scholarly journals Identification of Candidate Genes Involved in Curd Riceyness in Cauliflower

2020 ◽  
Vol 21 (6) ◽  
pp. 1999
Author(s):  
Zhenqing Zhao ◽  
Xiaoguang Sheng ◽  
Huifang Yu ◽  
Jiansheng Wang ◽  
Yusen Shen ◽  
...  
Keyword(s):  
Morphological Difference ◽  
Orthologous Gene ◽  
Target Sequence ◽  
Rna Seq ◽  
Flower Bud ◽  
Function Annotation ◽  
Breeding Lines ◽  
F2 Population ◽  
Candidate Loci ◽  
Precocious Development

“Riceyness” refers to the precocious development of flower bud initials over the curd surface of cauliflower, and it is regarded as undesirable for the market. The present study aimed to identify the candidate loci and genes responsible for the morphological difference in riceyness between a pair of cauliflower sister lines. Genetic analysis revealed that riceyness is controlled by a single dominant locus. An F2 population derived from the cross between these sister lines was used to construct “riceyness” and “non-riceyness” bulks, and then it was subjected to BSA-seq. On the basis of the results of Δ(SNP-index) analysis, a 4.0 Mb candidate region including 22 putative SNPs was mapped on chromosome C04. Combining the RNA-seq, gene function annotation, and target sequence analysis among two parents and other breeding lines, an orthologous gene of the Arabidopsis gene SOC1, Bo4g024850 was presumed as the candidate gene, and an upstream SNP likely resulted in riceyness phenotype via influencing the expression levels of Bo4g024850. These results are helpful to understand the genetic mechanism regulating riceyness, and to facilitate the molecular improvement on cauliflower curds.

scholarly journals Analysis and Mapping of Gene Families Encoding β-1,3-Glucanases of Soybean

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 445-452
Author(s):  
Wei Jin ◽  
Harry T Horner ◽  
Reid G Palmer ◽  
Randy C Shoemaker
Keyword(s):  
Gene Families ◽  
Mrna Levels ◽  
Linkage Groups ◽  
Flower Bud ◽  
Cross Hybridization ◽  
Coding Regions ◽  
F2 Population ◽  
Young Leaves ◽  
Glycine Max L ◽  
Stem Leaf

Abstract Oligonucleotide primers designed for conserved sequences from coding regions of β-1,3-glucanase genes from different species were used to amplify related sequences from soybean [Glycine max (L.) Merr.]. Sequencing and cross-hybridization of amplification products indicated that at least 12 classes of β-1,3-glucanase genes exist in the soybean. Members of classes mapped to 34 loci on five different linkage groups using an F2 population of 56 individuals. β-1,3-Glucanase genes are clustered onto regions of five linkage groups. Data suggest that more closely related genes are clustered together on one linkage group or on duplicated regions of linkage groups. Northern blot analyses performed on total RNA from root, stem, leaf, pod, flower bud, and hypocotyl using DNA probes for the different classes of β-1,3-glucanase genes revealed that the mRNA levels of all classes were low in young leaves. SGlu2, SGlu4, SGlu7, and SGlu12 mRNA were highly accumulated in young roots and hypocotyls. SGlu7 mRNA also accumulated in pods and flower buds.

scholarly journals Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

2010 ◽  
Vol 20 (9) ◽  
pp. 1238-1249 ◽  
Author(s):  
T. Lu ◽  
G. Lu ◽  
D. Fan ◽  
C. Zhu ◽  
W. Li ◽  
...  
Keyword(s):  
Rna Seq ◽  
Single Nucleotide ◽  
Function Annotation ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

scholarly journals Host-induced gene silencing involves transfer of dsRNA-derived siRNA via extracellular vesicles

