scholarly journals QTL-seq Analysis of Seed Size Trait in Grape Provides New Molecular Insight on Seedlessness

2020 ◽  
Author(s):  
Li Wang ◽  
Songlin Zhang ◽  
Chen Jiao ◽  
Zhi Li ◽  
Chonghuai Liu ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Seed Development ◽  
Seed Size ◽  
Expression Patterns ◽  
Grape Seed ◽  
Endosperm Development ◽  
Nonsynonymous Snps ◽  
Functional Study ◽  
Functional Variants ◽  
Seedless Grape

Abstract Background Seedlessness in grape ( Vitis vinifera ) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. Results In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified and analyzed with respect to published transcriptome data. All the DEGs containing nonsynonymous SNPs were further analyzed in terms of expression patterns, Gene Ontology and pathway enrichment. A potential QTL region associated with seed size was characterized based on SNP indices for both seedless and seeded progeny. Expression analysis of candidate genes during ovule development in multiple seeded and seedless grape cultivars further indicates their potential function in grape seed development. Conclusion In summary, DEGs containing nonsynonymous SNPs were mainly protein kinase, transcription factors, cytochrome P450 and other factors related to seed development, which were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, three genes were further identified as potential seedlessness-related genes. Overall the data cast light on the differences of seed development between seeded and sedless progeny in perspective of both functional variants and expression pattern,which provides valuable candidates for future functional study.

scholarly journals QTL-seq Analysis of Seed Size Trait in Grape Reveal New Insight on The Genetics of Seedlessness

2019 ◽  
Author(s):  
Li Wang ◽  
Songlin Zhang ◽  
Chen Jiao ◽  
Zhi Li ◽  
Chonghuai Liu ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Seed Development ◽  
Seed Size ◽  
Expression Patterns ◽  
Grape Seed ◽  
Endosperm Development ◽  
Nonsynonymous Snps ◽  
Functional Study ◽  
Functional Variants ◽  
Seedless Grape

Abstract Background Seedlessness in grape ( Vitis vinifera ) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. Results In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified and analyzed with respect to published transcriptome data. All the DEGs containing nonsynonymous SNPs were further analyzed in terms of expression patterns, Gene Ontology and pathway enrichment. A potential QTL region associated with seed size was characterized based on SNP indices for both seedless and seeded progeny. Expression analysis of candidate genes during ovule development in multiple seeded and seedless grape cultivars further indicates their potential function in grape seed development. Conclusion In summary, DEGs containing nonsynonymous SNPs were mainly protein kinase, transcription factors, cytochrome P450 and other factors related to seed development, which were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, three genes were further identified as potential seedlessness-related genes. Overall the data cast light on the differences of seed development between seeded and sedless progeny in perspective of both functional variants and expression pattern,which provides valuable candidates for future functional study.

scholarly journals QTL-seq Analysis of Seed Size Trait in Grape Provides New Molecular Insight on Seedlessness

2020 ◽  
Author(s):  
Li Wang ◽  
Songlin Zhang ◽  
Chen Jiao ◽  
Zhi Li ◽  
Chonghuai Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Development ◽  
Seed Size ◽  
Reproductive Organ ◽  
Endosperm Development ◽  
Nonsynonymous Snps ◽  
Functional Study ◽  
Ovule Development ◽  
Hormone Balance ◽  
Seedless Grape

Abstract Background: Seedlessness in grape (Vitis vinifera) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown.Results: In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified by genome sequencing and analyzed with published transcriptome data. Nonsynonymous SNPs were found in genes which were differential expressed during seeded and seedless grape ovule development, and corresponding Gene Ontology and pathway enrichment were conducted. A potential QTL region associated with seed size was characterized based on SNP-index for both seedless and seeded progeny. Expression analysis of SNP associated candidate genes during ovule development in multiple seeded and seedless grape cultivars were conducted and 3 SNP were further subjected to SNaPshot analysis in 40 progeny for validation.Conclusion: In summary, nonsynonymous SNPs happened in genes related seed development, which identified to be protein kinase, transcription factors, cytochrome P450 and showed differential expression during seeded and seedless grape ovule development. These nonsynonymous SNP associated genes were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, candidate genes in the QTL region were identified and a SNP in G8 showed 67.5% efficiency in the grape progeny validation. Overall, the data cast light on the differences of seed development between seeded and seedless progeny in genomic level, which provides valuable resources for future functional study and grape breeding.

scholarly journals Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development

