major quantitative trait loci (QTLs) for yield-related traits; however, few were previously isolated and characterized in maize. In this study, we divided a QTL for kernel row number (KRN), qKRN5, into two tightly linked loci, qKRN5a and qKRN5b, using advanced backcross populations derived from near-isogenic lines. KRN was greater in individuals that were homozygous for the NX531 allele, which showed coupling-phase linkage. The major QTL qKRN5b had an additive effect of approximately one kernel row. Furthermore, fine mapping narrowed qKRN5b within a 147.2-kb region. The upstream sequence Zm00001d013603 and its expression in the ear inflorescence showed obvious differences between qKRN5b near-isogenic lines. In situ hybridization located Zm00001d013603 on the primordia of the spikelet pair meristems and spikelet meristems, but not in the inflorescence meristem, which indicates a role in regulating the initiation of reproductive axillary meristems of ear inflorescences. Expression analysis and nucleotide sequence alignment revealed that Zm00001d013603, which encodes an endonuclease/exonuclease/phosphatase family protein that hydrolyzes phosphatidyl inositol diphosphates, is the causal gene of qKRN5b. These results provide insight into the genetic basis of KRN and have potential value for enhancing maize grain yield.
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Affiliation(s)
- Xiaomeng Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Ran Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Can Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Manfei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Hewei Du
- Hubei Collaborative Innovation Center for Grain Crops, Yangtze University, Jingzhou, 434025, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China.
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10
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Zhang D, Wang X, Li S, Wang C, Gosney MJ, Mickelbart MV, Ma J. A Post-domestication Mutation, Dt2, Triggers Systemic Modification of Divergent and Convergent Pathways Modulating Multiple Agronomic Traits in Soybean. MOLECULAR PLANT 2019; 12:1366-1382. [PMID: 31152912 DOI: 10.1016/j.molp.2019.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/28/2019] [Accepted: 05/19/2019] [Indexed: 05/28/2023]
Abstract
The semi-determinate stem growth habit in leguminous crops, similar to the "green revolution" semi-dwarf trait in cereals, is a key plant architecture trait that affects several other traits determining grain yield. In soybean semi-determinacy is modulated by a post-domestication gain-of-function mutation in the gene, Dt2, which encodes an MADS-box transcription factor. However, its role in systemic modification of stem growth and other traits is unknown. In this study, we show that Dt2 functions not only as a direct repressor of Dt1, which prevents terminal flowering, but also as a direct activator of putative floral integrator/identity genes including GmSOC1, GmAP1, and GmFUL, which likely promote flowering. We also demonstrate that Dt2 functions as a direct repressor of the putative drought-responsive transcription factor gene GmDREB1D, and as a direct activator of GmSPCH and GmGRP7, which are potentially associated with asymmetric division of young epidermal cells and stomatal opening, respectively, and may affect the plant's water-use efficiency (WUE). Intriguingly, Dt2 was found to be a direct activator or repressor of the precursors of eight microRNAs targeting genes potentially associated with meristem maintenance, flowering time, stomatal density, WUE, and/or stress responses. This study thus reveals the molecular basis of pleiotropy associated with plant productivity, adaptability, and environmental resilience.
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Affiliation(s)
- Dajian Zhang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA; College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Shuo Li
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA; School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Chaofan Wang
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Michael J Gosney
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Michael V Mickelbart
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA; Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
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11
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Varkonyi‐Gasic E, Wang T, Voogd C, Jeon S, Drummond RSM, Gleave AP, Allan AC. Mutagenesis of kiwifruit CENTRORADIALIS-like genes transforms a climbing woody perennial with long juvenility and axillary flowering into a compact plant with rapid terminal flowering. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:869-880. [PMID: 30302894 PMCID: PMC6587708 DOI: 10.1111/pbi.13021] [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: 03/17/2018] [Revised: 09/27/2018] [Accepted: 10/07/2018] [Indexed: 05/08/2023]
Abstract
Annualization of woody perennials has the potential to revolutionize the breeding and production of fruit crops and rapidly improve horticultural species. Kiwifruit (Actinidia chinensis) is a recently domesticated fruit crop with a short history of breeding and tremendous potential for improvement. Previously, multiple kiwifruit CENTRORADIALIS (CEN)-like genes have been identified as potential repressors of flowering. In this study, CRISPR/Cas9- mediated manipulation enabled functional analysis of kiwifruit CEN-like genes AcCEN4 and AcCEN. Mutation of these genes transformed a climbing woody perennial, which develops axillary inflorescences after many years of juvenility, into a compact plant with rapid terminal flower and fruit development. The number of affected genes and alleles and severity of detected mutations correlated with the precocity and change in plant stature, suggesting that a bi-allelic mutation of either AcCEN4 or AcCEN may be sufficient for early flowering, whereas mutations affecting both genes further contributed to precocity and enhanced the compact growth habit. CRISPR/Cas9-mediated mutagenesis of AcCEN4 and AcCEN may be a valuable means to engineer Actinidia amenable for accelerated breeding, indoor farming and cultivation as an annual crop.
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Affiliation(s)
- Erika Varkonyi‐Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
| | - Subin Jeon
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
| | - Revel S. M. Drummond
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
| | - Andrew P. Gleave
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research)AucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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12
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Rebah F, Ouhibi C, Alamer KH, Msilini N, Nasri MB, Stevens R, Attia H. Comparison of the responses to NaCl stress of three tomato introgression lines. ACTA BIOLOGICA HUNGARICA 2018; 69:464-480. [PMID: 30587018 DOI: 10.1556/018.69.2018.4.8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We aimed to examine the response of three tomato introgression lines (IL925.3, IL925.5 and IL925.6) to NaCl stress. These lines originated from a cross between M82 (Solanum lycopersicum) and the wild salttolerant tomato Solanum pennellii, each line containing a different fragment of the S.pennellii genome. Salt-sensitive phenotypes related to plant growth and physiology, and the response of antioxidants, pigments and antioxidant enzymes were measured. In general, salt stress decreased the fresh weight of leaves, leaf area and leaf number and an increase of Na+ accumulation in aerial parts was observed, which caused a reduction in the absorption of K+ and Ca2+. Salt stress also induced a decrease in chlorophyll, carotenoids and lipid peroxidation (MDA) and an increase in anthocyanins and reduced ascorbate, although some differences were seen between the lines, for example for carotenoid levels. Guaiacol peroxidase, catalase and glutathione reductase activity enhanced in aerial parts of the lines, but again some differences were seen between the three lines. It is concluded that IL925.5 might be the most sensitive line to salt stress as its dry weight loss was the greatest in response to salt and this line showed the highest Na+ ion accumulation in leaves.