2020 ◽  
Author(s):  
A Koch ◽  
T Schlemmer ◽  
L Höfle ◽  
BT Werner ◽  
C Preußer ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Extracellular Vesicles ◽  
Fungal Pathogens ◽  
Host Cells ◽  
Target Sequence ◽  
Rna Seq ◽  
Leaf Extracts ◽  
Transgenic Expression ◽  
Rna Molecules ◽  
Expression Host

AbstractSmall (s)RNA molecules are crucial factors in the communication between hosts and their interacting pathogens, where they function as effectors that can modulate both host defense and microbial virulence/pathogenicity through a mechanism termed cross-kingdom RNA interference (ckRNAi). Consistent with this recent knowledge, sRNAs and their double-stranded (ds)RNA precursors have been adopted to control diseases in crop plants through transgenic expression (host-induced gene silencing, HIGS) or exogenous application (spray-induced gene silencing, SIGS). While these strategies proved to be effective, the mechanism of RNA transfer at the plant - pathogen interface is widely unresolved. Here we show that extracellular vesicles (EVs) purified from Arabidopsis (Arabidopsis thaliana) leaf extracts and apoplastic fluids contain transgene-derived sRNAs. EVs from plants expressing CYP3RNA, a 791 nt long dsRNA, which was originally designed to target the three CYP51 genes of the fungal pathogen Fusarium graminearum, contain CYP3RNA-derived small interfering (si)RNAs as shown by RNA sequencing (RNA-seq) analysis. Notably, the EVs cargo retained the same CYP3RNA-derived siRNA profile as the respective leaf extracts, suggesting that there was no selective uptake of specific artificial sRNAs into EVs. In addition, mutants of the ESCRT-III complex were impaired in HIGS further indicating that endosomal vesicle trafficking supports transfer of transgene-derived siRNAs between donor host cells and recipient fungal cells. Further supporting the relevance of EV-mediated transport of sRNA, we demonstrate that HIGS plants, expressing a 100 nt dsRNA-target-sequence identified via EV-sRNA-seq of CYP3RNA Arabidopsis, confers strong resistance to F. graminearum. Together, these findings support the view that EVs are key mediators in the transport of HIGS-related sRNAs to reduce the virulence of interacting fungal pathogens during host-pathogen interaction.

scholarly journals Low Overnight Temperature-Induced Gibberellin Accumulation Increases Locule Number in Tomato

2019 ◽  
Vol 20 (12) ◽  
pp. 3042
Author(s):  
Yanbing Li ◽  
Meihua Sun ◽  
Hengzuo Xiang ◽  
Yudong Liu ◽  
Hui Li ◽  
...  
Keyword(s):  
Plant Hormone ◽  
Developmental Stages ◽  
Fruit Size ◽  
Ultra Performance Liquid Chromatography ◽  
Rna Seq ◽  
Flower Bud ◽  
Tomato Plants ◽  
Locule Number ◽  
Liquid Chromatography Tandem Mass ◽  
Flower Bud Differentiation

The number of locules in tomato affects fruit size, shape, and the incidence of malformation. Low temperature increases locule number and the incidences of malformation in tomato plants. In this study, three flower bud developmental stages (pre-flower bud differentiation, sepal and petal primordium formation, and carpel primordium formation) under different night temperatures (10, 15, and 20 °C) were used to analyze the reason behind locule number change using an RNA sequencing (RNA-seq) approach, Quantitative real-time PCR (qRT-PCR), and ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS). The results showed that the “plant hormone signal transduction”, “starch and sucrose metabolism”, and “diterpenoid biosynthesis” categories were remarkably activated during flower bud differentiation. Transcripts of gibberellin (GA)-related genes and endogenous levels of GAs were analyzed, and it was discovered that SlGA2ox genes were significantly downregulated and bioactive GA1 and GA4 accumulated at lower overnight temperature. Exogenous application of bioactive GA1, GA4, and PAC (paclobutrazol) showed that GA1 and GA4 increased the locule number, while PAC decreased the locule number. Taken together, our results suggest that lower overnight temperature reduced the expression of SlGA2ox genes, leading to GA1 and GA4 accumulation, thereby increasing locule number in tomato.

