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Khojasteh M, Darzi Ramandi H, Taghavi SM, Taheri A, Rahmanzadeh A, Chen G, Foolad MR, Osdaghi E. Unraveling the genetic basis of quantitative resistance to diseases in tomato: a meta-QTL analysis and mining of transcript profiles. PLANT CELL REPORTS 2024; 43:184. [PMID: 38951262 DOI: 10.1007/s00299-024-03268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
KEY MESSAGE Whole-genome QTL mining and meta-analysis in tomato for resistance to bacterial and fungal diseases identified 73 meta-QTL regions with significantly refined/reduced confidence intervals. Tomato production is affected by a range of biotic stressors, causing yield losses and quality reductions. While sources of genetic resistance to many tomato diseases have been identified and characterized, stability of the resistance genes or quantitative trait loci (QTLs) across the resources has not been determined. Here, we examined 491 QTLs previously reported for resistance to tomato diseases in 40 independent studies and 54 unique mapping populations. We identified 29 meta-QTLs (MQTLs) for resistance to bacterial pathogens and 44 MQTLs for resistance to fungal pathogens, and were able to reduce the average confidence interval (CI) of the QTLs by 4.1-fold and 6.7-fold, respectively, compared to the average CI of the original QTLs. The corresponding physical length of the CIs of MQTLs ranged from 56 kb to 6.37 Mb, with a median of 921 kb, of which 27% had a CI lower than 500 kb and 53% had a CI lower than 1 Mb. Comparison of defense responses between tomato and Arabidopsis highlighted 73 orthologous genes in the MQTL regions, which were putatively determined to be involved in defense against bacterial and fungal diseases. Intriguingly, multiple genes were identified in some MQTL regions that are implicated in plant defense responses, including PR-P2, NDR1, PDF1.2, Pip1, SNI1, PTI5, NSL1, DND1, CAD1, SlACO, DAD1, SlPAL, Ph-3, EDS5/SID1, CHI-B/PR-3, Ph-5, ETR1, WRKY29, and WRKY25. Further, we identified a number of candidate resistance genes in the MQTL regions that can be useful for both marker/gene-assisted breeding as well as cloning and genetic transformation.
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Affiliation(s)
- Moein Khojasteh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, University of Tehran, Karaj, 31587-77871, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, P.O. Box 657833131, Hamedan, Iran
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.
| | - Ayat Taheri
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Asma Rahmanzadeh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
- Department of Plant Protection, University of Tehran, Karaj, 31587-77871, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Majid R Foolad
- Department of Plant Science and the Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, 31587-77871, Iran.
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2
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Wanere SS, Phad AP, Jagtap RK, Rawal SK, Pyati PS, Lomate PR. Cost-effective and reliable genomic DNA extraction from plant seedlings for high-throughput genotyping in seed industries. Anal Biochem 2023; 676:115245. [PMID: 37429485 DOI: 10.1016/j.ab.2023.115245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Genetic purity of seeds is one of the critical aspects in the seed industry. Molecular seed testing laboratories are utilizing PCR based diagnostic tools for genetic purity analysis. High quality DNA is an essential prerequisite for such analyses. Here, we demonstrate a robust and inexpensive DNA extraction method to isolate genomic DNA from variety of crops. Current method (M2) was compared with four commonly used DNA isolation methods for PCR-based genetic characterization and High Resolution Melt (HRM) based hybridity analysis of cotton, okra, tomato and maize using SSR markers. DNA extracted through current method showed excellent yield and quality as compared to other methods. High quality, PCR ready DNA was isolated within 30-50 min and displayed best results for genetic purity analysis using HRM. In contrast, several genomic DNA samples extracted using other methods were found unsuitable for HRM analysis. Our method can be a perfect choice in seed industry, where thousands of samples are processed every day. Notably, using our method single technician can extract DNA from 96 leaf samples within 30-50 min, at a cost of only $0.11/sample. Overall, current DNA extraction method is a reliable and cost-effective solution for large-scale genotyping experiments in the agricultural industry.
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Affiliation(s)
- Shyamkumar S Wanere
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Archana P Phad
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Rameshwar K Jagtap
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Shuban K Rawal
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Prashant S Pyati
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
| | - Purushottam R Lomate
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
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3
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Kim SY, Kwak KW, Park JY, Park ES, Nam CJ, An KS, Kim HJ, Yoon HJ, Kim YS, Park K, Kim E, Ryu HY, Kim SD. Evaluation of subchronic oral dose toxicity and allergen of freeze-dried powder of Locusta migratoria (Orthoptera: Acrididae) as a novel food source. Toxicol Res 2023; 39:317-331. [PMID: 37008697 PMCID: PMC10050243 DOI: 10.1007/s43188-023-00171-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/19/2023] Open
Abstract
The migratory locust, Locusta migratoria (Orthoptera: Acrididae), is a well-known edible insect which may serve as new source of human food and animal feed. However, potential toxicity and food safety of L. migratoria had not been investigated extensively until now. Therefore, in this study, we aimed to investigate toxicity of freeze-dried powder of L. migratoria (fdLM) and identify allergic components in ELISA and PCR techniques. In this subchronic study, fdLM was administered once daily by oral gavage at the doses of 750, 1500, and 3000 mg/kg/day. No toxicological changes were observed in both sexes of rats for 13 weeks in accordance with the OECD guidelines and GLP conditions. In addition, fdLM did not induced increases of serum immunoglobulin E and 21 homologous proteins were not detected under our present conditions. In conclusion, the NOAEL (no-observed-adverse-effect level) was 3000 mg/kg/day and no target organ was identified in both sexes. In conclusion, we found that fdLM is safe with no adverse effects and offers the potential of its use as an edible ingredient or other biological uses.
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Affiliation(s)
- Sun Young Kim
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Kyu-Won Kwak
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Ji Yeong Park
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Eun-Sung Park
- Headquarters of GLP, Nonclinical Research Institute, Chemon Inc., 240, Nampyeong-Ro, Yangji-Myeon, Cheoin-Gu, Yongin-Si, Gyeonggi-Do 17162 Republic of Korea
| | - Chun-Ja Nam
- Headquarters of GLP, Nonclinical Research Institute, Chemon Inc., 240, Nampyeong-Ro, Yangji-Myeon, Cheoin-Gu, Yongin-Si, Gyeonggi-Do 17162 Republic of Korea
| | - Kyu Sup An
- Bioconvergence Technology Laboratory, Korea Conformity Laboratories, Incheon, 21999 Republic of Korea
| | - Hyun-Jin Kim
- Jeon-Nam Agricultural Research & Extension Services, Insect & Sericultural Research Institute, Jeonnam, 57214 Republic of Korea
| | - Hyung Joo Yoon
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Yong-Soon Kim
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Kwanho Park
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Eunsun Kim
- Industrial Insect Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Hyeon Yeol Ryu
- Bioconvergence Technology Laboratory, Korea Conformity Laboratories, Incheon, 21999 Republic of Korea
| | - Sun-Don Kim
- Headquarters of GLP, Nonclinical Research Institute, Chemon Inc., 240, Nampyeong-Ro, Yangji-Myeon, Cheoin-Gu, Yongin-Si, Gyeonggi-Do 17162 Republic of Korea
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Peters SA, Underwood CJ. Technology-driven approaches for meiosis research in tomato and wild relatives. PLANT REPRODUCTION 2023; 36:97-106. [PMID: 36149478 PMCID: PMC9957858 DOI: 10.1007/s00497-022-00450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Meiosis is a specialized cell division during reproduction where one round of chromosomal replication is followed by genetic recombination and two rounds of segregation to generate recombined, ploidy-reduced spores. Meiosis is crucial to the generation of new allelic combinations in natural populations and artificial breeding programs. Several plant species are used in meiosis research including the cultivated tomato (Solanum lycopersicum) which is a globally important crop species. Here we outline the unique combination of attributes that make tomato a powerful model system for meiosis research. These include the well-characterized behavior of chromosomes during tomato meiosis, readily available genomics resources, capacity for genome editing, clonal propagation techniques, lack of recent polyploidy and the possibility to generate hybrids with twelve related wild species. We propose that further exploitation of genome bioinformatics, genome editing and artificial intelligence in tomato will help advance the field of plant meiosis research. Ultimately this will help address emerging themes including the evolution of meiosis, how recombination landscapes are determined, and the effect of temperature on meiosis.
