scholarly journals Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Qiao ◽  
Qiming Cheng ◽  
Yutong Zhang ◽  
Wei Yan ◽  
Fengyan Yi ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Flower Color ◽  
Color Variation ◽  
Anthocyanin Synthesis ◽  
Flower Formation ◽  
Factors Affecting ◽  
Phenylpropanoid Biosynthesis ◽  
Molecular Information ◽  
Illumina Hiseq4000 ◽  
Insight Into

Abstract Background Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. Results Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the “flavonoid biosynthesis”and “phenylpropanoid biosynthesis” pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. Conclusions This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.

scholarly journals Time-Series Transcriptome Sheds Light on Anthocyanin Metabolism and Species Diversification Between two Lonicera Japonica Thunb Cultivars

2020 ◽  
Author(s):  
Jianjun Li ◽  
Chenglin Ye ◽  
Jingxiao Ma ◽  
Ting Cheng ◽  
Yan Lv ◽  
...  
Keyword(s):  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Lonicera Japonica ◽  
Pcr Analysis ◽  
Anthocyanin Synthesis ◽  
New Variety ◽  
Color Development ◽  
Phenylpropanoid Biosynthesis ◽  
New Varieties ◽  
Three Stages

Abstract Background：‘Yujin 2’ is new variety of Lonicera japonica Thunb and its flower color can change from red to yellow; hence, it is a good model for investigating flower color development mechanisms. Results：High throughput transcriptome sequencing of seven flower development stages of Yujin No.2 was carried out, and 133,487 unigenes were annotated, among which 73,088 were differentially expressed. Then the real-time PCR analysis was carried out. Further, the number of up-regulated DEGs was higher than those that were down-regulated. Of these annotated DEGs, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis were active throughout the flowering process during each stage, whereas carotenoid biosynthesis was inactive in the S1-6 stages. Furthermore, phenylalanine synthesis was enhanced in the S1 phase; however, anthocyanin synthesis was weakened in the S5 and S6 phases, which may be consistent with the changes in petal color of ‘Yujin 2’ from red (S1) to white (S5) and gold (S6). The results showed that 114 unigenes were associated with anthocyanin metabolism, and 72 were significantly upregulated or downregulated. According to the analysis of TFs in anthocyanin metabolism, we obtained 47 transcription factors, which belonged to 18 families. The LjDFR, LjABCB1, LjMYC6, LjDDB2, and LjANS genes rapidly increased during the first three stages. However, only LjF3'5'H expression was significantly down-regulated at S5, which was consistent with anthocyanin accumulation. Conclusions：This study developed a transcriptome profile of flower color generation for L. japonica as well as annotated unigene sets of seven anthesis phases, thereby providing possibilities for improving the germplasm of L. japonica with genetic engineering technologies and cultivating new varieties of different colors.

scholarly journals Comparative transcriptome analyses reveal genes related to pigmentation in the petals of a flower color variation cultivar of Rhododendron obtusum

2021 ◽  
Author(s):  
Xiaobo Sun ◽  
Lisi He ◽  
Zhenhao Guo ◽  
Jiale Su ◽  
Xiaoqing Liu ◽  
...  
Keyword(s):  
Flower Color ◽  
Development Stage ◽  
Color Variation ◽  
Strongly Correlated ◽  
Anthocyanin Pathway ◽  
Phenylpropanoid Biosynthesis ◽  
Genetic Mechanisms ◽  
Research Goal ◽  
Woody Ornamental Plant ◽  
R2r3 Myb

Abstract Rhododendron is an important woody ornamental plant and breeding varieties with different colors is vital research goal. In this study, a flower color variation cultivar ‘Yanzhi Mi’ (pink petals) and the wild-type (WT) cultivar ‘Dayuanyangjin’ (white petals with pink stripes) were used as research objects, the pigment and transcriptome of their petals during different flower development (stage S1, S2, S3, S4 and S5) were analyzed and compared. The results showed that the derivatives of cyanidin, peonidin and pelargonidin may be responsible for the pink of mutant petals and S2 stage (buds showing color at the top but with the scales still present) was the key stage of flower color formation of mutant. In total, 412,910 transcripts and 2,780 differentially expressed genes (DEGs) were identified in pairwise comparisons of WT and mutant petals. GO and KEGG enrichment analyses of the DEGs showed that the ‘DNA-binding transcription factor activity’, ‘Flavonoid biosynthesis’ and ‘Phenylpropanoid biosynthesis’ were more active in mutant petals. Early anthocyanin pathway candidate DEGs (CHS3-CHS6, CHI, F3Hs and F3’H) were strongly correlated and up-regulated expression in mutant petals than in WT petals at S2 stage. These genes may be the key structural genes for the pink coloration of mutant petals. In the petals of mutant, two R2R3-MYB unigene (TRINITY_DN59015_c3_g2 and TRINITY_DN49281_c1_g6) were identified as repressors involved in anthocyanin regulation and were significantly down-regulated at S2 stage. This study shed light on the biochemistry and genetic mechanisms underlying the flower coloration in two Rhododendron obtusum cultivars.