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Affiliation(s)
- Fedia Rebah
- Unité de Physiologie et Biochimie de la Réponse des Plantes aux Contraintes Abiotiques, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, 1068 Tunis, Tunisie
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Chayma Ouhibi
- Unité de Physiologie et Biochimie de la Réponse des Plantes aux Contraintes Abiotiques, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, 1068 Tunis, Tunisie
| | - K. H. Alamer
- Biology Department, Faculty of Science, Taif University, Kingdom of Saudi Arabia
| | - Najoua Msilini
- Unité de Physiologie et Biochimie de la Réponse des Plantes aux Contraintes Abiotiques, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, 1068 Tunis, Tunisie
| | - Mouhiba Ben Nasri
- Unité de Physiologie et Biochimie de la Réponse des Plantes aux Contraintes Abiotiques, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, 1068 Tunis, Tunisie
| | - Rebecca Stevens
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Houneida Attia
- Unité de Physiologie et Biochimie de la Réponse des Plantes aux Contraintes Abiotiques, Département de Biologie, Faculté des Sciences de Tunis, Université Tunis El Manar, 1068 Tunis, Tunisie
- Biology Department, Faculty of Science, Taif University, Kingdom of Saudi Arabia
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13
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Sagor GHM, Berberich T, Tanaka S, Nishiyama M, Kanayama Y, Kojima S, Muramoto K, Kusano T. A novel strategy to produce sweeter tomato fruits with high sugar contents by fruit-specific expression of a single bZIP transcription factor gene. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1116-26. [PMID: 26402509 DOI: 10.1111/pbi.12480] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/27/2015] [Accepted: 08/26/2015] [Indexed: 05/19/2023]
Abstract
Enhancement of sugar content and sweetness is desirable in some vegetables and in almost all fruits; however, biotechnological methods to increase sugar content are limited. Here, a completely novel methodological approach is presented that produces sweeter tomato fruits but does not have any negative effects on plant growth. Sucrose-induced repression of translation (SIRT), which is mediated by upstream open reading frames (uORFs), was initially reported in Arabidopsis AtbZIP11, a class S basic region leucine zipper (bZIP) transcription factor gene. Here, two AtbZIP11 orthologous genes, SlbZIP1 and SlbZIP2, were identified in tomato (Solanum lycopersicum). SlbZIP1 and SlbZIP2 contained four and three uORFs, respectively, in the cDNA 5'-leader regions. The second uORFs from the 5' cDNA end were conserved and involved in SIRT. Tomato plants were transformed with binary vectors in which only the main open reading frames (ORFs) of SlbZIP1 and SlbZIP2, without the SIRT-responsive uORFs, were placed under the control of the fruit-specific E8 promoter. Growth and morphology of the resulting transgenic tomato plants were comparable to those of wild-type plants. Transgenic fruits were approximately 1.5-fold higher in sugar content (sucrose/glucose/fructose) than nontransgenic tomato fruits. In addition, the levels of several amino acids, such as asparagine and glutamine, were higher in transgenic fruits than in wild-type fruits. This was expected because SlbZIP transactivates the asparagine synthase and proline dehydrogenase genes. This 'sweetening' technology is broadly applicable to other plants that utilize sucrose as a major translocation sugar.
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Affiliation(s)
- G H M Sagor
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Thomas Berberich
- Laboratory Center, Biodiversity and Climate Research Center, Frankfurt am Main, Germany
| | - Shun Tanaka
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Manabu Nishiyama
- Graduate School of Agricultural Science, Tohoku University, Aoba, Sendai, Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, Aoba, Sendai, Japan
| | - Seiji Kojima
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Koji Muramoto
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
| | - Tomonobu Kusano
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan
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14
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Ballester AR, Tikunov Y, Molthoff J, Grandillo S, Viquez-Zamora M, de Vos R, de Maagd RA, van Heusden S, Bovy AG. Identification of Loci Affecting Accumulation of Secondary Metabolites in Tomato Fruit of a Solanum lycopersicum × Solanum chmielewskii Introgression Line Population. FRONTIERS IN PLANT SCIENCE 2016; 7:1428. [PMID: 27733856 PMCID: PMC5040107 DOI: 10.3389/fpls.2016.01428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/07/2016] [Indexed: 05/21/2023]
Abstract
Semi-polar metabolites such as flavonoids, phenolic acids, and alkaloids are very important health-related compounds in tomato. As a first step to identify genes responsible for the synthesis of semi-polar metabolites, quantitative trait loci (QTLs) that influence the semi-polar metabolite content in red-ripe tomato fruit were identified, by characterizing fruits of a population of introgression lines (ILs) derived from a cross between the cultivated tomato Solanum lycopersicum and the wild species Solanum chmielewskii. By analyzing fruits of plants grown at two different locations, we were able to identify robust metabolite QTLs for changes in phenylpropanoid glycoconjugation on chromosome 9, for accumulation of flavonol glycosides on chromosome 5, and for alkaloids on chromosome 7. To further characterize the QTLs we used a combination of genome sequencing, transcriptomics and targeted metabolomics to identify candidate key genes underlying the observed metabolic variation.
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Affiliation(s)
| | - Yury Tikunov
- Wageningen University and Research CentreWageningen, Netherlands
| | - Jos Molthoff
- Wageningen University and Research CentreWageningen, Netherlands
| | - Silvana Grandillo
- Institute of Biosciences and Bioresources, National Research Council of ItalyPortici, Italy
| | | | - Ric de Vos
- Wageningen University and Research CentreWageningen, Netherlands
| | - Ruud A. de Maagd
- Wageningen University and Research CentreWageningen, Netherlands
| | | | - Arnaud G. Bovy
- Wageningen University and Research CentreWageningen, Netherlands
- Centre for Biosystems GenomicsWageningen, Netherlands
- *Correspondence: Arnaud G. Bovy,
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15
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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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16
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Liu Y, Zhang D, Ping J, Li S, Chen Z, Ma J. Innovation of a Regulatory Mechanism Modulating Semi-determinate Stem Growth through Artificial Selection in Soybean. PLoS Genet 2016; 12:e1005818. [PMID: 26807727 PMCID: PMC4726468 DOI: 10.1371/journal.pgen.1005818] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/28/2015] [Indexed: 11/27/2022] Open
Abstract
It has been demonstrated that Terminal Flowering 1 (TFL1) in Arabidopsis and its functional orthologs in other plants specify indeterminate stem growth through their specific expression that represses floral identity genes in shoot apical meristems (SAMs), and that the loss-of-function mutations at these functional counterparts result in the transition of SAMs from the vegetative to reproductive state that is essential for initiation of terminal flowering and thus formation of determinate stems. However, little is known regarding how semi-determinate stems, which produce terminal racemes similar to those observed in determinate plants, are specified in any flowering plants. Here we show that semi-determinacy in soybean is modulated by transcriptional repression of Dt1, the functional ortholog of TFL1, in SAMs. Such repression is fulfilled by recently enabled spatiotemporal expression of Dt2, an ancestral form of the APETALA1/FRUITFULL orthologs, which encodes a MADS-box factor directly binding to the regulatory sequence of Dt1. In addition, Dt2 triggers co-expression of the putative SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (GmSOC1) in SAMs, where GmSOC1 interacts with Dt2, and also directly binds to the Dt1 regulatory sequence. Heterologous expression of Dt2 and Dt1 in determinate (tfl1) Arabidopsis mutants enables creation of semi-determinacy, but the same forms of the two genes in the tfl1 and soc1 background produce indeterminate stems, suggesting that Dt2 and SOC1 both are essential for transcriptional repression of Dt1. Nevertheless, the expression of Dt2 is unable to repress TFL1 in Arabidopsis, further demonstrating the evolutionary novelty of the regulatory mechanism underlying stem growth in soybean.