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Affiliation(s)
- Sander A Peters
- Business Unit Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Charles J Underwood
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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5
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Kuang Q, Sheng W. The entire chloroplast genome sequence of Asparagus setaceus (Kunth) Jessop: Genome structure, gene composition, and phylogenetic analysis in Asparagaceae. Open Life Sci 2022; 17:1541-1554. [PMID: 36474705 PMCID: PMC9684740 DOI: 10.1515/biol-2022-0497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 09/08/2024] Open
Abstract
Asparagus setaceus (Kunth) Jessop is a horticultural plant of the genus Asparagus. Herein, the whole chloroplast (cp) genome of A. setaceus was sequenced with PacBio and Illumina sequencing systems. The cp genome shows a characteristic quadripartite structure with 158,076 bp. In total, 135 genes were annotated, containing 89 protein-coding, 38 tRNA, and 8 rRNA genes. Contrast with the previous cp genome of A. setaceus registered in NCBI, we identified 7 single-nucleotide polymorphisms and 15 indels, mostly situated in noncoding areas. Meanwhile, 36 repeat structures and 260 simple sequence repeats were marked out. A bias for A/T-ending codons was shown in this cp genome. Furthermore, we predicted 78 RNA-editing sites in 29 genes, which were all for C-to-U transitions. And it was also proven that positive selection was exerted on the rpoC1 gene of A. setaceus with the K a/K s data. Meanwhile, a conservative gene order and highly similar sequences of protein-coding genes were revealed within Asparagus species. Phylogenetic tree analysis indicated that A. setaceus was a sister to Asparagus cochinchinensis. Taken together, our released genome provided valuable information for the gene composition, genetics comparison, and the phylogeny studies of A. setaceus.
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Affiliation(s)
- Quan Kuang
- Department of Biological Technology, Nanchang Normal University, Nanchang, 330032, Jiangxi, China
| | - Wentao Sheng
- Department of Biological Technology, Nanchang Normal University, Nanchang, 330032, Jiangxi, China
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6
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Öztürk Hİ, Dönderalp V, Bulut H, Korkut R. Morphological and molecular characterization of some pumpkin (Cucurbita pepo L.) genotypes collected from Erzincan province of Turkey. Sci Rep 2022; 12:6814. [PMID: 35474245 PMCID: PMC9042938 DOI: 10.1038/s41598-022-11005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/07/2022] [Indexed: 11/09/2022] Open
Abstract
Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. To determine the genetic diversity among genotypes of Cucurbita pepo L. species of pumpkin, which is widely grown in Erzincan, 29 different pumpkin genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple Sequence Repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. In the evaluation performed using SSR markers, all primers exhibited polymorphism rate of %100. Seven SSR markers yielded a total of 15 polymorphic bands, the number of alleles per marker ranged from 2 to 3, and the mean number of alleles was 2.14. Polymorphic information content (PIC) ranged from 0.06 (GMT-M61) to 0.247 (GMT-P41), and the mean PIC value per marker was 0.152. Cluster analysis using Nei's genetic distance determined that 29 genotypes were divided into 4 major groups. The present findings have revealed the genetic diversity among pumpkin genotypes collected from Erzincan province and may form the basis for further breeding studies in pumpkin.
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Affiliation(s)
- Halil İbrahim Öztürk
- Vocational School of Health Services, Erzincan Binali Yıldırım University, Erzincan, Turkey.
| | | | - Hüseyin Bulut
- Vocational School of Health Services, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Recep Korkut
- Erzincan Horticultural Research Institute, Erzincan, Turkey
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7
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Shibaya T, Kuroda C, Nakayama S, Minami C, Obara A, Fujii T, Isobe S. Development of PCR-based DNA marker for detection of white carrot contamination caused by Y2 locus. BREEDING SCIENCE 2021; 71:201-207. [PMID: 34377068 PMCID: PMC8329877 DOI: 10.1270/jsbbs.20120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/25/2020] [Indexed: 06/13/2023]
Abstract
In carrot (Daucus carota L.), the taproot colors orange, yellow and white are determined mostly by the Y, Y2, and Or loci. One of the most severe issues in carrot seed production is contamination by wild white carrot. To evaluate the contamination ratio, easily detectable DNA markers for white carrot are desired. To develop PCR-based DNA markers for the Y2 locus, we have re-sequenced two orange-colored carrot cultivars at our company (Fujii Seed, Japan), as well as six white- and one light-orange-colored carrots that contaminated our seed products. Within the candidate region previously reported for the Y2 locus, only one DNA marker, Y2_7, clearly distinguished white carrots from orange ones in the re-sequenced samples. The Y2_7 marker was further examined in 12 of the most popular hybrid orange cultivars in Japan, as well as 'Nantes' and 'Chantenay Red Cored 2'. The Y2_7 marker showed that all of the orange cultivars examined had the orange allele except for 'Beta-441'. False white was detected in the orange-colored 'Beta-441'. The Y2_7 marker detected white root carrot contamination in an old open-pollinated Japanese cultivar, 'Nakamura Senkou Futo'. This marker would be a useful tool in a carrot seed quality control for some cultivars.
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Affiliation(s)
| | - Chika Kuroda
- Fujii Seed Co. Ltd., Osaka, Osaka 532-0023, Japan
| | | | - Chiharu Minami
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akiko Obara
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | | | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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8
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Safaei M, Olfati JA, Hamidoghli Y, Rabiei B, Yamamoto E, Shirasawa K. Four genetic loci control compact plant size with yellow pear-shaped fruit in ornamental tomato (Solanum lycopersicum L.). THE PLANT GENOME 2020; 13:e20017. [PMID: 33016615 DOI: 10.1002/tpg2.20017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
Tomato is an attractive fruiting vegetable crop that can be used as an ornamental plant. Agronomical traits have been subjected to extensive genetic dissection to enhance vegetable breeding programs. By contrast, there are few genetic studies of ornamental traits for the development of ornamental tomato varieties. To investigate genetic loci linked to desired ornamental traits, we performed genetic analyses using an intraspecific mapping population that segregated for fruit color (yellow or red), fruit shape (round or pear), and plant height (high or compact). A genetic map was constructed with 965 single nucleotide polymorphisms (SNPs) and 33 simple sequence repeat markers. Subsequent linkage analysis using quantitative locus analysis and genome-wide association study detected four genetic loci for the three selected traits, all of which were located near the reported genes. We performed KASP-kompetitive allele-specific PCR-to develop SNP markers that were tightly linked to the four loci. Highly accurate genotyping data were obtained from the four SNPs across 187 F2 plants, which enabled us to select two lines with homozygous alleles for compact plant size and yellow pear-shaped fruits. These newly developed SNP markers and genetic strategies could be used to accelerate breeding programs for ornamental tomato plants.
