Fine Mapping of the brachytic Locus on the Tomato Genome

Lee, Tong Geon; Hutton, Samuel F.; Shekasteband, Reza

doi:10.21273/jashs04423-18

Cited by 12 publications

(25 citation statements)

References 21 publications

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“…WHOLE-GENOME SEQUENCING. Plants were grown as previously described [Phenotype analysis section in the work by Lee et al (2018)]. Genomic DNA was extracted with a DNeasy Plant Mini Kit (Qiagen, Germantown, MD).…”

Section: Methodsmentioning

confidence: 99%

A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

Bhandari¹,

Lee²

2021

J. Amer. Soc. Hort. Sci.

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Genetic maps saturated with genetic markers are useful for genetic research and crop breeding; however, the genetic map for the large-fruited fresh-market tomato (Solanum lycopersicum) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. We constructed a novel fresh-market tomato genetic map by using 3614 single nucleotide polymorphism (SNP) markers and a 93 F2 segregating progeny derived from a cross between two United States large-fruited fresh-market tomato lines. The average distance between markers was less than 1 cM, and substantial recombination densities between markers were observed across the approximate centromere locations. A linkage panel for large-fruited fresh-market tomato was also established using the combined dataset of the genetic map and 58 SNP-genotyped core tomato lines. The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches.

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Section: Methodsmentioning

confidence: 99%

A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

Bhandari¹,

Lee²

2021

J. Amer. Soc. Hort. Sci.

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“…Plants were grown as previously described ("Phenotype analysis" section in Lee et al [16]. Field trials were conducted in three consecutive growing seasons during 2020 and 2021 at the Gulf Coast Research and Education Center (Wimauma, FL, USA) of the University of Florida, where conditions are representative of typical field fresh-market tomato production environments in the Southeastern U.S. During the spring of 2020, seed sowing in the greenhouse (S), seedling transplanting to the field (T), and fruit harvest (H) were performed on 22 January, 4 March, and 23 May, respectively.…”

Section: Phenotypic Data Collectionmentioning

confidence: 99%

Field Evaluation of CRISPR-Driven Jointless Pedicel Fresh-Market Tomatoes

Lee

Hutton

2021

Agronomy

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Clustered regularly interspaced short palindromic repeats (CRISPR)-driven traits are commonly introduced into tomato (Solanum lycopersicum) in less than a year. Although CRISPR technology is highly suitable for rapid incorporation of new traits into plants with superior breeding backgrounds, the usefulness of these traits must be demonstrated prior to large-scale distribution of any new variety possessing them. The jointless pedicel trait is crucial for stem-free harvest of tomato fruits and is therefore an essential requirement for developing low-labor tomato varieties. We aimed to evaluate the effect of CRISPR-driven jointless pedicel trait on the yield and horticultural traits of fresh-market tomatoes. We conducted field trials during three consecutive seasons using three related genotypes of two elite fresh-market tomatoes, namely a jointed pedicel tomato, a CRISPR-driven jointless pedicel mutant of the jointed pedicel tomato, and a conventionally-bred jointless pedicel near isogenic line (NIL) to the jointed pedicel tomato. Field evaluations confirmed that the total and medium-, large-, or extra-large-size fruit yields of the CRISPR-driven mutants were not statistically different for those corresponding to their backgrounds and that the fruit yield stratified by fruit size might be varied under different growth conditions. We did not observe any negative correlation between the genotype and the fruit/abscission joint detachment force for any of the genotypes under study.

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“…However, fresh-market tomatoes are usually grown on stakes or with strings in open fields or in protected agricultural areas (greenhouse, shade-house, and tunnel), requiring intensive labor for harvesting, staking, and tying. The compact growth habit (CGH) tomato with a lower plant height is an ideal fresh-market tomato architecture for mechanical harvest and reduces manual dependence (Frasca et al, 2014;Lee et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…It contains a mutation in a gene homolog to Arabidopsis ERECTA (ER) (Kwon et al, 2020). The br locus can reduce plant height and has been narrowed down to an interval of 763.1 kb on chromosome 1 (Lee et al, 2018), but the gene has not been cloned.…”

Section: Introductionmentioning

confidence: 99%

“…Several mutants related to plant height have been reported and some genes responsible for the phenotypes have been cloned in tomato. Mutants self-pruning ( sp ) ( MacArthur, 1932 ), semideterminate ( sdt ) ( Elkind et al, 1991 ), and suppressor of sp ( ssp ) ( Park et al, 2014 ) affect the number of internodes, while mutants brachytic ( br ) ( Lee et al, 2018 ), dwarf ( d ) ( Bishop et al, 1996 ), Elongated Internode ( EI ) ( Sun et al, 2019 ), gibberellin deficient-1 ( gib-1 ), gib-2 , gib-3 ( Koornneef et al, 1990 ), procera ( pro ) ( Jupe et al, 1988 ), short internode ( si ) ( Kwon et al, 2020 ), and tomato internode elongated -1 ( tie-1 ) ( Schrager-Lavelle et al, 2019 ) affect internode length. The sp mutant shows determinate growth habit.…”

Section: Introductionmentioning

confidence: 99%

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SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height

et al. 2020

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Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R 2), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL-qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL-qtph1.1 could not be rescued by exogenous GA 3 treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL-qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.

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Fine Mapping of the brachytic Locus on the Tomato Genome

Cited by 12 publications

References 21 publications

A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

Field Evaluation of CRISPR-Driven Jointless Pedicel Fresh-Market Tomatoes

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height

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