scholarly journals Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lin-Jiang Ye ◽  
Michael Mӧller ◽  
Ya-Huang Luo ◽  
Jia-Yun Zou ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Anthocyanin Biosynthesis ◽  
Flower Color ◽  
Indirect Measurement ◽  
Color Variation ◽  
Anthocyanin Synthesis ◽  
Anthocyanin Content ◽  
Nucleotide Polymorphisms ◽  
Expression Levels ◽  
Flower Color Polymorphism

Abstract Background The Rhododendron sanguineum complex is endemic to alpine mountains of northwest Yunnan and southeast Tibet of China. Varieties in this complex exhibit distinct flower colors even at the bud stage. However, the underlying molecular regulations for the flower color variation have not been well characterized. Here, we investigated this via measuring flower reflectance profiles and comparative transcriptome analyses on three coexisting varieties of the R. sanguineum complex, with yellow flush pink, bright crimson, and deep blackish crimson flowers respectively. We compared the expression levels of differentially-expressed-genes (DEGs) of the anthocyanin / flavonoid biosynthesis pathway using RNA-seq and qRT-PCR data. We performed clustering analysis based on transcriptome-derived Single Nucleotide Polymorphisms (SNPs) data, and finally analyzed the promoter architecture of DEGs. Results Reflectance spectra of the three color morphs varied distinctively in the range between 400 and 700 nm, with distinct differences in saturation, brightness, hue, and saturation/hue ratio, an indirect measurement of anthocyanin content. We identified 15,164 orthogroups that were shared among the three varieties. The SNP clustering analysis indicated that the varieties were not monophyletic. A total of 40 paralogous genes encoding 12 enzymes contributed to the flower color polymorphism. These anthocyanin biosynthesis-related genes were associated with synthesis, modification and transportation properties (RsCHS, RsCHI, RsF3H, RsF3′H, RsFLS, RsANS, RsAT, RsOMT, RsGST), as well as genes involved in catabolism and degradation (RsBGLU, RsPER, RsCAD). Variations in sequence and cis-acting elements of these genes might correlate with the anthocyanin accumulation, thus may contribute to the divergence of flower color in the R. sanguineum complex. Conclusions Our results suggested that the varieties are very closely related and flower color variations in the R. sanguineum complex correlate tightly with the differential expression levels of genes involved in the anabolic and catabolic synthesis network of anthocyanin. Our study provides a scenario involving intricate relationships between genetic mechanisms for floral coloration accompanied by gene flow among the varieties that may represent an early case of pollinator-mediated incipient sympatric speciation.

scholarly journals Mechanism Underlying Color Variation in Calla Lily Spathes Based on Transcriptomic Analysis

2021 ◽  
pp. 1-16
Author(s):  
Ying Fang ◽  
Ting Lei ◽  
Yanmei Wu ◽  
Xuehua Jin
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Flower Color ◽  
Transcriptomic Analysis ◽  
Color Variation ◽  
Anthocyanin Synthesis ◽  
Helix Loop Helix ◽  
Calla Lily ◽  
Unique Shape ◽  
Glutathione S Transferases