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Affiliation(s)
- Meysam Safaei
- Department of Horticultural Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Guilan, Iran
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Jamal-Ali Olfati
- Department of Horticultural Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Guilan, Iran
| | - Yousef Hamidoghli
- Department of Horticultural Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Guilan, Iran
| | - Babak Rabiei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Gilan Province, Iran
| | - Eiji Yamamoto
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
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9
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Identification of genomic regions associated with early plant vigour in lentil (Lens culinaris). J Genet 2020. [DOI: 10.1007/s12041-020-1182-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Wen G, Dang J, Xie Z, Wang J, Jiang P, Guo Q, Liang G. Molecular karyotypes of loquat ( Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity. PLANT METHODS 2020; 16:22. [PMID: 32123538 PMCID: PMC7041098 DOI: 10.1186/s13007-020-00568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/13/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. RESULTS Based on this imbalance in chromosome dosage, a new approach (referred to as 'SSR-qPCR') combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results. CONCLUSION SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.
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Affiliation(s)
- Guo Wen
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Zhongyi Xie
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jinying Wang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Pengfei Jiang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
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11
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Arafa RA, Rakha MT, Soliman NEK, Moussa OM, Kamel SM, Shirasawa K. Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. PLoS One 2017; 12:e0189951. [PMID: 29253902 PMCID: PMC5734779 DOI: 10.1371/journal.pone.0189951] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/05/2017] [Indexed: 11/19/2022] Open
Abstract
Tomato late blight caused by Phytophthora infestans (Mont.) de Bary, also known as the Irish famine pathogen, is one of the most destructive plant diseases. Wild relatives of tomato possess useful resistance genes against this disease, and could therefore be used in breeding to improve cultivated varieties. In the genome of a wild relative of tomato, Solanum habrochaites accession LA1777, we identified a new quantitative trait locus for resistance against blight caused by an aggressive Egyptian isolate of P. infestans. Using double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology, we determined 6,514 genome-wide SNP genotypes of an F2 population derived from an interspecific cross. Subsequent association analysis of genotypes and phenotypes of the mapping population revealed that a 6.8 Mb genome region on chromosome 6 was a candidate locus for disease resistance. Whole-genome resequencing analysis revealed that 298 genes in this region potentially had functional differences between the parental lines. Among of them, two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance. SNP and SSR markers linking to this region can be used in marker-assisted selection in future breeding programs for late blight disease, including introgression of new genetic loci from wild species. In addition, the approach developed in this study provides a model for identification of other genes for attractive agronomical traits.
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Affiliation(s)
- Ramadan A. Arafa
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Mohamed T. Rakha
- Department of Horticulture, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, Egypt
| | - Nour Elden K. Soliman
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Olfat M. Moussa
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Said M. Kamel
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Kenta Shirasawa
- Department of Frontier Science, Kazusa DNA Research Institute, Chiba, Japan
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12
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Ohyama A, Shirasawa K, Matsunaga H, Negoro S, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H, Hayashi T. Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F 1 hybrids of tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1601-1616. [PMID: 28477044 DOI: 10.1007/s00122-017-2913-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.
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Affiliation(s)
- Akio Ohyama
- National Agriculture and Food Research Organization (NARO), Institute of Vegetable and Floriculture Science (NIVFS), 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8519, Japan.
- NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | | | - Satomi Negoro
- NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Koji Miyatake
- NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | | | | | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyuki Fukuoka
- NARO, Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
- Takii & Company, Limited, 1360 Hari, Konan, Shiga, 520-3231, Japan
| | - Takeshi Hayashi
- NARO, Institute of Crop Science (NICS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
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Yamamoto E, Matsunaga H, Onogi A, Ohyama A, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H. Efficiency of genomic selection for breeding population design and phenotype prediction in tomato. Heredity (Edinb) 2017; 118:202-209. [PMID: 27624117 PMCID: PMC5234485 DOI: 10.1038/hdy.2016.84] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 11/09/2022] Open
Abstract
Genomic selection (GS), which uses estimated genetic potential based on genome-wide genotype data for a breeding selection, is now widely accepted as an efficient method to improve genetically complex traits. We assessed the potential of GS for increasing soluble solids content and total fruit weight of tomato. A collection of big-fruited F1 varieties was used to construct the GS models, and the progeny from crosses was used to validate the models. The present study includes two experiments: a prediction of a parental combination that generates superior progeny and the prediction of progeny phenotypes. The GS models successfully predicted a better parent even if the phenotypic value did not vary substantially between candidates. The GS models also predicted phenotypes of progeny, although their efficiency varied depending on the parental cross combinations and the selected traits. Although further analyses are required to apply GS in an actual breeding situation, our results indicated that GS is a promising strategy for future tomato breeding design.
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Affiliation(s)
- E Yamamoto
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - H Matsunaga
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - A Onogi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - A Ohyama
- Vegetable Production Technology Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - K Miyatake
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - H Yamaguchi
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - T Nunome
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - H Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - H Fukuoka
- Vegetable Breeding and Genome Division, Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, Tsu, Mie, Japan
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Bodanapu R, Gupta SK, Basha PO, Sakthivel K, Sreelakshmi Y, Sharma R. Nitric Oxide Overproduction in Tomato shr Mutant Shifts Metabolic Profiles and Suppresses Fruit Growth and Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1714. [PMID: 27965677 PMCID: PMC5124567 DOI: 10.3389/fpls.2016.01714] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/31/2016] [Indexed: 05/23/2023]
Abstract
Nitric oxide (NO) plays a pivotal role in growth and disease resistance in plants. It also acts as a secondary messenger in signaling pathways for several plant hormones. Despite its clear role in regulating plant development, its role in fruit development is not known. In an earlier study, we described a short root (shr) mutant of tomato, whose phenotype results from hyperaccumulation of NO. The molecular mapping localized shr locus in 2.5 Mb region of chromosome 9. The shr mutant showed sluggish growth, with smaller leaves, flowers and was less fertile than wild type. The shr mutant also showed reduced fruit size and slower ripening of the fruits post-mature green stage to the red ripe stage. Comparison of the metabolite profiles of shr fruits with wild-type fruits during ripening revealed a significant shift in the patterns. In shr fruits intermediates of the tricarboxylic acid (TCA) cycle were differentially regulated than WT indicating NO affected the regulation of TCA cycle. The accumulation of several amino acids, particularly tyrosine, was higher, whereas most fatty acids were downregulated in shr fruits. Among the plant hormones at one or more stages of ripening, ethylene, Indole-3-acetic acid and Indole-3-butyric acid increased in shr, whereas abscisic acid declined. Our analyses indicate that the retardation of fruit growth and ripening in shr mutant likely results from the influence of NO on central carbon metabolism and endogenous phytohormones levels.
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Ofner I, Lashbrooke J, Pleban T, Aharoni A, Zamir D. Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:151-60. [PMID: 27121752 DOI: 10.1111/tpj.13194] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/14/2016] [Indexed: 05/19/2023]
Abstract
We present a resource for fine mapping of traits derived from the wild tomato species Solanum pennellii (LA0716). The population of backcross inbred lines (BILs) is composed of 446 lines derived after a few generations of backcrosses of the wild species with cultivated tomato (cultivar M82; LA3475), followed by more than seven generations of self-pollination. The BILs were genotyped using the 10K SOL-CAP single nucleotide polymorphism (SNP) -Chip, and 3700 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs carry, on average, 2.7 introgressions per line, with a mean introgression length of 11.7 Mbp. Whereas the classic 76 introgression lines (ILs) partitioned the genome into 106 mapping bins, the BILs generated 633 bins, thereby enhancing the mapping resolution of traits derived from the wild species. We demonstrate the power of the BILs for rapid fine mapping of simple and complex traits derived from the wild tomato species.