scholarly journals Development and Application of a PCR-Based Molecular Marker for the Identification of High Temperature Tolerant Cabbage (Brassica oleracea var. capitata) Genotypes

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 116
Author(s):  
Hayoung Song ◽  
Myungjin Lee ◽  
Byung-Ho Hwang ◽  
Ching-Tack Han ◽  
Jong-In Park ◽  
...  
Keyword(s):  
High Temperature ◽  
Molecular Marker ◽  
Brassica Oleracea ◽  
Inbred Line ◽  
Genetic Basis ◽  
Soft Rot ◽  
Inbred Lines ◽  
Rna Seq ◽  
F2 Population ◽  
Pcr Based Molecular Marker

Global warming accelerates the development of high temperature (HT)- and high humidity (HH)-tolerant varieties. This is further facilitated by the identification of HTHH-tolerant genes and the development of molecular markers based on these genes. To identify genes involved in HTHH tolerance in cabbage (Brassica oleracea var. capitata), we performed RNA-seq analysis of two inbred lines, BN1 (HTHH-tolerant) and BN2 (HTHH-susceptible), and selected trehalose 6- phosphate phosphatase I-2 (BoTPPI-2) as one of the HTHH-tolerant-associated genes. We also developed a segregating F2 population from a cross between BN1 and BN2. RNA-seq results showed that BoTPPI-2 transcript levels were high in the HTHH-tolerant inbred line BN1, but not detectable in the HTHH-susceptible inbred line BN2. The expression pattern of BoTPPI-2 was not related to the expression of heat shock-related genes. Soft rot resistance, used as an indicator of HTHH tolerance, was higher in BN1 than in BN2. F2 individuals similar to BN1 with respect to phenotype appeared to be HTHH-tolerant, whereas BN2-types were susceptible to HTHH. Analysis of the genomic DNA revealed the presence of a long terminal repeat (LTR; ca. 4.6 kb) in the ninth intron of the BoTPPI-2_BN2 allele, thereby suppressing its transcription and exhibiting HTHH phenotype. Except for the LTR insertion, the sequence of BoTPPI-2_BN2 was almost identical to that of BoTPPI-2_BN1. On the basis of the LTR and BoTPPI-2 sequences, we developed a molecular marker to identify HTHH-tolerant genotypes and validated its efficiency using F2 individuals, inbred lines, and cultivars from diverse sources. The marker explained the genetic basis of HTHH tolerance in at least 80%, but not 100%, of the cabbage genotypes. Thus, additional markers associated with HTHH tolerance are needed for perfect selection.

scholarly journals Transcriptome profiling for floral development in reblooming cultivar ‘High Noon’ of Paeonia suffruticosa

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Yanting Chang ◽  
Tao Hu ◽  
Wenbo Zhang ◽  
Lin Zhou ◽  
Yan Wang ◽  
...  
Keyword(s):  
Flower Development ◽  
Floral Development ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Full Length ◽  
Rna Seq ◽  
Paeonia Suffruticosa ◽  
Tree Peony ◽  
Flower Bud ◽  
High Noon

Abstract Tree peony (Paeonia suffruticosa Andrew) is a popular ornamental plant due to its large, fragrant and colorful flowers. The floral development is the most important event in its lifecycle. To explore the mechanism that regulate flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea, using both full-length isoform-sequencing (ISO-seq) and RNA-seq were sequenced. A total of 15.94 Gb raw data were generated in full-length transcriptome sequencing of the 3 floral developmental stages, resulting 0.11 M protein-coding transcripts. Over 457.0 million reads were obtained by RNA-seq in the 3 floral buds. Here, we openly released the full-length transcriptome database of ‘High Noon’ and RNA-seq database of floral development. These databases can provide a fundamental genetic information of tree peony to investigate its transcript structure, variants and evolution. Data will facilitate to deep analyses of the transcriptome for flower development.

