Identification and Characterization of EI (Elongated Internode) Gene in Tomato (Solanum lycopersicum)

Sun, Xiaorong; Shu, Jinshuai; Mohamed, Ali Mohamed Ali; Deng, Xiaojie; Zhi, Xiaona; Bai, Jinrui; Cui, Yanan; Lu, Xiaoxiao; Du, Yan; Wang, Xiaoxuan; Huang, Zejun; Guo, Yanmei; Liu, Lei; Li, Junming

doi:10.3390/ijms20092204

Cited by 20 publications

(10 citation statements)

References 67 publications

(78 reference statements)

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“…Mutants deficient in GA biosynthesis can be rescued by exogenous application of bioactive GAs; however, it is not possible if the mutation is in the GA signaling pathway [70,71]. A number of GAR dwarf mutants has been isolated from various plant species, including watermelon, maize, pea, tomato, Arabidopsis, rice and wheat [5,68,[72][73][74]. In this study, the internode length and vine length increased in the short internode plants after exogenous GA 3 application.…”

Section: Discussionmentioning

confidence: 80%

Molecular Mapping and Candidate Gene Analysis for GA3 Responsive Short Internode in Watermelon (Citrullus lanatus)

Gebremeskel

Dou

et al. 2019

IJMS

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Plants with shorter internodes are suitable for high-density planting, lodging resistance and the preservation of land resources by improving yield per unit area. In this study, we identified a locus controlling the short internode trait in watermelon using Zhengzhouzigua (long internode) and Duan125 (short internode) as mapping parents. Genetic analysis indicated that F1 plants were consistent with long internode plants, which indicates that the long internode was dominant over the short internode. The observed F2 and BC1 individuals fitted the expected phenotypic segregation ratios of 3:1 and 1:1, respectively. The locus was mapped on chromosome 9 using a bulked segregant analysis approach. The region was narrowed down to 8.525 kb having only one putative gene, Cla015407, flanking by CAPS90 and CAPS91 markers, which encodes gibberellin 3β-hydroxylase (GA 3β-hydroxylase). The sequence alignment of the candidate gene between both parents revealed a 13 bp deletion in the short internode parent, which resulted in a truncated protein. Before GA3 application, significantly lower GA3 content and shorter cell length were obtained in the short internode plants. However, the highest GA3 content and significant increase in cell length were observed in the short internode plants after exogenous GA3 application. In the short internode plants, the expression level of the Cla015407 was threefold lower than the long internode plants in the stem tissue. In general, our results suggested that Cla015407 might be the candidate gene responsible for the short internode phenotype in watermelon and the phenotype is responsive to exogenous GA3 application.

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Section: Discussionmentioning

confidence: 80%

Molecular Mapping and Candidate Gene Analysis for GA3 Responsive Short Internode in Watermelon (Citrullus lanatus)

Gebremeskel

Dou

et al. 2019

IJMS

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“…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%

“…EI and tie-1 exhibit elongated internode. Both of them result from the loss function of the GA 2-beta-dioxygenase 7 ( SlGA2ox7 ) gene, which converts bioactive GAs to inactive GAs ( Schrager-Lavelle et al, 2019 ; Sun et al, 2019 ). The pro mutant displays higher plant height than the wild type (WT), which is similar to the phenotype of the WT treated with exogenous GA.…”

Section: Introductionmentioning

confidence: 99%

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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“…In recent years, with the rapid development of next-generation sequencing technology (NGS) and bioinformatics tools, the linkage and association mapping methods have been widely used for rapid detection of QTLs and candidate genes [15,16,17,18,19,20,21]. Furthermore, mutants have been proven to be very important materials for the study of the inheritance and molecular basis for complex agronomic traits [16,22,23,24,25], especially for diploid cultivated sesame with the smaller genome size of 354 Mb [2]. A sesame mutant simultaneously affecting the traits of seed number per capsule and CL named Yuzhi sn ( cs1 line) was created from the sesame cultivar Yuzhi 11 (selected as the reference genome for the Sesame Genome Project) using EMS mutagenesis in 2010.…”

Section: Introductionmentioning

confidence: 99%

A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame

Wei

Chun

Duan

et al. 2019

IJMS

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Seed number per capsule (SNC) is a major factor influencing seed yield and is an important trait with complex gene interaction effects. We first performed genetic analysis, gene cloning, and molecular mechanism study for an EMS-induced sesame mutant cs1 with fewer SNC and shorter capsule length (CL). The mutant traits were due to the pleiotropism of a regressive gene (Sics1). Capsule hormone determination showed that five out of 12 hormones, including auxin indole-3-acetic acid (IAA), had significantly different levels between wild type (WT) and mutant type (MT). KEGG pathway analysis showed that plant hormone signal transduction, especially the auxin signal transduction pathway, was the most abundant differentially expressed signaling pathway. After the cross-population association and regional genome screening, we found that three homozygous loci were retained in cs1. Further analysis of these three loci resulted in the identification of SiCRC as the candidate gene for cs1. SiCRC consists of seven exons and six introns encoding 163 amino acids. The SiCRC in cs1 showed a point mutation at intron 5 and exon 6 junction, resulting in the splice site being frame-shifted eight nucleotides further downstream, causing incorrect splicing. Taken together, we assumed the SNP mutation in SiCRC disrupted the function of the transcription factor, which might act downstream of the CRC-auxin signal transduction pathway, resulting in a shorter CL and less SNC mutation of cs1 in sesame. Our results highlight the molecular framework underlying the transcription factor CRC-mediated role of auxin transduction in SNC and CL development.

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Identification and Characterization of EI (Elongated Internode) Gene in Tomato (Solanum lycopersicum)

Cited by 20 publications

References 67 publications

Molecular Mapping and Candidate Gene Analysis for GA3 Responsive Short Internode in Watermelon (Citrullus lanatus)

Molecular Mapping and Candidate Gene Analysis for GA3 Responsive Short Internode in Watermelon (Citrullus lanatus)

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

A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame

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