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Affiliation(s)
- Itai Ofner
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Justin Lashbrooke
- Department of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, 38010, TN, Italy
| | - Tzili Pleban
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dani Zamir
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
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Yamamoto E, Matsunaga H, Onogi A, Kajiya-Kanegae H, Minamikawa M, Suzuki A, Shirasawa K, Hirakawa H, Nunome T, Yamaguchi H, Miyatake K, Ohyama A, Iwata H, Fukuoka H. A simulation-based breeding design that uses whole-genome prediction in tomato. Sci Rep 2016; 6:19454. [PMID: 26787426 PMCID: PMC4726135 DOI: 10.1038/srep19454] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/08/2015] [Indexed: 11/14/2022] Open
Abstract
Efficient plant breeding methods must be developed in order to increase yields and feed a growing world population, as well as to meet the demands of consumers with diverse preferences who require high-quality foods. We propose a strategy that integrates breeding simulations and phenotype prediction models using genomic information. The validity of this strategy was evaluated by the simultaneous genetic improvement of the yield and flavour of the tomato (Solanum lycopersicum), as an example. Reliable phenotype prediction models for the simulation were constructed from actual genotype and phenotype data. Our simulation predicted that selection for both yield and flavour would eventually result in morphological changes that would increase the total plant biomass and decrease the light extinction coefficient, an essential requirement for these improvements. This simulation-based genome-assisted approach to breeding will help to optimise plant breeding, not only in the tomato but also in other important agricultural crops.
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Affiliation(s)
- Eiji Yamamoto
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Hiroshi Matsunaga
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Mai Minamikawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Akinori Suzuki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tsukasa Nunome
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Hirotaka Yamaguchi
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Koji Miyatake
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Akio Ohyama
- NARO Institute of Vegetable and Tea Science (NIVTS), 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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17
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Okabe Y, Ariizumi T. Mutant Resources and TILLING Platforms in Tomato Research. BIOTECHNOLOGY IN AGRICULTURE AND FORESTRY 2016. [DOI: 10.1007/978-3-662-48535-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Shirasawa K, Hirakawa H, Nunome T, Tabata S, Isobe S. Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:51-60. [PMID: 25689669 PMCID: PMC5023996 DOI: 10.1111/pbi.12348] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/15/2014] [Accepted: 12/26/2014] [Indexed: 05/20/2023]
Abstract
Genome-wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro-Tom genome were identified by a whole-genome shotgun sequencing analysis to estimate the spectrum and distribution of whole-genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired-end reads for four EMS-induced mutants and three gamma-ray-irradiated lines as well as a wild-type line were obtained by next-generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma-ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1,140,687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild-type Micro-Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild-type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse-genetic approaches.
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Affiliation(s)
| | | | - Tsukasa Nunome
- NARO Institute of Vegetable and Tea Sciences, Tsu, Japan
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19
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Shirasawa K, Hand ML, Henderson ST, Okada T, Johnson SD, Taylor JM, Spriggs A, Siddons H, Hirakawa H, Isobe S, Tabata S, Koltunow AMG. A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts. ANNALS OF BOTANY 2015; 115:567-80. [PMID: 25538115 PMCID: PMC4343286 DOI: 10.1093/aob/mcu249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. METHODS RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. KEY RESULTS A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. CONCLUSIONS A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Melanie L Hand
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Steven T Henderson
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Takashi Okada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Susan D Johnson
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Taylor
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Andrew Spriggs
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Hayley Siddons
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Anna M G Koltunow
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
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20
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Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H. Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res 2014; 21:649-60. [PMID: 25233906 PMCID: PMC4263298 DOI: 10.1093/dnares/dsu027] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/12/2014] [Indexed: 11/28/2022] Open
Abstract
Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.
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Affiliation(s)
- Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Miyatake
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Tsukasa Nunome
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satomi Negoro
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Akio Ohyama
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Hirotaka Yamaguchi
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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Shirasawa K, Isobe S, Tabata S, Hirakawa H. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants. BREEDING SCIENCE 2014; 64:264-71. [PMID: 25320561 PMCID: PMC4154615 DOI: 10.1270/jsbbs.64.264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/08/2014] [Indexed: 05/06/2023]
Abstract
In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.
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Ariizumi T, Kishimoto S, Kakami R, Maoka T, Hirakawa H, Suzuki Y, Ozeki Y, Shirasawa K, Bernillon S, Okabe Y, Moing A, Asamizu E, Rothan C, Ohmiya A, Ezura H. Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:453-65. [PMID: 24888879 DOI: 10.1111/tpj.12570] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 05/18/2023]
Abstract
Xanthophylls, the pigments responsible for yellow to red coloration, are naturally occurring carotenoid compounds in many colored tissues of plants. These pigments are esterified within the chromoplast; however, little is known about the mechanisms underlying their accumulation in flower organs. In this study, we characterized two allelic tomato (Solanum lycopersicum L.) mutants, pale yellow petal (pyp) 1-1 and pyp1-2, that have reduced yellow color intensity in the petals and anthers due to loss-of-function mutations. Carotenoid analyses showed that the yellow flower organs of wild-type tomato contained high levels of xanthophylls that largely consisted of neoxanthin and violaxanthin esterified with myristic and/or palmitic acids. Functional disruption of PYP1 resulted in loss of xanthophyll esters, which was associated with a reduction in the total carotenoid content and disruption of normal chromoplast development. These findings suggest that xanthophyll esterification promotes the sequestration of carotenoids in the chromoplast and that accumulation of these esters is important for normal chromoplast development. Next-generation sequencing coupled with map-based positional cloning identified the mutant alleles responsible for the pyp1 phenotype. PYP1 most likely encodes a carotenoid modifying protein that plays a vital role in the production of xanthophyll esters in tomato anthers and petals. Our results provide insight into the molecular mechanism underlying the production of xanthophyll esters in higher plants, thereby shedding light on a longstanding mystery.
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Affiliation(s)
- Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
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Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3-GENES GENOMES GENETICS 2014; 4:1395-405. [PMID: 24879607 PMCID: PMC4132171 DOI: 10.1534/g3.114.011197] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome–fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps.
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Chen AL, Liu CY, Chen CH, Wang JF, Liao YC, Chang CH, Tsai MH, Hwu KK, Chen KY. Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of Phytophthora infestans. PLoS One 2014; 9:e96417. [PMID: 24788810 PMCID: PMC4008630 DOI: 10.1371/journal.pone.0096417] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/04/2014] [Indexed: 12/22/2022] Open
Abstract
Tomato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are associated with migration of new and more aggressive populations of P. infestans in the field. The objective of this study was to reassess late blight resistance in the wild tomato accession L3708 (Solanum pimpinellifolium L.) against pathogens of different aggressiveness. An F2:3 genetic mapping population was developed using L3708 as the paternal parent. Two isolates of P. infestans, Pi39A and Pi733, were used for inoculation. Pi733 is a highly aggressive genotype that defeats three known late blight resistance genes, Ph-1, Ph-2, and Ph-5t in tomato. In contrast, Pi39A is a less aggressive genotype that defeats only Ph-1. Restriction site Associated DNA Sequencing (RAD-Seq) technology was used to massively sequence 90 bp nucleotides adjacent to both sides of PstI restriction enzyme cutting sites in the genome for all individuals in the genetic mapping population. The RAD-seq data were used to construct a genetic linkage map containing 440 single nucleotide polymorphism markers. Quantitative trait locus (QTL) analysis identified a new disease-resistant QTL specific to Pi733 on chromosome 2. The Ph-3 gene located on chromosome 9 could be detected whichever isolates were used. This study demonstrated the feasibility and efficiency of RAD-Seq technology for conducting a QTL mapping experiment using an F2:3 mapping population, which allowed the identification of a new late blight resistant QTL in tomato.