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Affiliation(s)
- Yunfeng Liu
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Dajian Zhang
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Jieqing Ping
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Shuai Li
- College of Life Sciences, Qingdao Agricultural University, Qiangdao, Shandong, China
| | - Zhixiang Chen
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
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17
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Vicente MH, Zsögön A, de Sá AFL, Ribeiro RV, Peres LEP. Semi-determinate growth habit adjusts the vegetative-to-reproductive balance and increases productivity and water-use efficiency in tomato (Solanum lycopersicum). JOURNAL OF PLANT PHYSIOLOGY 2015; 177:11-19. [PMID: 25659332 DOI: 10.1016/j.jplph.2015.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/04/2015] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Tomato (Solanum lycopersicum) shows three growth habits: determinate, indeterminate and semi-determinate. These are controlled mainly by allelic variation in the self-pruning (SP) gene family, which also includes the "florigen" gene single flower TRUSS (SFT). Determinate cultivars have synchronized flower and fruit production, which allows mechanical harvesting in the tomato processing industry, whereas indeterminate ones have more vegetative growth with continuous flower and fruit formation, being thus preferred for fresh market tomato production. The semi-determinate growth habit is poorly understood, although there are indications that it combines advantages of determinate and indeterminate growth. Here, we used near-isogenic lines (NILs) in the cultivar Micro-Tom (MT) with different growth habit to characterize semi-determinate growth and to determine its impact on developmental and productivity traits. We show that semi-determinate genotypes are equivalent to determinate ones with extended vegetative growth, which in turn impacts shoot height, number of leaves and either stem diameter or internode length. Semi-determinate plants also tend to increase the highly relevant agronomic parameter Brix × ripe yield (BRY). Water-use efficiency (WUE), evaluated either directly as dry mass produced per amount of water transpired or indirectly through C isotope discrimination, was higher in semi-determinate genotypes. We also provide evidence that the increases in BRY in semi-determinate genotypes are a consequence of an improved balance between vegetative and reproductive growth, a mechanism analogous to the conversion of the overly vegetative tall cereal varieties into well-balanced semi-dwarf ones used in the Green Revolution.
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Affiliation(s)
- Mateus Henrique Vicente
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11, CP 09, 13418-900 Piracicaba, SP, Brazil
| | - Agustin Zsögön
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11, CP 09, 13418-900 Piracicaba, SP, Brazil
| | - Ariadne Felicio Lopo de Sá
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11, CP 09, 13418-900 Piracicaba, SP, Brazil
| | - Rafael V Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), R. Monteiro Lobato, 255, 13083-862, Campinas, SP, Brazil
| | - Lázaro E P Peres
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11, CP 09, 13418-900 Piracicaba, SP, Brazil.
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18
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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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Haggard JE, Johnson EB, St Clair DA. Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11. G3 (BETHESDA, MD.) 2014; 5:219-33. [PMID: 25504736 PMCID: PMC4321030 DOI: 10.1534/g3.114.014654] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/06/2014] [Indexed: 11/18/2022]
Abstract
Previously, a Phytophthora infestans resistance QTL from Solanum habrochaites chromosome 11 was introgressed into cultivated tomato (S. lycopersicum). Fine mapping of this resistance QTL using near-isogenic lines (NILs) revealed some co-located QTL with undesirable effects on plant size, canopy density, and fruit size traits. Subsequently, higher-resolution mapping with sub-NILs detected multiple P. infestans resistance QTL within this 9.4-cM region of chromosome 11. In our present study, these same sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over 2 years. The horticultural trait QTL originally detected by fine mapping each fractionated into two or more QTL at higher resolution. A total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL × environment interactions (QTL × E). QTL for many traits were co-located, suggesting either pleiotropic effects or tight linkage among genes controlling these traits. Recombination in the pericentromeric region of the introgression between markers TG147 and At4g10050 was suppressed to approximately 29.7 Mbp per cM, relative to the genomewide average of 750 kbp per cM. The genetic architecture of many of the horticultural and P. infestans resistance traits that mapped within this chromosome 11 S. habrochaites region is complex. Complicating factors included fractionation of QTL, pleiotropy or tight linkage of QTL for multiple traits, pericentromeric chromosomal location(s), and/or QTL × E. High-resolution mapping of QTL in this region would be needed to determine which specific target QTL could be useful in breeding cultivated tomato.
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Affiliation(s)
- J Erron Haggard
- Plant Sciences Department, University of California-Davis, Davis, California 95616
| | - Emily B Johnson
- Plant Sciences Department, University of California-Davis, Davis, California 95616
| | - Dina A St Clair
- Plant Sciences Department, University of California-Davis, Davis, California 95616
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Osorio S, Ruan YL, Fernie AR. An update on source-to-sink carbon partitioning in tomato. FRONTIERS IN PLANT SCIENCE 2014; 5:516. [PMID: 25339963 PMCID: PMC4186278 DOI: 10.3389/fpls.2014.00516] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/14/2014] [Indexed: 05/18/2023]
Abstract
Plant growth and carbon metabolism are closely associated since carbohydrate in the form of sucrose generated by photosynthesis, provides the primary source of building blocks and energy for the production and maintenance of biomass. Regulation of carbon partitioning between source and sink tissues is important because it has a vast influence on both plant growth and development. The regulation of carbon partitioning at the whole plant level is directly linked to the cellular pathways of assimilate transport and the metabolism and allocation of sugars, mainly sucrose and hexoses in source leaves, and sink organs such as roots and fruit. By using tomato plant as a model, this review documents and discusses our current understanding of source-sink interactions from molecular to physiological perspectives focusing on those that regulate the growth and development of both vegetative and reproductive organs. It furthermore discusses the impact that environmental conditions play in maintenance of this balance in an attempt to address the link between physiological and ecological aspects of growth.
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Affiliation(s)
- Sonia Osorio
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Department of Molecular Biology and Biochemistry, University of Malaga – Consejo Superior de InvestigacionesCientíficas, Málaga, Spain
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Yong-Ling Ruan
- Australia–China Research Centre for Crop Improvement, The University of NewcastleCallaghan, NSW, Australia
- School of Environmental and Life Sciences, The University of NewcastleCallaghan, NSW, Australia
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
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Díaz A, Zarouri B, Fergany M, Eduardo I, Álvarez JM, Picó B, Monforte AJ. Mapping and introgression of QTL involved in fruit shape transgressive segregation into ‘piel de sapo’ melon (cucumis melo l.) [corrected]. PLoS One 2014; 9:e104188. [PMID: 25126852 PMCID: PMC4134209 DOI: 10.1371/journal.pone.0104188] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 07/10/2014] [Indexed: 11/19/2022] Open
Abstract
A mapping F2 population from the cross ‘Piel de Sapo’ × PI124112 was selectively genotyped to study the genetic control of morphological fruit traits by QTL (Quantitative Trait Loci) analysis. Ten QTL were identified, five for FL (Fruit Length), two for FD (Fruit Diameter) and three for FS (Fruit Shape). At least one robust QTL per character was found, flqs8.1 (LOD = 16.85, R2 = 34%), fdqs12.1 (LOD = 3.47, R2 = 11%) and fsqs8.1 (LOD = 14.85, R2 = 41%). flqs2.1 and fsqs2.1 cosegregate with gene a (andromonoecious), responsible for flower sex determination and with pleiotropic effects on FS. They display a positive additive effect (a) value, so the PI124112 allele causes an increase in FL and FS, producing more elongated fruits. Conversely, the negative a value for flqs8.1 and fsqs8.1 indicates a decrease in FL and FS, what results in rounder fruits, even if PI124112 produces very elongated melons. This is explained by a significant epistatic interaction between fsqs2.1 and fsqs8.1, where the effects of the alleles at locus a are attenuated by the additive PI124112 allele at fsqs8.1. Roundest fruits are produced by homozygous for PI124112 at fsqs8.1 that do not carry any dominant A allele at locus a (PiPiaa). A significant interaction between fsqs8.1 and fsqs12.1 was also detected, with the alleles at fsqs12.1 producing more elongated fruits. fsqs8.1 seems to be allelic to QTL discovered in other populations where the exotic alleles produce elongated fruits. This model has been validated in assays with backcross lines along 3 years and ultimately obtaining a fsqs8.1-NIL (Near Isogenic Line) in ‘Piel de Sapo’ background which yields round melons.
