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The major origin of seedless grapes is associated with a missense mutation in the MADS-box gene VviAGL11

ABSTRACT: Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE106668 | GEO | 2018/07/31

REPOSITORIES: GEO

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Analysis of the origin of stenospermocarpy under the control of the major seedlessness locus in grapevine

Project description:Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding.

2018-07-31 | GSE107014 | GEO

Transcriptome profiling for seed abortion in Ponkan (Citrus reticulata)

Project description:Seed developmental arrest is one of the early phenotypes of seed abortion. However, the molecular mechanism underlying seed developmental arrest of citrus is still unclear. In this study, laser capture microdissection (LCM) was used to accurately divide the seeds of seedless Ponkan ‘Huagan No.4’ (Citrus reticulata) (HG) and seeded Ponkan ‘Egan No.1’ (Citrus reticulata) (EG) into nucellus and integument/seed coat tissues. The captured tissues were used for subsequent RNA-seq. Moreover, single-molecule real-time (SMRT) sequencing was used to generate full-length transcripts of EG, which were used as reference transcripts for RNA-seq. These data can be utilized to analyse the causes of citrus seedlessness formation and the molecular regulatory network in the process of seed abortion.

2023-05-08 | GSE197716 | GEO

Laser capture microdissection-based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in Ponkan (Citrus reticulate)

Project description:Seed abortion is one of the important reasons for the formation of seedless characters in citrus. However, the molecular mechanism of seed abortion in citrus is still unclear. We identified several genes that may play an important role in seed abortion of 'Huagan 4', such as CrWRKY74. The downstream regulatory network of CrWRKY74 was identified based on DAP seq analysis to gain insight into the molecular mechanism related to seed abortion.

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Comparative transcript profiling of gene expression between seedless Ponkan mandarin (Citrus reticulata Blanco) and its seedy wild type during floral organ development

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2012-05-21 | E-GEOD-38094 | biostudies-arrayexpress

Comparative transcript profiling of gene expression between seedless Ponkan mandarin (Citrus reticulata Blanco) and its seedy wild type during floral organ development

2012-05-22 | GSE38094 | GEO

Total transcriptome assays were performed on ovules and developing seeds derived from two seeded (Italia and Red globe) and two seedless (Thompson Seedless and Autumn Royal) table grape varieties

Project description:VviAGL11, the Arabidopsis SEEDSTICK homolog, has been proposed to have a causative role in grapevine stenospermocarpy. An association between a mutation in the coding sequence (CDS) and the seedless phenotype was reported, however, no working mechanisms have been demonstrated yet. We performed a deep investigation of the full VviAGL11 gene sequence in a collection of grapevine varieties belonging to several seedlessness classes that revealed three different promoter-CDS combinations. By investigating the expression of the three VviAGL11 alleles, and by evaluating their ability to activate the promoter region, we observed that VviAGL11 self-activates in a specific promoter-CDS combination manner. Furthermore, by transcriptomic analyses on ovule and developing seeds in seeded and seedless varieties and co-expression approaches, candidate VviAGL11 targets were identified and further validated through luciferase assay and in situ hybridization. We demonstrated that VviAGL11 Wild Type CDS activates Methyl jasmonate esterase and Indole-3-acetate beta-glucosyltransferase, both involved in hormone signaling and Isoflavone reductase, involved in secondary metabolism. The dominant-negative effect of the mutated CDS was also functionally ectopically validated in target induction. VviAGL11 was shown to co-localize with its targets in the outer seed coat integument, supporting its direct involvement in seed development, possibly by orchestrating the crosstalk among MeJA, auxin, and isoflavonoids synthesis. In conclusion, the VviAGL11 expression level depends on the promoter-CDS allelic combination, and this will likely affect its ability to activate important triggers of the seed coat development. The dominant-negative effect of the mutated VviAGL11 CDS on the target genes activation was molecularly validated. A new regulatory mechanism correlating VviAGL11 haplotype assortment and seedlessness class in grapevine is proposed.

2022-06-14 | GSE186838 | GEO

Transcriptome analysis during seed development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and it seedless somatic variant.

Project description:We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine:Â E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources. Examination of absolute expression count for every gene at three key time-points in a seeded grapevine variety and its seedless somatic variant.

2014-12-31 | E-GEOD-58061 | biostudies-arrayexpress

Soybean cultivars,Soybean Hydrophobic Protein(HPS) comparison

Project description:The Hydrophobic protein from soybean (HPS) locus is polymorphic among soybean cultivars and copy-number changes in the tandem array at this locus are directly correlated with expression level and seed coat luster phenotypes. Keywords: comparative genomic hybridization

2006-03-21 | GSE3810 | GEO

Transcriptome analysis during seed development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and it seedless somatic variant.

Project description:We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine: E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources.

2014-12-31 | GSE58061 | GEO

An epigenetic role for disrupted paternal gene expression in postzygotic seed abortion in Arabidopsis interspecific hybrids

Project description:Interspecific hybrids in Arabidopsis result in seed abortion that causes reproductive barrier. To investigate the allelic expression pattern at transcriptome level during early seed abortion stage, we performed RNA-seq analysis in F1 interspecific hybrids with three different ecotypes in A. thaliana as maternal and A. arenosa as paternal and identified MEGs and PEGs. Interestingly, PEGs showed distinct expression pattern in several aspects, compared to MEGs: PEGs showed ecotype-specific expression pattern, suggesting a role for PEGs in ecotype-dependent seed lethality. 35% of previously known MEGs in non-lethal hybrids were found as PEGs in our lethal interspecific hybrids, implying the presence of abnormal paternal allelic upregulation. The correlation test between the upregulation of PEGs and previously reported paternal-excess interploidy cross (2X6) which exhibited seed abortion showed that dosage disruption by abnormal paternal upregulation is correlated with seed abortion. Moreover, epigenetic disruption appears to cause some of abnormal upregulation of paternal alleles in PEGs via mis-regulation of MEA-mediated PcG2 and MET1-mediated DNA methylation. The results provide clue on the critical role of PEGs in seed abortion via disruption of dosage balance and epigenetic regulation.

2015-10-01 | GSE41391 | GEO

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