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Affiliation(s)
- Ai-Lin Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Chu-Yin Liu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Chien-Hua Chen
- AVRDC - The World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Jaw-Fen Wang
- AVRDC - The World Vegetable Center, Shanhua, Tainan, Taiwan
| | | | | | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Kae-Kang Hwu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Kai-Yi Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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Chusreeaeom K, Ariizumi T, Asamizu E, Okabe Y, Shirasawa K, Ezura H. A novel tomato mutant, Solanum lycopersicum elongated fruit1 (Slelf1), exhibits an elongated fruit shape caused by increased cell layers in the proximal region of the ovary. Mol Genet Genomics 2014; 289:399-409. [PMID: 24519535 DOI: 10.1007/s00438-014-0822-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022]
Abstract
Genes controlling fruit morphology offer important insights into patterns and mechanisms determining organ shape and size. In cultivated tomato (Solanum lycopersicum L.), a variety of fruit shapes are displayed, including round-, bell pepper-, pear-, and elongate-shaped forms. In this study, we characterized a tomato mutant possessing elongated fruit morphology by histologically analyzing its fruit structure and genetically analyzing and mapping the genetic locus. The mutant line, Solanum lycopersicum elongated fruit 1 (Slelf1), was selected in a previous study from an ethylmethane sulfonate-mutagenized population generated in the background of Micro-Tom, a dwarf and rapid-growth variety. Histological analysis of the Slelf1 mutant revealed dramatically increased elongation of ovary and fruit. Until 6 days before flowering, ovaries were round and they began to elongate afterward. We also determined pericarp thickness and the number of cell layers in three designated fruit regions. We found that mesocarp thickness, as well as the number of cell layers, was increased in the proximal region of immature green fruits, making this the key sector of fruit elongation. Using 262 F2 individuals derived from a cross between Slelf1 and the cultivar Ailsa Craig, we constructed a genetic map, simple sequence repeat (SSR), cleaved amplified polymorphism sequence (CAPS), and derived CAPS (dCAPS) markers and mapped to the 12 tomato chromosomes. Genetic mapping placed the candidate gene locus within a 0.2 Mbp interval on the long arm of chromosome 8 and was likely different from previously known loci affecting fruit shape.
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Affiliation(s)
- Katarut Chusreeaeom
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
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Todorovska E, Ivanova A, Ganeva D, Pevicharova G, Molle E, Bojinov B, Radkova M, Danailov Z. Assessment of genetic variation in Bulgarian tomato ( Solanum lycopersicum L.) genotypes, using fluorescent SSR genotyping platform. BIOTECHNOL BIOTEC EQ 2014; 28:68-76. [PMID: 26019490 PMCID: PMC4433931 DOI: 10.1080/13102818.2014.901683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Genetic variability in modern crops is limited due to domestication and selection processes. Genetic variation in eight Bulgarian tomato varieties and breeding lines (variety Plovdivska karotina, variety IZK Alya, L21β, L53β, L1140, L1116, L975, L984) differing in their morphological and biochemical composition was assessed using a highly efficient and low-cost fluorescent simple sequence repeat (SSR) genotyping platform. Genotyping was conducted with 165 publicly available microsatellite markers developed from different research groups under a number of projects in tomato (SOL Genomics SSRs, Kazusa TGS and TES, SLM, TMS and LEMDDNa) among which only five (3.03%) failed to amplify the expected PCR fragments. Of the remaining markers, 81 (50.62%) were polymorphic in the whole collection of eight genotypes. Among the marker groups used, SLM markers were most polymorphic, followed by TMS and SOL Genomics SSR markers. The total number of amplified alleles was 299, with a mean of 1.869; and the average polymorphic information content (PIC) was 0.196. The genetic diversity within the collection was relatively low (0.2222). Nei's genetic distance varied from 0.0953 to 0.3992. Cluster analysis using the un-weighted pair group method with arithmetic mean (UPGMA) method indicated that the studied tomato genotypes are grouped in four main clusters, which is to some extent consistent with the morpho- and hemo-types of the studied tomatoes. Variety IZK Alya (cherry type) and two of the breeding lines (L1140, L1116) formed three separate and more distant clusters. The fourth cluster includes the other five genotypes. The observed grouping of these genotypes in two sub-clusters reflects their similar morphological and biochemical composition. The genetic distance information from this study might be useful for further implementation of breeding strategies and crosses among these inbred lines.
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Affiliation(s)
| | - Albena Ivanova
- Agricultural Academy, AgroBioInstitute , Sofia , Bulgaria
| | - Daniela Ganeva
- Agricultural Academy, Maritsa Vegetable Crops Research Institute , Plovdiv , Bulgaria
| | - Galina Pevicharova
- Agricultural Academy, Maritsa Vegetable Crops Research Institute , Plovdiv , Bulgaria
| | - Emil Molle
- Faculty of Ecology and Landscape Architecture, University of Forestry, Sofia , Bulgaria
| | - Bojin Bojinov
- Faculty of Agronomy, Agricultural University, Plovdiv , Bulgaria
| | | | - Zhivko Danailov
- Bulgarian Academy of Sciences, Institute of Plant Physiology and Genetics , Sofia , Bulgaria
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Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S. Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. PLANT & CELL PHYSIOLOGY 2014; 55:e8. [PMID: 24363285 PMCID: PMC3894704 DOI: 10.1093/pcp/pct189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.
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Affiliation(s)
- Erika Asamizu
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Hisako Ichihara
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Akihiro Nakaya
- Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8585 Japan
| | - Yasukazu Nakamura
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Hideki Hirakawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takahiro Ishii
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takuro Tamura
- LINE Co., Ltd., 5-201 Kandamatsunaga-cho, Tokyo, 101-0023 Japan
| | | | - Yukari Nakajima
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
- *Corresponding author: Fax: +81-438-52-3918; E-mail,
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Long W, Li Y, Zhou W, Ling HQ, Zheng S. Sequence-based SSR marker development and their application in defining the Introgressions of LA0716 (Solanum pennellii) in the background of cv. M82 (Solanum lycopersicum). PLoS One 2013; 8:e81091. [PMID: 24339899 PMCID: PMC3855227 DOI: 10.1371/journal.pone.0081091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/18/2013] [Indexed: 12/02/2022] Open
Abstract
The introgression lines (ILs) from cv. M82 (Solanum lycopersicum) × LA0716 (S. pennellii) have been proven to be exceptionally useful for genetic analysis and gene cloning. The introgressions were originally defined by RFLP markers at their development. The objectives of this study are to develop polymorphic SSR markers, and to re-define the DNA introgression from LA0716 in the ILs. Tomato sequence data was scanned by software to generate SSR markers. In total, 829 SSRs, which could be robustly amplified by PCR, were developed. Among them, 658 SSRs were dinucleotide repeats, 162 were trinucleotide repeats, and nine were tetranucleotide repeats. The 829 SSRs together with 96 published RFLPs were integrated into the physical linkage map of S. lycopersicum. Introgressions of DNA fragments from LA0716 were re-defined among the 75 ILs using the newly developed SSRs. A specific introgression of DNA fragment from LA0716 was identified in 72 ILs as described previously by RFLP, whereas the specific DNA introgression described previously were not detected in the ILs LA4035, LA4059 and LA4091. The physical location of each investigated DNA introgression was finely determined by SSR mapping. Among the 72 ILs, eight ILs showed a shorter and three ILs (IL3-2, IL12-3 and IL12-3-1) revealed a longer DNA introgression than that framed by RFLPs. Furthermore, 54 previously undefined segments were found in 21 ILs, ranging from 1 to 11 DNA introgressions per IL. Generally, the newly developed SSRs provide additional markers for genetic studies of tomatoes, and the fine definition of DNA introgressions from LA0716 would facilitate the use of the ILs for genetic analysis and gene cloning.