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Affiliation(s)
- Aurora Díaz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- * E-mail: (AD); (AJM)
| | - Belkacem Zarouri
- Laboratorio de Biología Molecular. Dpto. Investigación Agroalimentaria. Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcalá de Henares, Madrid, Spain
| | - Mohamed Fergany
- Centre de Recerca en Agrigenòmica (CRAG), IRTA-CSIC-UAB, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), IRTA-CSIC-UAB, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
| | - José M. Álvarez
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
| | - Belén Picó
- COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitad Politécnica de Valencia, Valencia, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- * E-mail: (AD); (AJM)
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Ping J, Liu Y, Sun L, Zhao M, Li Y, She M, Sui Y, Lin F, Liu X, Tang Z, Nguyen H, Tian Z, Qiu L, Nelson RL, Clemente TE, Specht JE, Ma J. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. THE PLANT CELL 2014; 26:2831-42. [PMID: 25005919 PMCID: PMC4145117 DOI: 10.1105/tpc.114.126938] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/03/2012] [Accepted: 06/18/2014] [Indexed: 05/20/2023]
Abstract
Similar to Arabidopsis thaliana, the wild soybeans (Glycine soja) and many cultivars exhibit indeterminate stem growth specified by the shoot identity gene Dt1, the functional counterpart of Arabidopsis TERMINAL FLOWER1 (TFL1). Mutations in TFL1 and Dt1 both result in the shoot apical meristem (SAM) switching from vegetative to reproductive state to initiate terminal flowering and thus produce determinate stems. A second soybean gene (Dt2) regulating stem growth was identified, which, in the presence of Dt1, produces semideterminate plants with terminal racemes similar to those observed in determinate plants. Here, we report positional cloning and characterization of Dt2, a dominant MADS domain factor gene classified into the APETALA1/SQUAMOSA (AP1/SQUA) subfamily that includes floral meristem (FM) identity genes AP1, FUL, and CAL in Arabidopsis. Unlike AP1, whose expression is limited to FMs in which the expression of TFL1 is repressed, Dt2 appears to repress the expression of Dt1 in the SAMs to promote early conversion of the SAMs into reproductive inflorescences. Given that Dt2 is not the gene most closely related to AP1 and that semideterminacy is rarely seen in wild soybeans, Dt2 appears to be a recent gain-of-function mutation, which has modified the genetic pathways determining the stem growth habit in soybean.
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Affiliation(s)
- Jieqing Ping
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Yunfeng Liu
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Lianjun Sun
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Yinghui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maoyun She
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Yi Sui
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Feng Lin
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Xiaodong Liu
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Zongxiang Tang
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Hanh Nguyen
- Department of Agronomy and Horticulture/Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68583
| | - Zhixi Tian
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Randall L Nelson
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Thomas E Clemente
- Department of Agronomy and Horticulture/Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68583
| | - James E Specht
- Department of Agronomy and Horticulture/Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68583
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
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Shatalina M, Messmer M, Feuillet C, Mascher F, Paux E, Choulet F, Wicker T, Keller B. High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:573-586. [PMID: 24306318 DOI: 10.1007/s00122-013-2240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/19/2013] [Indexed: 06/02/2023]
Abstract
Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars 'Arina' and 'Forno', the physical map of chromosome 3B of cultivar 'Chinese Spring' and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs.
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Affiliation(s)
- Margarita Shatalina
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites. G3-GENES GENOMES GENETICS 2013; 3:2131-46. [PMID: 24122052 PMCID: PMC3852376 DOI: 10.1534/g3.113.007195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ∼30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.
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de Bossoreille de Ribou S, Douam F, Hamant O, Frohlich MW, Negrutiu I. Plant science and agricultural productivity: why are we hitting the yield ceiling? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:159-76. [PMID: 23849123 DOI: 10.1016/j.plantsci.2013.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/26/2013] [Accepted: 05/16/2013] [Indexed: 05/11/2023]
Abstract
Trends in conventional plant breeding and in biotechnology research are analyzed with a focus on production and productivity of individual organisms. Our growing understanding of the productive/adaptive potential of (crop) plants is a prerequisite to increasing this potential and also its expression under environmental constraints. This review concentrates on growth rate, ribosome activity, and photosynthetic rate to link these key cellular processes to plant productivity. Examples of how they may be integrated in heterosis, organ growth control, and responses to abiotic stresses are presented. The yield components in rice are presented as a model. The ultimate goal of research programs, that concentrate on yield and productivity and integrating the panoply of systems biology tools, is to achieve "low input, high output" agriculture, i.e. shifting from a conventional "productivist" agriculture to an efficient sustainable agriculture. This is of critical, strategic importance, because the extent to which we, both locally and globally, secure and manage the long-term productive potential of plant resources will determine the future of humanity.
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26
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Liu R, Jia H, Cao X, Huang J, Li F, Tao Y, Qiu F, Zheng Y, Zhang Z. Fine mapping and candidate gene prediction of a pleiotropic quantitative trait locus for yield-related trait in Zea mays. PLoS One 2012. [PMID: 23185451 PMCID: PMC3504098 DOI: 10.1371/journal.pone.0049836] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The yield of maize grain is a highly complex quantitative trait that is controlled by multiple quantitative trait loci (QTLs) with small effects, and is frequently influenced by multiple genetic and environmental factors. Thus, it is challenging to clone a QTL for grain yield in the maize genome. Previously, we identified a major QTL, qKNPR6, for kernel number per row (KNPR) across multiple environments, and developed two nearly isogenic lines, SL57-6 and Ye478, which differ only in the allelic constitution at the short segment harboring the QTL. Recently, qKNPR6 was re-evaluated in segregating populations derived from SL57-6×Ye478, and was narrowed down to a 2.8 cM interval, which explained 56.3% of the phenotypic variance of KNPR in 201 F2∶3 families. The QTL simultaneously affected ear length, kernel weight and grain yield. Furthermore, a large F2 population with more than 12,800 plants, 191 recombinant chromosomes and 10 overlapping recombinant lines placed qKNPR6 into a 0.91 cM interval corresponding to 198Kb of the B73 reference genome. In this region, six genes with expressed sequence tag (EST) evidence were annotated. The expression pattern and DNA diversity of the six genes were assayed in Ye478 and SL57-6. The possible candidate gene and the pathway involved in inflorescence development were discussed.
