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Siddique MI, Silverman E, Louws F, Panthee DR. Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes. PLANTS (BASEL, SWITZERLAND) 2024; 13:876. [PMID: 38592886 PMCID: PMC10976105 DOI: 10.3390/plants13060876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Bacterial wilt (BW) of tomatoes, caused by Ralstonia solanacearum, is a devastating disease that results in large annual yield losses worldwide. Management of BW of tomatoes is difficult due to the soil-borne nature of the pathogen. One of the best ways to mitigate the losses is through breeding for disease resistance. Moreover, plant height (PH) is a crucial element related to plant architecture, which determines nutrient management and mechanical harvesting in tomatoes. An intraspecific F2 segregating population (NC 11212) of tomatoes was developed by crossing NC 84173 (tall, BW susceptible) × CLN1466EA (short, BW resistant). We performed quantitative trait loci (QTL) mapping using single nucleotide polymorphic (SNP) markers and the NC 11212 F2 segregating population. The QTL analysis for BW resistance revealed a total of three QTLs on chromosomes 1, 2, and 3, explaining phenotypic variation (R2) ranging from 3.6% to 14.9%, whereas the QTL analysis for PH also detected three QTLs on chromosomes 1, 8, and 11, explaining R2 ranging from 7.1% to 11%. This work thus provides information to improve BW resistance and plant architecture-related traits in tomatoes.
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Affiliation(s)
- Muhammad Irfan Siddique
- Mountain Horticultural Crops Research and Extension Center, Department of Horticultural Science, North Carolina State University, 455 Research Dr., Mills River, NC 28759, USA
| | - Emily Silverman
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Frank Louws
- Mountain Horticultural Crops Research and Extension Center, Department of Horticultural Science, North Carolina State University, 455 Research Dr., Mills River, NC 28759, USA
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dilip R. Panthee
- Mountain Horticultural Crops Research and Extension Center, Department of Horticultural Science, North Carolina State University, 455 Research Dr., Mills River, NC 28759, USA
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Adhikari P, Siddique MI, Louws FJ, Panthee DR. Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.). PLoS One 2023; 18:e0295551. [PMID: 38079392 PMCID: PMC10712892 DOI: 10.1371/journal.pone.0295551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Bacterial spot of tomato is a serious disease caused by at least four species and four races of Xanthomonas- X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (race T3 and T4), and X. gardneri, with X. perforans race T4 being predominant in the southeast USA. Practical management of this disease is challenging because of the need for more effective chemicals and commercially resistant cultivars. Identification of genetic resistance is the first step to developing a disease-resistant variety. The objective of this study was to identify quantitative trait loci (QTL) conferring resistance to race T4 in two independent recombinant inbred lines (RILs) populations NC 10204 (intra-specific) and NC 13666 (interspecific) developed by crossing NC 30P x NC22L-1(2008) and NC 1CELBR x PI 270443, respectively. Seven QTLs on chromosomes 2, 6, 7, 11, and 12 were identified in NC 10204. The QTL on chromosome 6 explained the highest percentage of phenotypic variance (up to 21.3%), followed by the QTL on chromosome 12 (up to 8.2%). On the other hand, the QTLs on chromosomes 1, 3, 4, 6, 7, 8, 9, and 11 were detected in NC 13666. The QTLs on chromosomes 6, 7, and 11 were co-located in NC 10204 and NC 13666 populations. The donor of the resistance associated with these QTL in NC 10204 is a released breeding line with superior horticultural traits. Therefore, both the donor parent and the QTL information will be useful in tomato breeding programs as there will be minimal linkage drag associated with the bacterial spot resistance.
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Affiliation(s)
- Pragya Adhikari
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
- Bayer Crop Science, Huxley, Iowa, United States of America
| | - Muhammad Irfan Siddique
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
| | - Frank J. Louws
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
- Department of Horticultural Science and Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Dilip R. Panthee
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
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Shahwar D, Khan Z, Park Y. Molecular Marker-Assisted Mapping, Candidate Gene Identification, and Breeding in Melon ( Cucumis melo L.): A Review. Int J Mol Sci 2023; 24:15490. [PMID: 37895169 PMCID: PMC10607903 DOI: 10.3390/ijms242015490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Melon (Cucumis melo L.) is an important crop that is cultivated worldwide for its fleshy fruit. Understanding the genetic basis of a plant's qualitative and quantitative traits is essential for developing consumer-favored varieties. This review presents genetic and molecular advances related to qualitative and quantitative phenotypic traits and biochemical compounds in melons. This information guides trait incorporation and the production of novel varieties with desirable horticultural and economic characteristics and yield performance. This review summarizes the quantitative trait loci, candidate genes, and development of molecular markers related to plant architecture, branching patterns, floral attributes (sex expression and male sterility), fruit attributes (shape, rind and flesh color, yield, biochemical compounds, sugar content, and netting), and seed attributes (seed coat color and size). The findings discussed in this review will enhance demand-driven breeding to produce cultivars that benefit consumers and melon breeders.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
| | - Zeba Khan
- Center for Agricultural Education, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India;
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
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Adhikari TB, Siddique MI, Louws FJ, Sim SC, Panthee DR. Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes. FRONTIERS IN PLANT SCIENCE 2023; 14:1135884. [PMID: 37324699 PMCID: PMC10267708 DOI: 10.3389/fpls.2023.1135884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F2 and F2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F2 population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes.
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Affiliation(s)
- Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Muhammad Irfan Siddique
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC, United States
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul, Republic of Korea
| | - Dilip R. Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC, United States
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Zhao H, Zhang T, Meng X, Song J, Zhang C, Gao P. Genetic Mapping and QTL Analysis of Fruit Traits in Melon ( Cucumis melo L.). Curr Issues Mol Biol 2023; 45:3419-3433. [PMID: 37185748 PMCID: PMC10137213 DOI: 10.3390/cimb45040224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Melon (Cucumis melo L.) is an important horticultural cash crop and its quality traits directly affect consumer choice and market price. These traits are controlled by genetic as well as environmental factors. In this study, a quantitative trait locus (QTL) mapping strategy was used to identify the potential genetic loci controlling quality traits of melons (i.e., exocarp and pericarp firmness and soluble solid content) based on newly derived whole-genome single nucleotide polymorphism-based cleaved amplified polymorphic sequence (SNP-CAPS) markers. Specifically, SNPs of two melon varieties, M4-5 and M1-15, as revealed by whole-genome sequencing, were converted to the CAPS markers, which were used to construct a genetic linkage map comprising 12 chromosomes with a total length of 1414.88 cM, in the F2 population of M4-5 and M1-15. The six identified QTLs included: SSC6.1 and SSC11.1 related to soluble solid content; EF12.1 associated with exocarp firmness; and EPF3.1, EPF3.2 and EPF7.1 related to edible pericarp firmness. These genes were located on five chromosomes (3, 6, 7, 11, and 12) in the flanking regions of the CAPS markers. Moreover, the newly developed CAPS markers will be useful in guiding genetic engineering and molecular breeding in melon.
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Affiliation(s)
- Haiyong Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Taifeng Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Xiaobing Meng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Jiayan Song
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
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Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane. Genes (Basel) 2022; 13:genes13081477. [PMID: 36011388 PMCID: PMC9408448 DOI: 10.3390/genes13081477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding
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