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Affiliation(s)
- Wenbo Long
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ye Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (H-QL); (SZ)
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (H-QL); (SZ)
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Causse M, Desplat N, Pascual L, Le Paslier MC, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M, Brunel D, Bouchet JP. Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 2013; 14:791. [PMID: 24228636 PMCID: PMC4046683 DOI: 10.1186/1471-2164-14-791] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 11/07/2013] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of genetic variation present in the tomato genome. Like many self-pollinated crops, cultivated tomato accessions show a low molecular but high phenotypic diversity. Here we describe the whole-genome resequencing of eight accessions (four cherry-type and four large fruited lines) chosen to represent a large range of intra-specific variability and the identification and annotation of novel polymorphisms. RESULTS The eight genomes were sequenced using the GAII Illumina platform. Comparison of the sequences with the reference genome yielded more than 4 million single nucleotide polymorphisms (SNPs). This number varied from 80,000 to 1.5 million according to the accessions. Almost 128,000 InDels were detected. The distribution of SNPs and InDels across and within chromosomes was highly heterogeneous revealing introgressions from wild species and the mosaic structure of the genomes of the cherry tomato accessions. In-depth annotation of the polymorphisms identified more than 16,000 unique non-synonymous SNPs. In addition 1,686 putative copy-number variations (CNVs) were identified. CONCLUSIONS This study represents the first whole genome resequencing experiment in cultivated tomato. Substantial genetic differences exist between the sequenced tomato accessions and the reference sequence. The heterogeneous distribution of the polymorphisms may be related to introgressions that occurred during domestication or breeding. The annotated SNPs, InDels and CNVs identified in this resequencing study will serve as useful genetic tools, and as candidate polymorphisms in the search for phenotype-altering DNA variations.
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Affiliation(s)
- Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, BP94, Montfavet F-84143, France.
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30
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Zhang C, Liu L, Zheng Z, Sun Y, Zhou L, Yang Y, Cheng F, Zhang Z, Wang X, Huang S, Xie B, Du Y, Bai Y, Li J. Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2643-53. [PMID: 23921955 DOI: 10.1007/s00122-013-2162-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/12/2013] [Indexed: 05/23/2023]
Abstract
Late blight, caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary, is a devastating disease for tomato and potato crops. In the past decades, many late blight resistance (R) genes have been characterized in potato. In contrast, less work has been conducted on tomato. The Ph-3 gene from Solanum pimpinellifolium was introgressed into cultivated tomatoes and conferred broad-spectrum resistance to P. infestans. It was previously assigned to the long arm of chromosome 9. In this study, a high-resolution genetic map covering the Ph-3 locus was constructed using an F2 population of a cross between Solanum lycopersicum CLN2037B (containing Ph-3) and S. lycopersicum LA4084. Ph-3 was mapped in a 0.5 cM interval between two markers, Indel_3 and P55. Eight putative genes were found in the corresponding 74 kb region of the tomato Heinz1706 reference genome. Four of these genes are resistance gene analogs (RGAs) with a typical nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 domain. Each RGA showed high homology to the late blight R gene Rpi-vnt1.1 from Solanum venturii. Transient gene silencing indicated that a member of this RGA family is required for Ph-3-mediated resistance to late blight in tomato. Furthermore, this RGA family was also found in the potato genome, but the number of the RGAs was higher than in tomato.
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Affiliation(s)
- Chunzhi Zhang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
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Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, Isobe S, Tabata S. Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato. DNA Res 2013; 20:593-603. [PMID: 23903436 PMCID: PMC3859326 DOI: 10.1093/dnares/dst033] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
With the aim of understanding relationship between genetic and phenotypic variations in cultivated tomato, single nucleotide polymorphism (SNP) markers covering the whole genome of cultivated tomato were developed and genome-wide association studies (GWAS) were performed. The whole genomes of six tomato lines were sequenced with the ABI-5500xl SOLiD sequencer. Sequence reads covering ∼13.7× of the genome for each line were obtained, and mapped onto tomato reference genomes (SL2.40) to detect ∼1.5 million SNP candidates. Of the identified SNPs, 1.5% were considered to confer gene functions. In the subsequent Illumina GoldenGate assay for 1536 SNPs, 1293 SNPs were successfully genotyped, and 1248 showed polymorphisms among 663 tomato accessions. The whole-genome linkage disequilibrium (LD) analysis detected highly biased LD decays between euchromatic (58 kb) and heterochromatic regions (13.8 Mb). Subsequent GWAS identified SNPs that were significantly associated with agronomical traits, with SNP loci located near genes that were previously reported as candidates for these traits. This study demonstrates that attractive loci can be identified by performing GWAS with a large number of SNPs obtained from re-sequencing analysis.
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Affiliation(s)
- Kenta Shirasawa
- 1 Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
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Du FK, Xu F, Qu H, Feng S, Tang J, Wu R. Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database. PLoS One 2013; 8:e61337. [PMID: 23593466 PMCID: PMC3623821 DOI: 10.1371/journal.pone.0061337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/08/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL FINDINGS A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html). CONCLUSIONS The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.
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Affiliation(s)
- Fang K. Du
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fang Xu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hong Qu
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
| | - Sisi Feng
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
| | - Rongling Wu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami JF, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 2013; 20:173-84. [PMID: 23315685 PMCID: PMC3628447 DOI: 10.1093/dnares/dss042] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/21/2012] [Indexed: 02/02/2023] Open
Abstract
The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
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Shirasawa K, Hirakawa H. DNA marker applications to molecular genetics and genomics in tomato. BREEDING SCIENCE 2013; 63:21-30. [PMID: 23641178 PMCID: PMC3621441 DOI: 10.1270/jsbbs.63.21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 08/23/2012] [Indexed: 05/23/2023]
Abstract
Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding.
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Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S, Tabata S. Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 31:101-110. [PMID: 23316112 PMCID: PMC3538017 DOI: 10.1007/s11032-012-9774-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/01/2012] [Indexed: 05/04/2023]
Abstract
Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-012-9774-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
| | - Kohei Ishii
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | - Cholgwang Kim
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | | | - Takashi Ito
- Osaka University, Suita, Osaka, 565-0871 Japan
| | | | | | - Noriko Nagata
- Japan Women’s University, Bunkyo, Tokyo, 112-8681 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
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Asamizu E, Shirasawa K, Hirakawa H, Sato S, Tabata S, Yano K, Ariizumi T, Shibata D, Ezura H. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:437026. [PMID: 23227037 PMCID: PMC3514829 DOI: 10.1155/2012/437026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/18/2012] [Indexed: 05/29/2023]
Abstract
A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, "Heinz 1706." By referring to the "Heinz 1706" physical map and by eliminating redundant or nonsignificant hits, 28,804 "unique pair ends" and 8,263 "unique ends" were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.