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Affiliation(s)
- Ruixiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Haitao Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoliang Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jun Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Feng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongsheng Tao
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yonglian Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Tang Z, Xiao J, Hu W, Yu B, Xu C. Bin-based model construction and analytical strategies for dissecting complex traits with chromosome segment substitution lines. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5195-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Carrera J, Fernández del Carmen A, Fernández-Muñoz R, Rambla JL, Pons C, Jaramillo A, Elena SF, Granell A. Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Comput Biol 2012; 8:e1002528. [PMID: 22685389 PMCID: PMC3369923 DOI: 10.1371/journal.pcbi.1002528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/06/2012] [Indexed: 11/18/2022] Open
Abstract
Considering cells as biofactories, we aimed to optimize its internal processes by using the same engineering principles that large industries are implementing nowadays: lean manufacturing. We have applied reverse engineering computational methods to transcriptomic, metabolomic and phenomic data obtained from a collection of tomato recombinant inbreed lines to formulate a kinetic and constraint-based model that efficiently describes the cellular metabolism from expression of a minimal core of genes. Based on predicted metabolic profiles, a close association with agronomic and organoleptic properties of the ripe fruit was revealed with high statistical confidence. Inspired in a synthetic biology approach, the model was used for exploring the landscape of all possible local transcriptional changes with the aim of engineering tomato fruits with fine-tuned biotechnological properties. The method was validated by the ability of the proposed genomes, engineered for modified desired agronomic traits, to recapitulate experimental correlations between associated metabolites.
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Affiliation(s)
- Javier Carrera
- Instituto de Biologa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, Valencia, Spain
- Synth-Bio Group, Institute of Systems and Synthetic Biology, Universite d'Evry Val d'Essonne - Genopole - CNRS UPS3201, Evry, France
- * E-mail: (JC); (AG)
| | - Asun Fernández del Carmen
- Instituto de Biologa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, Valencia, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” (IHSM-UMA-CSIC), Algarrobo-Costa, Malaga, Spain
| | - Jose Luis Rambla
- Instituto de Biologa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, Valencia, Spain
| | - Clara Pons
- Instituto de Biologa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, Valencia, Spain
| | - Alfonso Jaramillo
- Synth-Bio Group, Institute of Systems and Synthetic Biology, Universite d'Evry Val d'Essonne - Genopole - CNRS UPS3201, Evry, France
| | - Santiago F. Elena
- Instituto de Biologa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, Valencia, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Antonio Granell
- Instituto de Biologa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, Valencia, Spain
- * E-mail: (JC); (AG)
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Steinhauser MC, Steinhauser D, Gibon Y, Bolger M, Arrivault S, Usadel B, Zamir D, Fernie AR, Stitt M. Identification of enzyme activity quantitative trait loci in a Solanum lycopersicum x Solanum pennellii introgression line population. PLANT PHYSIOLOGY 2011; 157:998-1014. [PMID: 21890649 PMCID: PMC3252166 DOI: 10.1104/pp.111.181594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/27/2011] [Indexed: 05/03/2023]
Abstract
Activities of 28 enzymes from central carbon metabolism were measured in pericarp tissue of ripe tomato fruits from field trials with an introgression line (IL) population generated by introgressing segments of the genome of the wild relative Solanum pennellii (LA0716) into the modern tomato cultivar Solanum lycopersicum M82. Enzyme activities were determined using a robotized platform in optimized conditions, where the activities largely reflect the level of the corresponding proteins. Two experiments were analyzed from years with markedly different climate conditions. A total of 27 quantitative trait loci were shared in both experiments. Most resulted in increased enzyme activity when a portion of the S. lycopersicum genome was substituted with the corresponding portion of the genome of S. pennellii. This reflects the change in activity between the two parental genotypes. The mode of inheritance was studied in a heterozygote IL population. A similar proportion of quantitative trait loci (approximately 30%) showed additive, recessive, and dominant modes of inheritance, with only 5% showing overdominance. Comparison with the location of putative genes for the corresponding proteins indicates a large role of trans-regulatory mechanisms. These results point to the genetic control of individual enzyme activities being under the control of a complex program that is dominated by a network of trans-acting genes.
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Cherel P, Pires J, Glénisson J, Milan D, Iannuccelli N, Hérault F, Damon M, Le Roy P. Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs. BMC Genet 2011; 12:76. [PMID: 21875434 PMCID: PMC3175459 DOI: 10.1186/1471-2156-12-76] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 08/29/2011] [Indexed: 11/10/2022] Open
Abstract
Background Detection of quantitative trait loci (QTLs) affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effects. We report on a microsatellite-based QTL detection scan including all autosomes for pig meat quality and carcass composition traits in an F2 population of 1,000 females and barrows resulting from an intercross between a Pietrain and a Large White-Hampshire-Duroc synthetic sire line. Our QTL detection design allowed side-by-side comparison of the RYR1 and PRKAG3 mutation effects seen as QTLs when segregating at low frequencies (0.03-0.08), with independent QTL effects detected from most of the same population, excluding any carrier of these mutations. Results Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait. Conclusions Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the influence of major-effect mutations on the least affected traits, but is one order of magnitude lower than effect on variance of traits primarily affected by these causative mutations. This suggests that uncovering physiological traits directly affected by genetic polymorphisms would be an appropriate approach for further characterization of QTLs.
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Affiliation(s)
- Pierre Cherel
- INRA, UMR0598, Génétique Animale, 35042 Rennes cedex, France
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Genomic resources in horticultural crops: Status, utility and challenges. Biotechnol Adv 2011; 29:199-209. [DOI: 10.1016/j.biotechadv.2010.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 09/04/2010] [Accepted: 09/26/2010] [Indexed: 01/02/2023]
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JIA JZ, TIAN LP, XUE L, WEI YN. Dynamic QTL and correlated characters of tomato soluble solid content. YI CHUAN = HEREDITAS 2011; 32:1077-83. [DOI: 10.3724/sp.j.1005.2010.01077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G. Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 2010; 11:656. [PMID: 21106060 PMCID: PMC3091774 DOI: 10.1186/1471-2164-11-656] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/24/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics. RESULTS In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene. CONCLUSIONS The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.
