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

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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A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.)

Scientific Reports ◽

10.1038/s41598-020-71861-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yuyan Sun ◽

Huiqing Zhang ◽

Min Fan ◽

Yanjun He ◽

Pingan Guo

Keyword(s):

Citrullus Lanatus ◽

Recessive Gene ◽

Labor Cost ◽

Chromosome 9 ◽

Splice Acceptor Site ◽

Acceptor Site ◽

Splice Acceptor ◽

Subcellular Targeting ◽

Lodging Resistance ◽

Intron Splice

Abstract Dwarf architecture is an important trait associated with plant yield, lodging resistance and labor cost. Here, we aimed to identify a gene causing dwarfism in watermelon. The ‘w106’ (dwarf) and ‘Charleston Gray’ (vine) were used as parents to construct F1 and F2 progeny. Dwarf architecture of ‘w106’ was mainly caused by longitudinal cell length reduction and was controlled by a single recessive gene. Whole-genome sequencing of two parents and two bulk DNAs of F2 population localized this gene to a 2.63-Mb region on chromosome 9; this was further narrowed to a 541-kb region. Within this region, Cla015407, encoding a gibberellin 3β-hydroxylase (GA3ox), was the candidate gene. Cla015407 had a SNP mutation (G → A) in the splice acceptor site of the intron, leading to altered splicing event and generating two splicing isoforms in dwarf plants. One splicing isoform retained the intron sequences, while the other had a 13-bp deletion in the second exon of GA3ox transcript, both resulting in truncated proteins and loss of the functional Fe2OG dioxygenase domain in dwarf plants. RNA-Seq analysis indicated that expression of Cla015407 and other GA biosynthetic and metabolic genes were mostly up-regulated in the shoots of dwarf plants compared with vine plants in F2 population. Measurement of endogenous GA levels indicated that bioactive GA4 was significantly decreased in the shoots of dwarf plants. Moreover, the dwarf phenotype can be rescued by exogenous applications of GA3 or GA4+7, with the latter having a more distinct effect than the former. Subcellular localization analyses of GA3ox proteins from two parents revealed their subcellular targeting in nucleus and cytosol. Here, a GA3ox gene controlling dwarf architecture was identified, and loss function of GA3ox leads to GA4 reduction and dwarfism phenotype in watermelon.

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Fine Mapping of Cla015407 Controlling Plant Height in Watermelon

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04934-20 ◽

2021 ◽

pp. 1-26

Author(s):

Taifeng Zhang ◽

Jiajun Liu ◽

Sikandar Amanullah ◽

Zhuo Ding ◽

Haonan Cui ◽

...

Keyword(s):

Gibberellic Acid ◽

Fine Mapping ◽

Growth Habit ◽

Gene Annotation ◽

Bulked Segregant Analysis ◽

Citrullus Lanatus ◽

Chromosome 9 ◽

Land Utilization ◽

Site Mutation ◽

Significant Difference

The plant compact and dwarf growth habit is an important agronomic trait when breeding watermelon (Citrullus lanatus) cultivars because of their reduced vine length, high-density planting, and better land utilization; however, the genetic basis of the dwarf growth habit is not well-known. In this study, the plant population of six generations, P1, P2, F1, F2, BC1P1, and BC1P2, were studied. A genetic segregation analysis demonstrated that dwarfism is mainly controlled by a single recessive Cldw gene. Furthermore, whole-genome sequencing of two distinct watermelon cultivars, W1-1 (P1) and 812 (P2), was performed and preliminarily mapped through a bulked segregant analysis of F2 individuals that revealed the Cldw gene locus on chromosome 9. Two candidate genes, Cla015407 and Cla015408, were discovered at the delimited region of 43.2 kb by fine mapping, and gene annotation exposed that the Cla015407 gene encodes gibberellic acid 3β-hydroxylase protein. In addition, a comparative analysis of gene sequence and cultivars sequences across the reference genome of watermelon revealed the splice site mutation in the intron region of the Cldw gene in dwarf-type cultivar 812. The quantitative real-time polymerase chain reaction exhibited a significantly higher expression of the Cla015407 gene in cultivar W1-1 compared with 812. There was no significant difference in the vine length of both cultivars after gibberellic acid treatment. In brief, our fine mapping demonstrated that Cla015407 is a candidate gene controlling dwarfism of watermelon plants.