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Affiliation(s)
- Erika Asamizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki 214-8571, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
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Sun YD, Liang Y, Wu JM, Li YZ, Cui X, Qin L. Dynamic QTL analysis for fruit lycopene content and total soluble solid content in a Solanum lycopersicum x S. pimpinellifolium cross. GENETICS AND MOLECULAR RESEARCH 2012; 11:3696-710. [PMID: 22930431 DOI: 10.4238/2012.august.17.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruit lycopene content and total soluble solid content are important factors determining fruit quality of tomatoes; however, the dynamic quantitative trait loci (QTL) controlling lycopene and soluble solid content have not been well studied. We mapped the chromosomal regions controlling these traits in different periods in F(2:3) families derived from a cross between the domestic and wild tomato species Solanum lycopersicum and S. pimpinellifolium. Fifteen QTLs for lycopene and soluble solid content and other related traits analyzed at three different fruit ripening stages were detected with a composite interval mapping method. These QTLs explained 7-33% of the individual phenotypic variation. QTLs detected in the color-changing period were different from those detected in the other two periods. On chromosome 1, the soluble solid content QTL was located in the same region during the color-changing and full-ripe periods. On chromosome 4, the same QTL for lycopene content was found during the color-changing and full-ripe periods. The QTL for lycopene content on chromosome 4 co-located with the QTL for soluble solid content during the full-ripe period. Co-location of lycopene content QTL and soluble solid content QTLs may be due to pleiotropic effects of a single gene or a cluster of genes via physiological relationships among traits. On chromosome 9, the same two QTLs for lycopene content at two different fruit ripening periods may reflect genes controlling lycopene content that are always expressed in tomato fruit development.
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Affiliation(s)
- Y D Sun
- Key Laboratory of Horticulture Plant Germplasm and Genetic Improvement, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, Shaanxi, China
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Moe KT, Kwon SW, Park YJ. Trends in genomics and molecular marker systems for the development of some underutilized crops. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0049-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Labate JA, Robertson LD. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. BMC PLANT BIOLOGY 2012; 12:133. [PMID: 22871151 PMCID: PMC3462117 DOI: 10.1186/1471-2229-12-133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/30/2012] [Indexed: 05/05/2023]
Abstract
BACKGROUND Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. RESULTS Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. CONCLUSION Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.
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Affiliation(s)
- Joanne A Labate
- USDA-ARS Plant Genetic Resources Unit, 630 W. North Street, Geneva, NY 14456, USA.
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Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 2012; 19:357-73. [PMID: 22864163 PMCID: PMC3473369 DOI: 10.1093/dnares/dss018] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.
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Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India
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Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A. Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:47-56. [PMID: 22350090 DOI: 10.1007/s00122-012-1815-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 01/31/2012] [Indexed: 05/07/2023]
Abstract
We constructed an integrated DNA marker linkage map of eggplant (Solanum melongena L.) using DNA marker segregation data sets obtained from two independent intraspecific F(2) populations. The linkage map consisted of 12 linkage groups and encompassed 1,285.5 cM in total. We mapped 952 DNA markers, including 313 genomic SSR markers developed by random sequencing of simple sequence repeat (SSR)-enriched genomic libraries, and 623 single-nucleotide polymorphisms (SNP) and insertion/deletion polymorphisms (InDels) found in eggplant-expressed sequence tags (ESTs) and related genomic sequences [introns and untranslated regions (UTRs)]. Because of their co-dominant inheritance and their highly polymorphic and multi-allelic nature, the SSR markers may be more versatile than the SNP and InDel markers for map-based genetic analysis of any traits of interest using segregating populations derived from any intraspecific crosses of practical breeding materials. However, we found that the distribution of microsatellites in the genome was biased to some extent, and therefore a considerable part of the eggplant genome was first detected when gene-derived SNP and InDel markers were mapped. Of the 623 SNP and InDel markers mapped onto the eggplant integrated map, 469 were derived from eggplant unigenes contained within Solanum orthologous (SOL) gene sets (i.e., sets of orthologous unigenes from eggplant, tomato, and potato). Out of the 469 markers, 326 could also be mapped onto the tomato map. These common markers will be informative landmarks for the transfer of tomato's more saturated genomic information to eggplant and will also provide comparative information on the genome organization of the two solanaceous species. The data are available from the DNA marker database of vegetables, VegMarks (http://vegmarks.nivot.affrc.go.jp).
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Affiliation(s)
- Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science (NIVTS), National Agriculture and Food Research Organization, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
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Choudhary S, Gaur R, Gupta S. EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1449-62. [PMID: 22301907 DOI: 10.1007/s00122-012-1800-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/05/2012] [Indexed: 05/17/2023]
Abstract
Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.
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Affiliation(s)
- Shalu Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No 10531, New Delhi 110067, India
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Yu X, Li X, Ma Y, Yu Z, Li Z. A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers. Genome 2012; 55:327-335. [PMID: 22462407 DOI: 10.1139/g2012-014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Using a population of 105 interspecific F2 hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. ‘Fairway’ as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future.
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Affiliation(s)
- Xiaoxia Yu
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010019, China
- Key Laboratory of Crop Genomics and Genetic Improvement, Ministry of Agriculture, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, China
| | - Xiaolei Li
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Yanhong Ma
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Zhuo Yu
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Zaozhe Li
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010019, China
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Sturbois B, Dubrana-Ourabah MP, Gombert J, Lasseur B, Macquet A, Faure C, Bendahmane A, Baurès I, Candresse T. Identification and characterization of tomato mutants affected in the Rx-mediated resistance to PVX isolates. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:341-54. [PMID: 22088194 DOI: 10.1094/mpmi-07-11-0181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Five tomato mutants affected in the Rx-mediated resistance against Potato virus X (PVX) were identified by screening a mutagenized population derived from a transgenic, Rx1-expressing 'Micro-Tom' line. Contrary to their parental line, they failed to develop lethal systemic necrosis upon infection with the virulent PVX-KH2 isolate. Sequence analysis and quantitative reverse-transcription polymerase chain reaction experiments indicated that the mutants are not affected in the Rx1 transgene or in the Hsp90, RanGap1 and RanGap2, Rar1 and Sgt1 genes. Inoculation with the PVX-CP4 avirulent isolate demonstrated that the Rx1 resistance was still effective in the mutants. In contrast, the virulent PVX-KH2 isolate accumulation was readily detectable in all mutants, which could further be separated in two groups depending on their ability to restrict the accumulation of PVX-RR, a mutant affected at two key positions for Rx1 elicitor activity. Finally, transient expression of the viral capsid protein elicitor indicated that the various mutants have retained the ability to mount an Rx1-mediated hypersensitive response. Taken together, the results obtained are consistent with a modification of the specificity or intensity of the Rx1-mediated response. The five Micro-Tom mutants should provide very valuable resources for the identification of novel tomato genes affecting the functioning of the Rx gene.
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Affiliation(s)
- Bénédicte Sturbois
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry d'Essonne, INRA, France.