The calla lily (Zantedeschia hybrida) is a valued ornamental plant due to its unique shape and color variations. To determine the mechanisms responsible for color development in the calla lily spathe, we conducted a comparative transcriptomic analysis of the spathes of the black [Black Girl (B)], pink [Romantic (P)], and white [Ventura (W)] cultivars. The gene expression patterns in six spathe colors, including the preceding three colors as well as the amaranth [Promise (N)], red [Figo (F)], and yellow [Sun Club (Y)] cultivars were analyzed by real-time quantitative polymerase chain reaction (PCR). Transcriptomic analysis identified 25,165 differentially expressed genes. The transcription abundance and expression level of genes annotated as anthocyanidin reductase (ANR1, ANR2), basic-helix-loop-helix (bHLH1), and glutathione S-transferases (GST1) were significantly upregulated in B, and the expression of anthocyanidin synthase (ANS) was highest in B except for N. However, chalcone isomerase (CHI2) and dihydroflavonol 4-reductase (DFR1, DFR2) were expressed at significantly lower levels in P, W, and Y. Correlation analysis revealed that bHLH1 might act as a positive regulator of ANS expression, promoting anthocyanin synthesis. Moreover, GST1-encoded proteins may be related to the accumulation and transport of both anthocyanin and procyanidin in the calla lily spathe. It is speculated that the formation of the black spathe is related to the accumulation of anthocyanins and procyanidins. However, the low expression of CHI2, DFR1, and DFR2 may result in the inhibition of anthocyanin synthesis, which may lead to lightening of the spathe color. This preliminary study revealed the mechanism responsible for calla lily spathe color, identifying the key genes involved, thus providing effective gene resources and a theoretical basis for flower color molecular breeding.

Relationship Between the Composition of Anthocyanins and Flower Color Variation in Hardy Water Lily (Nymphaea spp.) Cultivars

2013 ◽  
Vol 47 (5) ◽  
pp. 437-453
Author(s):  
Zhu Manlan ◽  
Wang Liangsheng ◽  
Zhang Huijin ◽  
Xu Yanjun ◽  
Zheng Xuchen ◽  
...  
Keyword(s):  
Flower Color ◽  
Color Variation ◽  
Water Lily

scholarly journals Factors affecting presence and relative abundance of the Endangered volcano rabbit Romerolagus diazi, a habitat specialist

Oryx ◽  
2021 ◽  
pp. 1-10
Author(s):  
Felipe Osuna ◽  
Roger Guevara ◽  
Enrique Martínez-Meyer ◽  
Raúl Alcalá ◽  
Alejandro Espinosa de los Monteros
Keyword(s):  
Sierra Nevada ◽  
Relative Abundance ◽  
Linear Models ◽  
Cattle Grazing ◽  
Patch Occupancy ◽  
Factors Affecting ◽  
Rock Cover ◽  
Volcanic Fields ◽  
Mountain Grasslands ◽  
Insight Into

Abstract Habitat specialists are particularly vulnerable to extinction when habitat conditions are altered. Information on the habitat use of such species is thus important because it provides insight into factors that influence distribution and abundance, which is crucial for conservation. Here, we aimed to identify factors that influence the patterns of presence and abundance of the Endangered volcano rabbit Romerolagus diazi, a rare leporid with a patchy distribution. Through exhaustive sampling of its range in the Sierra Chichinautzin and Sierra Nevada volcanic fields, Mexico, and using generalized linear models, we found that the probability of patch occupancy was higher where bunchgrass cover exceeded 75%, rock cover exceeded 5%, no cattle grazing was observed and human settlements were at least 7 km away. Patches with greater relative abundance were those with similar characteristics, but located at elevations > 3,600 m, and with rock cover < 15%. Cattle grazing was identified as a major threat to local populations of the volcano rabbit, particularly in the Sierra Chichinautzin. Because of the significance of bunchgrasses for this species, the protection of the mountain grasslands is required in both volcanic fields.

Bioinfomatics Analysis of the Anthocyanidin synthase Gene in Tree Peony

2014 ◽  
Vol 1010-1012 ◽  
pp. 1181-1184
Author(s):  
Yan Zhao Zhang ◽  
Yan Wei Cheng ◽  
Hui Yuan Ya ◽  
Chao Yun ◽  
Jian Ming Han ◽  
...  
Keyword(s):  
Plant Species ◽  
Structure Prediction ◽  
Biosynthetic Pathway ◽  
Resistance Breeding ◽  
Flower Color ◽  
Anthocyanin Synthesis ◽  
Tree Peony ◽  
Reading Frame ◽  
Transcriptome Database ◽  
Color Modification

Anthocyanin mainly responsible for flowers color in many plant species, it also accumulated in response to lots of environmental stress to reduce the damage to plant cell. Anthocyanin synthesis (ANS) protein is an important synthetase participated in anthocyanin biosynthetic pathway. In this study, we isolated the PsANS gene from transcriptome database built by our previous study. The PsANS gene contain an 1050bp open reading frame encoding 349 amino acid, phylogenetic analysis revealed that PsANS was segrated into a group with ANS from others plant species. Secondary and thri-dimension structure prediction also revealed that it may have similar function with ANS in others plant species. The identified PsANS gene would be helpful for further research in flower color modification and resistance breeding.

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