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QTL Mapping Identifies Novel Source of Resistance to Fusarium Wilt Race 1 in Citrullus amarus

Plant Disease ◽

10.1094/pdis-09-18-1677-re ◽

2019 ◽

Vol 103 (5) ◽

pp. 984-989 ◽

Cited By ~ 4

Author(s):

Sandra E. Branham ◽

Amnon Levi ◽

W. Patrick Wechter

Keyword(s):

Fusarium Wilt ◽

Citrullus Lanatus ◽

Recombinant Inbred Lines ◽

The United States ◽

Chromosome 9 ◽

Mapping Study ◽

Sources Of Resistance ◽

Race 1 ◽

Genetic Source ◽

Genetic Mapping Study

Fusarium wilt race 1, caused by the soilborne fungus Fusarium oxysporum Schlechtend.: Fr. f. sp. niveum (E.F. Sm.) W.C. Snyder & H.N. Hans (Fon), is a major disease of watermelon (Citrullus lanatus) in the United States and throughout the world. Although Fusarium wilt race 1 resistance has been incorporated into several watermelon cultivars, identification of additional genetic sources of resistance is crucial if a durable and sustainable level of resistance is to be continued over the years. We conducted a genetic mapping study to identify quantitative trait loci (QTLs) associated with resistance to Fon race 1 in segregating populations (F2:3 and recombinant inbred lines) of Citrullus amarus (citron melon) derived from the Fon race 1 resistant and susceptible parents USVL246-FR2 and USVL114, respectively. A major QTL (qFon1-9) associated with resistance to Fon race 1 was identified on chromosome 9 of USVL246-FR2. This discovery provides a novel genetic source of resistance to Fusarium wilt race 1 in watermelon and, thus, an additional host-resistance option for watermelon breeders to further the effort to mitigate this serious phytopathogen.

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Molecular mapping and identification of a candidate gene for new locus Hg2 conferring hairy glume in wheat

Plant Science ◽

10.1016/j.plantsci.2021.110879 ◽

2021 ◽

Vol 307 ◽

pp. 110879

Author(s):

Peipei Wu ◽

Li Yang ◽

Guanghao Guo ◽

Jinghuang Hu ◽

Dan Qiu ◽

...

Keyword(s):

Candidate Gene ◽

Molecular Mapping

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Molecular mapping of a thermosensitive genetic male sterility gene in rice using bulked segregant analysis

Genome ◽

10.1139/g97-027 ◽

1997 ◽

Vol 40 (2) ◽

pp. 188-194 ◽

Cited By ~ 59

Author(s):

P. K. Subudhi ◽

R. P. Borkakati ◽

S. S. Virmani ◽

N. Huang

Keyword(s):