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Sonnante G, Gatto A, Morgese A, Montemurro F, Sarli G, Blanco E, Pignone D. Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1215-29. [PMID: 21800142 DOI: 10.1007/s00122-011-1661-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/09/2011] [Indexed: 05/07/2023]
Abstract
An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F(1) progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.
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Affiliation(s)
- Gabriella Sonnante
- Institute of Plant Genetics, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy.
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Trujillo-Moya C, Gisbert C, Vilanova S, Nuez F. Localization of QTLs for in vitro plant regeneration in tomato. BMC PLANT BIOLOGY 2011; 11:140. [PMID: 22014149 PMCID: PMC3209458 DOI: 10.1186/1471-2229-11-140] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 10/20/2011] [Indexed: 05/24/2023]
Abstract
BACKGROUND Low regeneration ability limits biotechnological breeding approaches. The influence of genotype in the regeneration response is high in both tomato and other important crops. Despite the various studies that have been carried out on regeneration genetics, little is known about the key genes involved in this process. The aim of this study was to localize the genetic factors affecting regeneration in tomato. RESULTS We developed two mapping populations (F2 and BC1) derived from a previously selected tomato cultivar (cv. Anl27) with low regeneration ability and a high regeneration accession of the wild species Solanum pennellii (PE-47). The phenotypic assay indicated dominance for bud induction and additive effects for both the percentage of explants with shoots and the number of regenerated shoots per explant. Two linkage maps were developed and six QTLs were identified on five chromosomes (1, 3, 4, 7 and 8) in the BC1 population by means of the Interval Mapping and restricted Multiple QTL Mapping methods. These QTLs came from S. pennellii, with the exception of the minor QTL located on chromosome 8, which was provided by cv. Anl27. The main QTLs correspond to those detected on chromosomes 1 and 7. In the F2 population, a QTL on chromosome 7 was identified on a similar region as that detected in the BC1 population. Marker segregation distortion was observed in this population in those areas where the QTLs of BC1 were detected. Furthermore, we located two tomato candidate genes using a marker linked to the high regeneration gene: Rg-2 (a putative allele of Rg-1) and LESK1, which encodes a serine/threonine kinase and was proposed as a marker for regeneration competence. As a result, we located a putative allele of Rg-2 in the QTL detected on chromosome 3 that we named Rg-3. LESK1, which is also situated on chromosome 3, is outside Rg-3. In a preliminary exploration of the detected QTL peaks, we found several genes that may be related to regeneration. CONCLUSIONS In this study we have identified new QTLs related to the complex process of regeneration from tissue culture. We have also located two candidate genes, discovering a putative allele of the high regeneration gene Rg-1 in the QTL on chromosome 3. The identified QTLs could represent a significant step toward the understanding of this process and the identification of other related candidate genes. It will also most likely facilitate the development of molecular markers for use in gene isolation.
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Affiliation(s)
- Carlos Trujillo-Moya
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV) Universitat Politècnica de València, Camino de Vera, 14 46022 Valencia, Spain
| | - Carmina Gisbert
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV) Universitat Politècnica de València, Camino de Vera, 14 46022 Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV) Universitat Politècnica de València, Camino de Vera, 14 46022 Valencia, Spain
| | - Fernando Nuez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV) Universitat Politècnica de València, Camino de Vera, 14 46022 Valencia, Spain
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Shokeen B, Choudhary S, Sethy NK, Bhatia S. Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus. ANNALS OF BOTANY 2011; 108:321-336. [PMID: 21788377 PMCID: PMC3143056 DOI: 10.1093/aob/mcr162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/27/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Catharanthus roseus is a plant of great medicinal importance, yet inadequate knowledge of its genome structure and the unavailability of genomic resources have been major impediments in the development of improved varieties. The aims of this study were to develop co-dominant sequence-tagged microsatellite sites (STMS) and gene-targeted markers (GTMs) and utilize them for the construction of a framework intraspecific linkage map of C. roseus. METHODS For simple sequence repeat (SSR) isolation, a genomic library enriched for (GA)(n) repeats was constructed from C. roseus 'Nirmal' (CrN1). In addition, GTMs were also designed from 12 genes of the TIA (terpenoid indole alkaloid) pathway - the medicinally most significant pathway in C. roseus. An F(2) mapping population was also generated by crossing two diverse accessions of C. roseus CrN1 (Nirmal)×CrN82 (Kew). KEY RESULTS A new set of 314 STMS markers and 64 GTMs were developed in this study. A segregating F(2) mapping population consisting of 111 F(2) individuals was generated. For generating the linkage map, a set of 423 co-dominant markers (378 newly developed and 45 published earlier) were screened for polymorphism between the parental genotypes, of which 134 were identified to be polymorphic. A total of 114 markers were mapped on eight linkage groups that spanned a 632·7 cM region of the genome with an average marker distance of 5·55 cM. Further, the mechanism of hypervariability at the gene-targeted loci was investigated at the sequence level. CONCLUSIONS For the first time, a large array of STMS markers and GTMs was generated in the model medicinal plant C. roseus. Moreover, the first microsatellite marker-based linkage map was described in this study. Together, these will serve as a foundation for future genomics studies related to quantitative trait loci analysis and molecular breeding in C. roseus.
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Affiliation(s)
- Bhumika Shokeen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Shalu Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Niroj Kumar Sethy
- Peptide and Proteomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Timarpur, Delhi-110054, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
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Bindler G, Plieske J, Bakaher N, Gunduz I, Ivanov N, Van der Hoeven R, Ganal M, Donini P. A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:219-30. [PMID: 21461649 PMCID: PMC3114088 DOI: 10.1007/s00122-011-1578-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 03/15/2011] [Indexed: 05/19/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco genome. The genetic map was generated using an F2 mapping population derived from the intervarietal cross of Hicks Broadleaf × Red Russian and merges the polymorphic markers from this new set with those from a smaller set previously used to produce a lower density map. The genetic map described here contains 2,317 microsatellite markers and 2,363 loci, resulting in an average distance between mapped microsatellite markers which is less than 2 million base pairs or 1.5 cM. With this new and expanded marker resource, a sufficient number of markers are now available for multiple applications ranging from tobacco breeding to comparative genome analysis. The genetic map of tobacco is now comparable in marker density and resolution with the best characterized genomes of the Solanaceae: tomato and potato.
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Affiliation(s)
- Gregor Bindler
- Applied Research Department, Philip Morris International, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Jörg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466 Gatersleben, Germany
| | - Nicolas Bakaher
- Applied Research Department, Philip Morris International, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Irfan Gunduz
- Applied Research Department, Philip Morris International, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nikolai Ivanov
- Applied Research Department, Philip Morris International, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Rutger Van der Hoeven
- Applied Research Department, Philip Morris International, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
- Present Address: KWS SAAT AG, P.O. Box 1463, 37555 Einbeck, Germany
| | - Martin Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466 Gatersleben, Germany
| | - Paolo Donini
- Applied Research Department, Philip Morris International, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
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Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S. An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 2011; 18:221-32. [PMID: 21669962 PMCID: PMC3158468 DOI: 10.1093/dnares/dsr013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon.
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Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 2011; 12:304. [PMID: 21663628 PMCID: PMC3128069 DOI: 10.1186/1471-2164-12-304] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/10/2011] [Indexed: 11/10/2022] Open
Abstract
Background The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant. Results RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci. Conclusion The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.
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Affiliation(s)
- Lorenzo Barchi
- DIVAPRA Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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