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Affiliation(s)
- Jianjun Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Qiang Zhao
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Peina Du
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Baohe Wang
- Lixiahe Region Agricultural Research Institute of Jiangsu, 225007, Yangzhou, PR China
| | - Qi Feng
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
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Do PT, Prudent M, Sulpice R, Causse M, Fernie AR. The influence of fruit load on the tomato pericarp metabolome in a Solanum chmielewskii introgression line population. PLANT PHYSIOLOGY 2010; 154:1128-42. [PMID: 20841452 PMCID: PMC2971594 DOI: 10.1104/pp.110.163030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 09/13/2010] [Indexed: 05/19/2023]
Abstract
It has been recently demonstrated, utilizing interspecific introgression lines of tomato, generated from the cross between Solanum lycopersicum and the wild species Solanum pennellii, that the efficiency of photosynthate partitioning exerts a considerable influence on the metabolic composition of tomato fruit pericarp. In order to further evaluate the influence of source-sink interaction, metabolite composition was determined by gas chromatography-mass spectrometry in a different population. For this purpose, we used 23 introgression lines resulting from an interspecific cross between S. lycopersicum and the wild species Solanum chmielewskii under high (unpruned trusses) and low (trusses pruned to one fruit) fruit load conditions. Following this strategy, we were able to contrast the metabolite composition of fruits from plants cultivated at both fruit loads as well as to compare the network behavior of primary metabolism in the introgression line population. The study revealed that while a greater number of metabolic quantitative trait loci were observed under high fruit load (240) than under low fruit load (128) cultivations, the levels of metabolites were more highly correlated under low fruit load cultivation. Finally, an analysis of genotype × fruit load interactions indicated a greater influence of development and cultivation than genotype on fruit composition. Comparison with previously documented transcript profiles from a subset of these lines revealed that changes in metabolite levels did not correlate with changes in the levels of genes associated with their metabolism. These findings are discussed in the context of our current understanding of the genetic and environmental influence on metabolic source-sink interactions in tomato, with particular emphasis given to fruit amino acid content.
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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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Zanor MI, Osorio S, Nunes-Nesi A, Carrari F, Lohse M, Usadel B, Kühn C, Bleiss W, Giavalisco P, Willmitzer L, Sulpice R, Zhou YH, Fernie AR. RNA interference of LIN5 in tomato confirms its role in controlling Brix content, uncovers the influence of sugars on the levels of fruit hormones, and demonstrates the importance of sucrose cleavage for normal fruit development and fertility. PLANT PHYSIOLOGY 2009; 150:1204-18. [PMID: 19439574 PMCID: PMC2705052 DOI: 10.1104/pp.109.136598] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 05/09/2009] [Indexed: 05/18/2023]
Abstract
It has been previously demonstrated, utilizing intraspecific introgression lines, that Lycopersicum Invertase5 (LIN5), which encodes a cell wall invertase, controls total soluble solids content in tomato (Solanum lycopersicum). The physiological role of this protein, however, has not yet been directly studied, since evaluation of data obtained from the introgression lines is complicated by the fact that they additionally harbor many other wild species alleles. To allow a more precise comparison, we generated transgenic tomato in which we silenced the expression of LIN5 using the RNA interference approach. The transformants were characterized by an altered flower and fruit morphology, displaying increased numbers of petals and sepals per flower, an increased rate of fruit abortion, and a reduction in fruit size. Evaluation of the mature fruit revealed that the transformants were characterized by a reduction of seed number per plant. Furthermore, detailed physiological analysis revealed that the transformants displayed aberrant pollen morphology and a reduction in the rate of pollen tube elongation. Metabolite profiling of ovaries and green and red fruit revealed that metabolic changes in the transformants were largely confined to sugar metabolism, whereas transcript and hormone profiling revealed broad changes both in the hormones themselves and in transcripts encoding their biosynthetic enzymes and response elements. These results are discussed in the context of current understanding of the role of sugar during the development of tomato fruit, with particular focus given to its impact on hormone levels and organ morphology.
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Affiliation(s)
- María Inés Zanor
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
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Doroszuk A, Snoek LB, Fradin E, Riksen J, Kammenga J. A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans. Nucleic Acids Res 2009; 37:e110. [PMID: 19542186 PMCID: PMC2760803 DOI: 10.1093/nar/gkp528] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recombinant inbred lines (RILs) derived from Caenorhabditis elegans wild-type N2 and CB4856 are increasingly being used for mapping genes underlying complex traits. To speed up mapping and gene discovery, introgression lines (ILs) offer a powerful tool for more efficient QTL identification. We constructed a library of 90 ILs, each carrying a single homozygous CB4856 genomic segment introgressed into the genetic background of N2. The ILs were genotyped by 123 single-nucleotide polymorphism (SNP) markers. The proportion of the CB4856 segments in most lines does not exceed 3%, and together the introgressions cover 96% of the CB4856 genome. The value of the IL library was demonstrated by identifying novel loci underlying natural variation in two ageing-related traits, i.e. lifespan and pharyngeal pumping rate. Bin mapping of lifespan resulted in six QTLs, which all have a lifespan-shortening effect on the CB4856 allele. We found five QTLs for the decrease in pumping rate, of which four colocated with QTLs found for average lifespan. This suggests pleiotropic or closely linked QTL associated with lifespan and pumping rate. Overall, the presented IL library provides a versatile resource toward easier and efficient fine mapping and functional analyses of loci and genes underlying complex traits in C. elegans.
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Affiliation(s)
- Agnieszka Doroszuk
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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38
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Yu S, Yang C, Fan Y, Zhuang J, Li X. Genetic dissection of a thousand-grain weight quantitative trait locus on rice chromosome 1. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0281-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Stevens R, Page D, Gouble B, Garchery C, Zamir D, Causse M. Tomato fruit ascorbic acid content is linked with monodehydroascorbate reductase activity and tolerance to chilling stress. PLANT, CELL & ENVIRONMENT 2008; 31:1086-96. [PMID: 18433441 DOI: 10.1111/j.1365-3040.2008.01824.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Quantitative trait loci (QTL) mapping is a step towards the identification of factors regulating traits such as fruit ascorbic acid content. A previously identified QTL controlling variations in tomato fruit ascorbic acid has been fine mapped and reveals that the QTL has a polygenic and epistatic architecture. A monodehydroascorbate reductase (MDHAR) allele is a candidate for a proportion of the increase in fruit ascorbic acid content. The MDHAR enzyme is active in different stages of fruit ripening, shows increased activity in the introgression lines containing the wild-type (Solanum pennellii) allele, and responds to chilling injury in tomato along with the reduced/oxidized ascorbate ratio. Low temperature storage of different tomato introgression lines with all or part of the QTL for ascorbic acid and with or without the wild MDHAR allele shows that enzyme activity explains 84% of the variation in the reduced ascorbic acid levels of tomato fruit following storage at 4 degrees C, compared with 38% at harvest under non-stress conditions. A role is indicated for MDHAR in the maintenance of ascorbate levels in fruit under stress conditions. Furthermore, an increased fruit MDHAR activity and a lower oxidation level of the fruit ascorbate pool are correlated with decreased loss of firmness because of chilling injury.
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Affiliation(s)
- R Stevens
- INRA, UR1052, Unité de génétique et amélioration des fruits et légumes, Domaine St Maurice BP94, 84143 Montfavet, France.
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40
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Kammenga JE, Phillips PC, De Bono M, Doroszuk A. Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends Genet 2008; 24:178-85. [PMID: 18325626 DOI: 10.1016/j.tig.2008.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 01/04/2008] [Accepted: 01/04/2008] [Indexed: 01/30/2023]
Abstract
Induced mutants in the nematode Caenorhabditis elegans are used to study genetic pathways of processes ranging from aging to behavior. The effects of such mutations are usually analyzed in a single wildtype background: N2. However, studies in other species demonstrate that the phenotype(s) of induced mutations can vary widely depending on the genetic background. Moreover, induced mutations in one genetic background do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Because other wildtype Caenorhabditis spp., including C. elegans, are now available, we review how current mapping resources and methodologies within and between species support the use of Caenorhabditis spp. for studying genetic variation, with a focus on pathways associated with human disease.