Male Sterility ◽

Molecular Mapping ◽

Bulked Segregant Analysis ◽

Pcr Primers ◽

Rflp Markers ◽

Arbitrary Primers ◽

Repulsion Phase ◽

Genetic Male Sterility ◽

True Breeding ◽

Efficient Alternative

The thermosensitive genetic male sterility (TGMS) system is considered to be a more efficient alternative to the cytoplasmic male sterility (CMS) system for hybrid rice. An F2 population from a cross between a TGMS mutant line (IR32364TGMS) and IR68 was used to map the TGMS gene tms3(t). Fertile and sterile bulks were constructed following the classification of F2 plants into true breeding sterile, fertile, and segregating fertile plants based on F3 family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF182600, OPB19750, and OPAA7550, were linked to tms3(t) in repulsion phase and one, OPAC3640, was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF182600 and OPAC3640 on one side and by OPAA7550 and OPB19750 on the other side. All four markers were low-copy sequences and two of them (OPF182600 and OPAC3640) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3640 was mapped to the short arm of chromosome 6 using a mapping population available at IRRI. However, no RFLP markers from this region showed linkage to tms3(t) owing to the lack of polymorphism between the parents. All RAPD fragments were cloned and partially sequenced from both ends. Thus, PCR primers can be designed to develop PCR markers for marker-assisted breeding to facilitate the transfer of tms3(t) from one genetic background to another.Key words: bulked segregant analysis, gene tagging, marker-assisted selection, RAPD, TGMS.

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Molecular mapping and candidate gene analysis for fruit epidermal structure in cucumber

Plant Breeding ◽

10.1111/pbr.12510 ◽

2017 ◽

Vol 136 (5) ◽

pp. 767-774 ◽

Cited By ~ 1

Author(s):

Song Zhang ◽

Han Miao ◽

Zichao Song ◽

Panna Liu ◽

Ye Wang ◽

...

Keyword(s):

Candidate Gene ◽

Molecular Mapping ◽

Gene Analysis ◽

Epidermal Structure ◽

Candidate Gene Analysis

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Genetic Mapping and Discovery of the Candidate Gene for Black Seed Coat Color in Watermelon (Citrullus lanatus)

Frontiers in Plant Science ◽

10.3389/fpls.2019.01689 ◽

2020 ◽

Vol 10 ◽

Cited By ~ 1

Author(s):

Bingbing Li ◽

Xuqiang Lu ◽

Haileslassie Gebremeskel ◽

Shengjie Zhao ◽

Nan He ◽

...

Keyword(s):

Genetic Mapping ◽

Candidate Gene ◽

Seed Coat ◽

Coat Color ◽

Citrullus Lanatus ◽

Seed Coat Color ◽

Black Seed ◽

Black Seed Coat

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Molecular Mapping of the Stb4 Gene for Resistance to Septoria tritici Blotch in Wheat

Phytopathology ◽

10.1094/phyto.2004.94.11.1198 ◽

2004 ◽

Vol 94 (11) ◽

pp. 1198-1206 ◽

Cited By ~ 58

Author(s):

Tika B. Adhikari ◽

Jessica R. Cavaletto ◽

Jorge Dubcovsky ◽

Jorge Omar Gieco ◽

Ana Rosa Schlatter ◽

...

Keyword(s):

Molecular Mapping ◽

Bulked Segregant Analysis ◽

Recombinant Inbred Lines ◽

Single Gene ◽

Effective Means ◽

Wheat Chromosome ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

Adult Plant ◽

Field Season

Breeding wheat for resistance is the most effective means to control Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola (anamorph Septoria tritici). At least eight genes that confer resistance to STB in wheat have been identified. Among them, the Stb4 locus from the wheat cv. Tadinia showed resistance to M. graminicola at both seedling and adult-plant stages. However, no attempt has been made to map the Stb4 locus in the wheat genome. A mapping population of 77 F10 recombinant-inbred lines (RILs) derived from a three-way cross between the resistant cv. Tadinia and the susceptible parent (Yecora Rojo × UC554) was evaluated for disease resistance and molecular mapping. The RILs were tested with Argentina isolate I 89 of M. graminicola for one greenhouse season in Brazil during 1999, with an isolate from Brazil (IPBr1) for one field season in Piracicaba (Brazil) during 2000, and with Indiana tester isolate IN95-Lafayette-1196-WW-1-4 in the greenhouse during 2000 and 2001. The ratio of resistant:susceptible RILs was 1:1 in all three tests, confirming the single-gene model for control of resistance to STB in Tadinia. However, the patterns of resistance and susceptibility were different between the Indiana isolate and those from South America. For example, the ratio of RILs resistant to both the Indiana and Argentina isolates, resistant to one but susceptible to the other, and susceptible to both isolates was approximately 1:1:1:1, indicating that Tadinia may contain at least two genes for resistance to STB. A similar pattern was observed between the Indiana and Brazil isolates. The gene identified with the Indiana tester isolate was assumed to be the same as Stb4, whereas that revealed by the South American isolates may be new. Bulked-segregant analysis was used to identify amplified fragment length polymorphism (AFLP) and microsatellite markers linked to the presumed Stb4 gene. The AFLP marker EcoRI-ACTG/MseI-CAAA5 and microsatellite Xgwm111 were closely linked to the Stb4 locus in coupling at distances of 2.1 and 0.7 centimorgans (cM), respectively. A flanking marker, AFLP EAGG/ M-CAT10, was 4 cM from Stb4. The Stb4 gene was in a potential supercluster of resistance genes near the centromere on the short arm of wheat chromosome 7D that also contained Stb5 plus five previously identified genes for resistance to Russian wheat aphid. The microsatellite marker Xgwm111 identified in this study may be useful for facilitating the transfer of Stb4 into improved cultivars of wheat.