2020 ◽  
Vol 21 (20) ◽  
pp. 7603
Author(s):  
Shuo Sun ◽  
Changyu Yi ◽  
Jing Ma ◽  
Shoudong Wang ◽  
Marta Peirats-Llobet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Glycine Max ◽  
Seed Development ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Soybean Seed ◽  
Endosperm Development ◽  
A Genome ◽  
Early Seed Development ◽  
Spatio Temporal

Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.

scholarly journals Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 408 ◽  
Author(s):  
Jing-Yao Yu ◽  
Zhan-Guo Zhang ◽  
Shi-Yu Huang ◽  
Xue Han ◽  
Xin-Yu Wang ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Seed Development ◽  
Small Rna ◽  
Target Genes ◽  
Soybean Seed ◽  
Regulatory Genes ◽  
Small Rna Sequencing ◽  
Grain Development ◽  
Regulatory Relationship ◽  
Novel Mirna

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

scholarly journals Analysis of maxillopedia Expression Pattern and Larval Cuticular Phenotype in Wild-Type and Mutant Tribolium

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 721-731 ◽  
Author(s):  
Teresa D Shippy ◽  
Jianhua Guo ◽  
Susan J Brown ◽  
Richard W Beeman ◽  
Robin E Denell
Keyword(s):  
Rna Interference ◽  
Expression Pattern ◽  
Tribolium Castaneum ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Homeotic Gene ◽  
Wild Type ◽  
Double Stranded Rna ◽  
Similar Expression ◽  
Mutant Phenotypes

Abstract The Tribolium castaneum homeotic gene maxillopedia (mxp) is the ortholog of Drosophila proboscipedia (pb). Here we describe and classify available mxp alleles. Larvae lacking all mxp function die soon after hatching, exhibiting strong transformations of maxillary and labial palps to legs. Hypomorphic mxp alleles produce less severe transformations to leg. RNA interference with maxillopedia double-stranded RNA results in phenocopies of mxp mutant phenotypes ranging from partial to complete transformations. A number of gain-of-function (GOF) mxp alleles have been isolated based on transformations of adult antennae and/or legs toward palps. Finally, we have characterized the mxp expression pattern in wild-type and mutant embryos. In normal embryos, mxp is expressed in the maxillary and labial segments, whereas ectopic expression is observed in some GOF variants. Although mxp and Pb display very similar expression patterns, pb null embryos develop normally. The mxp mutant larval phenotype in Tribolium is consistent with the hypothesis that an ancestral pb-like gene had an embryonic function that was lost in the lineage leading to Drosophila.

scholarly journals Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jorge A. Ramírez-Tejero ◽  
Jaime Jiménez-Ruiz ◽  
Alicia Serrano ◽  
Angjelina Belaj ◽  
Lorenzo León ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Expression Level ◽  
Resistant Cultivars ◽  
Pathogen Invasion ◽  
Wide Range ◽  
Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

scholarly journals Comparison of Nodule Induction in Legume and Actinorhizal Symbioses: The Induction of Actinorhizal Nodules Does Not Involve ENOD40

2003 ◽  
Vol 16 (9) ◽  
pp. 808-816 ◽  
Author(s):  
Carole Santi ◽  
Uritza von Groll ◽  
Ana Ribeiro ◽  
Maurizio Chiurazzi ◽  
Florence Auguy ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Host Plants ◽  
Root Nodule ◽  
Higher Plants ◽  
Expression Patterns ◽  
Lotus Japonicus ◽  
Casuarina Glauca ◽  
Actinorhizal Plant ◽  
Allocasuarina Verticillata ◽  
Actinorhizal Nodules

Two types of root nodule symbioses are known for higher plants, legume and actinorhizal symbioses. In legume symbioses, bacterial signal factors induce the expression of ENOD40 genes. We isolated an ENOD40 promoter from an actinorhizal plant, Casuarina glauca, and compared its expression pattern in a legume (Lotus japonicus) and an actinorhizal plant (Allocasuarina verticillata) with that of an ENOD40 promoter from the legume soybean (GmENOD402). In the actinorhizal Allocasuarina sp., CgENOD40-GUS and GmENOD40-2-GUS showed similar expression patterns in both vegetative and symbiotic development, and neither promoter was active during nodule induction. The nonsymbiotic expression pattern of CgENOD40-GUS in the legume genus Lotus resembled the nonsymbiotic expression patterns of legume ENOD40 genes however, in contrast to GmENOD40-2-GUS, CgENOD40-GUS was not active during nodule induction. The fact that only legume, not actinorhizal, ENOD40 genes are induced during legume nodule induction can be linked to the phloem unloading mechanisms established in the zones of nodule induction in the roots of both types of host plants.

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