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Affiliation(s)
- Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
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41
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Schauer N, Semel Y, Balbo I, Steinfath M, Repsilber D, Selbig J, Pleban T, Zamir D, Fernie AR. Mode of inheritance of primary metabolic traits in tomato. THE PLANT CELL 2008; 20:509-23. [PMID: 18364465 PMCID: PMC2329927 DOI: 10.1105/tpc.107.056523] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 01/24/2008] [Accepted: 03/10/2008] [Indexed: 05/18/2023]
Abstract
To evaluate components of fruit metabolic composition, we have previously metabolically phenotyped tomato (Solanum lycopersicum) introgression lines containing segmental substitutions of wild species chromosome in the genetic background of a cultivated variety. Here, we studied the hereditability of the fruit metabolome by analyzing an additional year's harvest and evaluating the metabolite profiles of lines heterozygous for the introgression (ILHs), allowing the evaluation of putative quantitative trait locus (QTL) mode of inheritance. These studies revealed that most of the metabolic QTL (174 of 332) were dominantly inherited, with relatively high proportions of additively (61 of 332) or recessively (80 of 332) inherited QTL and a negligible number displaying the characteristics of overdominant inheritance. Comparison of the mode of inheritance of QTL revealed that several metabolite pairs displayed a similar mode of inheritance of QTL at the same chromosomal loci. Evaluation of the association between morphological and metabolic traits in the ILHs revealed that this correlation was far less prominent, due to a reduced variance in the harvest index within this population. These data are discussed in the context of genomics-assisted breeding for crop improvement, with particular focus on the exploitation of wide biodiversity.
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Affiliation(s)
- Nicolas Schauer
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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42
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Liu LL, Yan XY, Jiang L, Zhang WW, Wang MQ, Zhou SR, Shen Y, Shen YY, Liu SJ, Chen LM, Wang JK, Wan JM. Identification of stably expressed quantitative trait loci for cooked rice elongation in non-Basmati varieties. Genome 2008; 51:104-12. [DOI: 10.1139/g07-106] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The elongation of the cooked grain determines the cooking and eating quality of Basmati rice. The identification of stable quantitative trait loci (QTLs), especially those from non-Basmati types, will extend the genetic basis of the Basmati type and facilitate the breeding of high-quality varieties. A set of recombinant inbred lines derived from an indica × japonica hybrid was used to identify QTLs controlling the elongation ratio (ER), elongation index (EI), and water absorption (WA) of the cooked grain. Three ER QTLs on chromosomes 2, 4, and 12, two EI QTLs on chromosomes 2 and 5, and two WA QTLs on chromosomes 2 and 6 were detected. Four of these QTLs were validated using a set of established chromosome segment substitution lines. The genetic effect of qER-2 was explored in an analysis of segregating generations, using 8 newly developed simple sequence repeat markers. Two tightly linked loci (qER-2a and qER-2b) were identified on chromosome 2.
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Affiliation(s)
- L. L. Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - X. Y. Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - L. Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - W. W. Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - M. Q. Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - S. R. Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - Y. Shen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - Y. Y. Shen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - S. J. Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - L. M. Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - J. K. Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - J. M. Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 10081, China
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Lippman ZB, Semel Y, Zamir D. An integrated view of quantitative trait variation using tomato interspecific introgression lines. Curr Opin Genet Dev 2007; 17:545-52. [PMID: 17723293 DOI: 10.1016/j.gde.2007.07.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 07/17/2007] [Indexed: 02/02/2023]
Abstract
Resolving natural phenotypic variation into genetic and molecular components is a major objective in biology. Over the past decade, tomato interspecific introgression lines (ILs), each carrying a single 'exotic' chromosome segment from a wild species, have exposed thousands of quantitative trait loci (QTL) affecting plant adaptation, morphology, yield, metabolism, and gene expression. QTL for fruit size and sugar composition were isolated by map-based cloning, while others were successfully implemented in marker-assisted breeding programs. More recently, integrating the multitude of IL-QTL into a single database has unraveled some unifying principles about the architecture of complex traits in plants.
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Affiliation(s)
- Zachary B Lippman
- The Hebrew University of Jerusalem, Faculty of Agriculture, Institute of Plant Sciences, Rehovot, Israel.
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44
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Jiménez-Gómez JM, Alonso-Blanco C, Borja A, Anastasio G, Angosto T, Lozano R, Martínez-Zapater JM. Quantitative genetic analysis of flowering time in tomato. Genome 2007; 50:303-15. [PMID: 17502904 DOI: 10.1139/g07-009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial selection of cultivated tomato (Solanum lycopersicum L.) has resulted in the generation of early-flowering, day-length-insensitive cultivars, despite its close relationship to other Solanum species that need more time and specific photoperiods to flower. To investigate the genetic mechanisms controlling flowering time in tomato and related species, we performed a quantitative trait locus (QTL) analysis for flowering time in an F2 mapping population derived from S. lycopersicum and its late-flowering wild relative S. chmielewskii. Flowering time was scored as the number of days from sowing to the opening of the first flower (days to flowering), and as the number of leaves under the first inflorescence (leaf number). QTL analyses detected 2 QTLs affecting days to flowering, which explained 55.3% of the total phenotypic variance, and 6 QTLs for leaf number, accounting for 66.7% of the corresponding phenotypic variance. Four of the leaf number QTLs had not previously been detected for this trait in tomato. Colocation of some QTLs with flowering-time genes included in the genetic map suggests PHYB2, FALSIFLORA, and a tomato FLC-like sequence as candidate genes that might have been targets of selection during the domestication of tomato.
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Affiliation(s)
- José M Jiménez-Gómez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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45
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Zhang FZ, Wagstaff C, Rae AM, Sihota AK, Keevil CW, Rothwell SD, Clarkson GJJ, Michelmore RW, Truco MJ, Dixon MS, Taylor G. QTLs for shelf life in lettuce co-locate with those for leaf biophysical properties but not with those for leaf developmental traits. JOURNAL OF EXPERIMENTAL BOTANY 2007; 58:1433-49. [PMID: 17347132 DOI: 10.1093/jxb/erm006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Developmental and biophysical leaf characteristics that influence post-harvest shelf life in lettuce, an important leafy crop, have been examined. The traits were studied using 60 informative F9 recombinant inbed lines (RILs) derived from a cross between cultivated lettuce (Lactuca sativa cv. Salinas) and wild lettuce (L. serriola acc. UC96US23). Quantitative trait loci (QTLs) for shelf life co-located most closely with those for leaf biophysical properties such as plasticity, elasticity, and breakstrength, suggesting that these are appropriate targets for molecular breeding for improved shelf life. Significant correlations were found between shelf life and leaf size, leaf weight, leaf chlorophyll content, leaf stomatal index, and epidermal cell number per leaf, indicating that these pre-harvest leaf development traits confer post-harvest properties. By studying the population in two contrasting environments in northern and southern Europe, the genotype by environment interaction effects of the QTLs relevant to leaf development and shelf life were assessed. In total, 107 QTLs, distributed on all nine linkage groups, were detected from the 29 traits. Only five QTLs were common in both environments. Several areas where many QTLs co-located (hotspots) on the genome were identified, with relatively little overlap between developmental hotspots and those relating to shelf life. However, QTLs for leaf biophysical properties (breakstrength, plasticity, and elasticity) and cell area correlated well with shelf life, confirming that the ideal ideotype lettuce should have small cells with strong cell walls. The identification of QTLs for leaf development, strength, and longevity will lead to a better understanding of processability at a genetic and cellular level, and allow the improvement of salad leaf quality through marker-assisted breeding.