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Identification and mapping of a leaf rust resistance gene in barley line Q21861

Genome ◽

10.1139/g97-033 ◽

1997 ◽

Vol 40 (2) ◽

pp. 236-241 ◽

Cited By ~ 31

Author(s):

I. G. Borovkova ◽

B. J. Steffenson ◽

Y. Jin ◽

A. Kilian ◽

A. Kleinhofs ◽

...

Keyword(s):

Leaf Rust ◽

Molecular Mapping ◽

Bulked Segregant Analysis ◽

Dominant Gene ◽

Puccinia Hordei ◽

Doubled Haploid Population ◽

Leaf Rust Resistance Gene ◽

Resistance Locus ◽

Sequence Tagged Sites ◽

Barley Line

Barley line Q21861 possesses an incompletely dominant gene (RphQ) for resistance to leaf rust caused by Puccinia hordei. To investigate the allelic and linkage relations between RphQ and other known Rph genes, F2 populations from crosses between Q21861 and donors of Rph1 to Rph14 (except for Rph8) were evaluated for leaf rust reaction at the seedling stage. Results indicate that RphQ is either allelic with or closely linked to the Rph2 locus. A doubled haploid population derived from a cross between Q21861 and SM89010 (a leaf rust susceptible line) was used for molecular mapping of the resistance locus. Bulked segregant analysis was used to identify markers linked to RphQ, using random amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and sequence tagged sites (STSs). Of 600 decamer primers screened, amplified fragments generated by 9 primers were found to be linked to the RphQ locus; however, only 4 of them were within 10 cM of the target. The RphQ locus was mapped to the centromeric region of chromosome 7, with a linkage distance of 3.5 cM from the RFLP marker CDO749. Rrn2, an RFLP clone from the ribosomal RNA intergenic spacer region, was found to be very closely linked with RphQ, based on bulked segregant analysis. An STS marker, ITS1, derived from Rrn2, was also closely linked (1.6 cM) to RphQ.Key words: Hordeum vulgare, Puccinia hordei, allelism testing, linkage, molecular markers.

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Fine-Mapping And Identification of A Candidate Gene Controlling Seed Coat Color In Melon (Cucumis Melo L. Var. Chinensis Pangalo)

10.21203/rs.3.rs-720440/v1 ◽

2021 ◽

Author(s):

Zhicheng Hu ◽

Xueyin Shi ◽

Xuemiao Chen ◽

Jing Zheng ◽

Aiai Zhang ◽

...

Keyword(s):

Candidate Gene ◽

Seed Coat ◽

Coat Color ◽

Bulked Segregant Analysis ◽

Dominant Gene ◽

Seed Coat Color ◽

Gene Encoding ◽

Yellow Seed ◽

Homeobox Protein ◽

Yellow Seed Coat

Abstract Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon was controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene was located at 11,860,000–15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A→T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 was related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.

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