scholarly journals Microsatellites markers associated with resistance to flower bud thrips in a cowpea F2 population derived from genotypes TVU-123 and WC36

2018 ◽  
Vol 17 (25) ◽  
pp. 767-778
Author(s):  
Agbahoungba Symphorien ◽  
Karungi Jeninah ◽  
Sadik Kassim ◽  
Gibson Paul ◽  
Edema Richard ◽  
...  
Keyword(s):  
Flower Bud ◽  
Microsatellites Markers ◽  
F2 Population

scholarly journals Genetic Variation and Association Mapping in the F2 Population of the Perilla Crop (Perilla Frutescens L.) using new Developed Perilla SSR Markers

2021 ◽  
Author(s):  
Ju Keon Kim ◽  
Kyu Jin Sa ◽  
Ye Ju Ha ◽  
Ju Kyong Lee
Keyword(s):  
Ssr Markers ◽  
Association Analysis ◽  
Transcriptome Sequencing ◽  
Morphological Characteristics ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Dinucleotide Repeats ◽  
Breeding Programs ◽  
F2 Population ◽  
Primer Sets

Abstract The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of SSR markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that dinucleotide repeats were the most abundant (62.0%) type, followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. A total of 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, a total of 40 individuals from the F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. In an association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population, we identified 12 and 11 SSR markers associated with leaf-related traits and plant-related traits, respectively. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.

Interactive effects of light, temperature and cultivar on photosynthesis in evening primrose (Oenothera spp.) crops

2005 ◽  
Vol 52 (4) ◽  
pp. 333-342 ◽  
Author(s):  
A. F. Fieldsend
Keyword(s):  
Low Temperature ◽  
Biomass Accumulation ◽  
Interactive Effects ◽  
Clear Correlation ◽  
Oilseed Crop ◽  
Temperature Dependent ◽  
Flower Bud ◽  
Response Curves ◽  
Breeding Lines ◽  
Evening Primrose

The photosynthetic performance of evening primrose (Oenothera spp.), a temperate oilseed crop, was assessed during the period of rapid biomass accumulation and flower bud formation. Light response curves constructed from field-grown plants harvested in late May, late June and late July were similar, suggesting that the photosynthetic capacity of evening primrose leaves is not readily susceptible to low temperatures. The maximum quantum efficiency of CO2 assimilation and light-saturated rate of CO2 assimilation data were comparable to other C3 species. Short-term changes in photosynthetic efficiency, measured as the ratio of variable to maximal chlorophyll fluorescence, Fv/Fm, were assessed on field-grown plants of five breeding lines during late May and early June, and on glasshouse-grown plants under controlled temperatures and light levels. Low temperature-dependent photoinhibition (measured as a decline in Fv/Fm) occurred in both field and controlled-environment studies. Differences were observed between breeding lines in the rate of recovery upon a return to more favourable conditions. A clear correlation between Fv/Fm and CO2 assimilation was demonstrated, suggesting that low temperature-dependent photoinhibition could lead to reduced biomass accumulation in evening primrose crops grown in cool temperate climates.

scholarly journals Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hao Rong ◽  
Wenjing Yang ◽  
Haotian Zhu ◽  
Bo Jiang ◽  
Jinjin Jiang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Genomic Imprinting ◽  
Castor Bean ◽  
Imprinted Genes ◽  
Reciprocal Hybrid ◽  
Rna Seq ◽  
Flower Bud ◽  
Gene Imprinting ◽  
Parent Of Origin ◽  
Stem Leaf

Abstract Background Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. napus will enrich the knowledge of genomic imprinting in dicotyledon plants. Results In this study, we performed reciprocal crosses between B. napus L. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted in Arabidopsis, rice, castor bean, maize, B. rapa, and other B. napus lines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud of B. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5 AGLs and 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm. Conclusion This research provided a comprehensive identification of imprinted genes in B. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.

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