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Affiliation(s)
- Fang Z Zhang
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton S016 7PX, UK
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Petreikov M, Shen S, Yeselson Y, Levin I, Bar M, Schaffer AA. Temporally extended gene expression of the ADP-Glc pyrophosphorylase large subunit (AgpL1) leads to increased enzyme activity in developing tomato fruit. PLANTA 2006; 224:1465-79. [PMID: 16770584 DOI: 10.1007/s00425-006-0316-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 05/04/2006] [Indexed: 05/10/2023]
Abstract
Tomato plants (Solanum lycopersicum) harboring the allele for the AGPase large subunit (AgpL1) derived from the wild species Solanum habrochaites (AgpL1 ( H )) are characterized by higher AGPase activity and increased starch content in the immature fruit, as well as higher soluble solids in the mature fruit following the breakdown of the transient starch, as compared to fruits from plants harboring the cultivated tomato allele (AgpL1 ( E )). Comparisons of AGPase subunit gene expression and protein levels during fruit development indicate that the increase in AGPase activity correlates with a prolonged expression of the AgpL1 gene in the AgpL1 ( H ) high starch line, leading to an extended presence of the L1 protein. The S1 (small subunit) protein also remained for an extended period of fruit development in the AgpL1 ( H ) fruit, linked to the presence of the L1 protein. There were no discernible differences between the kinetic characteristics of the partially purified AGPase-L1(E) and AGPase-L1(H) enzymes. The results indicate that the increased activity of AGPase in the AgpL1 ( H ) tomatoes is due to the extended expression of the regulatory L1 and to the subsequent stability of the heterotetramer in the presence of the L1 protein, implying a role for the large subunit not only in the allosteric control of AGPase activity but also in the stability of the AGPase L1-S1 heterotetramer. The introgression line of S. lycopersicum containing the wild species AgpL1 ( H ) allele is a novel example of transgressive heterosis in which the hybrid multimeric enzyme shows higher activity due to a modulated temporal expression of one of the subunits.
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Affiliation(s)
- Marina Petreikov
- Department of Vegetable Crops and Genetics, Agricultural Research Organization, Volcani Center, Bet Dagan, 50250, Israel
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47
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Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J, Willmitzer L, Zamir D, Fernie AR. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 2006; 24:447-54. [PMID: 16531992 DOI: 10.1038/nbt1192] [Citation(s) in RCA: 443] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 01/05/2006] [Indexed: 11/08/2022]
Abstract
Tomato represents an important source of fiber and nutrients in the human diet and is a central model for the study of fruit biology. To identify components of fruit metabolic composition, here we have phenotyped tomato introgression lines (ILs) containing chromosome segments of a wild species in the genetic background of a cultivated variety. Using this high-diversity population, we identify 889 quantitative fruit metabolic loci and 326 loci that modify yield-associated traits. The mapping analysis indicates that at least 50% of the metabolic loci are associated with quantitative trait loci (QTLs) that modify whole-plant yield-associated traits. We generate a cartographic network based on correlation analysis that reveals whole-plant phenotype associated and independent metabolic associations, including links with metabolites of nutritional and organoleptic importance. The results of our genomic survey illustrate the power of genome-wide metabolic profiling and detailed morphological analysis for uncovering traits with potential for crop breeding.
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Affiliation(s)
- Nicolas Schauer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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Chaïb J, Lecomte L, Buret M, Causse M. Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:934-44. [PMID: 16402187 DOI: 10.1007/s00122-005-0197-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 12/14/2005] [Indexed: 05/06/2023]
Abstract
The efficiency of marker-assisted backcross for the introgression of a quantitative trait locus (QTL) from a donor line into a recipient line depends on the stability of QTL expression. QTLs for six quality traits in tomato (fruit weight, firmness, locule number, soluble solid content, sugar content and titratable acidity) were studied in order to investigate their individual effect and their stability over years, generations and genetic backgrounds. Five chromosome regions carrying fruit quality QTLs were transferred following a marker-assisted backcross scheme from a cherry tomato line into three modern lines with larger fruits. Three sets of genotypes corresponding to three generations were compared: (1) an RIL population, which contained 50% of each parental genome, (2) three BC3S1 populations which segregated simultaneously for the five regions of interest but were almost fully homozygous for the recipient genome on the eight chromosomes carrying no QTL and (3) three sets of QTL-NILs (BC3S3 lines) which differed from the recipient line only in one of the five regions. QTL detection was performed in each generation, in each genetic background and during 2 successive years for QTL-NILs. About half of the QTLs detected in QTL-NILs were detected in both years. Eight of the ten QTLs detected in RILs were recovered in the QTL-NILs with the genetic background used for the initial QTL mapping experiment, with the exception of two QTLs for fruit firmness. Several new QTLs were detected. In the two other genetic backgrounds, the number of QTLs in common with the RILs was lower, but several new QTLs were also detected in advanced generations.
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Affiliation(s)
- J Chaïb
- INRA, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, BP94, 84143 Montfavet Cedex, France
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Thomson MJ, Edwards JD, Septiningsih EM, Harrington SE, McCouch SR. Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics 2006; 172:2501-14. [PMID: 16452146 PMCID: PMC1456415 DOI: 10.1534/genetics.105.050500] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.
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Affiliation(s)
- Michael J Thomson
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
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Pestsova EG, Börner A, Röder MS. Development and QTL assessment of Triticum aestivum-Aegilops tauschii introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:634-47. [PMID: 16341683 DOI: 10.1007/s00122-005-0166-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 11/17/2005] [Indexed: 05/05/2023]
Abstract
A set of 84 bread wheat lines, each containing a single homozygous introgression of the Aegilops tauschii genome was produced in the 'Chinese Spring' background via backcrossing of the D-genome chromosome substitution lines 'Chinese Spring'/Sears's 'Synthetic 6x' with the recurrent parent and subsequent selfing. The development of the lines was accompanied by microsatellite marker assisted selection. With the exception of three telomeric regions at chromosomes 1DL, 4DL and 7DS, and a region of less than 24 cM on the chromosome arm 3DL, the genome of Ae. tauschii is fully represented in these lines. The newly developed lines were used for the discovery of morphological and agronomical quantitative trait loci (QTLs) from the wild species. Fifty-two introgression lines were grown in the field and evaluated for six traits including flowering time, plant height, ear length, spikelet number, fertility and grain weight per ear. Seventeen significant QTLs were detected, Ae. tauschii contributed favourable alleles at nine loci influencing five traits. The whole set of 84 homozygous lines provides a tool for further testing the effects and stability of the detected QTLs and for the evaluation of new traits.
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Affiliation(s)
- Elena G Pestsova
- Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany.
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