scholarly journals Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar ‘Qiannan Guifei’

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12265
Author(s):  
Qi Cui ◽  
Junhua Huang ◽  
Fan Wu ◽  
Dong-ze Li ◽  
Liqun Zheng ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Metabolic Pathways ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Chloroplast Ultrastructure ◽  
Carotenoid Biosynthesis ◽  
Leaf Color ◽  
Color Changes ◽  
Leaf Coloration ◽  
Transcriptional Changes

Background Osmanthus fragrans (Oleaceae) is one of the most important ornamental plant species in China. Many cultivars with different leaf color phenotypes and good ornamental value have recently been developed. For example, a new cultivar ‘Qiannan Guifei’, presents a rich variety of leaf colors, which change from red to yellow-green and ultimately to green as leaves develop, making this cultivar valuable for landscaping. However, the biochemical characteristics and molecular mechanisms underlying leaf color changes of these phenotypes have not been elucidated. It has been hypothesized that the biosynthesis of different pigments in O. fragrans might change during leaf coloration. Here, we analyzed transcriptional changes in genes involved in chlorophyll (Chl), flavonoid, and carotenoid metabolic pathways and identified candidate genes responsible for leaf coloration in the new cultivar ‘Qiannan Guifei’. Methods Leaf samples were collected from ‘Qiannan Guifei’ plants at the red (R), yellow-green (YG) and green (G) leaf stages. We compared the different-colored leaves via leaf pigment concentrations, chloroplast ultrastructure, and transcriptomic data. We further analyzed differentially expressed genes (DEGs) involved in the Chl, flavonoid, and carotenoid metabolic pathways. In addition, we used qRT-PCR to validate expression patterns of the DEGs at the three stages. Results We found that, compared with those at the G stage, chloroplasts at the R and YG stages were less abundant and presented abnormal morphologies. Pigment analyses revealed that the leaves had higher flavonoid and anthocyanin levels at the R stage but lower Chl and carotenoid concentrations. Similarly, Chl and carotenoid concentrations were lower at the YG stage than at the G stage. By using transcriptomic sequencing, we further identified 61 DEGs involved in the three pigment metabolic pathways. Among these DEGs, seven structural genes (OfCHS, OfCHI, OfF3H, OfDFR, OfANS, OfUGT andOf3AT) involved in the flavonoid biosynthesis pathway were expressed at the highest level at the R stage, thereby increasing the biosynthesis of flavonoids, especially anthocyanins. Six putativeOfMYB genes, including three flavonoid-related activators and three repressors, were also highly expressed at the R stage, suggesting that they might coordinately regulate the accumulation of flavonoids, including anthocyanins. Additionally, expressions of the Chl biosynthesis-related genes OfHEMA, OfCHLG and OfCAO and the carotenoid biosynthesis-related genes OfHYB and OfZEP were upregulated from the R stage to the G stage, which increased the accumulation of Chl and carotenoids throughout leaf development. In summary, we screened the candidate genes responsible for the leaf color changes of ‘Qiannan Guifei’, improved current understanding of the regulatory mechanisms underlying leaf coloration and provided potential targets for future leaf color improvement in O. fragrans.

scholarly journals Simultaneous changes in anthocyanin, chlorophyll, and carotenoid contents produce green variegation in pink–leaved ornamental kale

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yang Liu ◽  
Xin Feng ◽  
Yuting Zhang ◽  
Fuhui Zhou ◽  
Pengfang Zhu
Keyword(s):  
Molecular Mechanisms ◽  
Color Change ◽  
Anthocyanin Biosynthesis ◽  
Carotenoid Biosynthesis ◽  
Anthocyanin Content ◽  
Leaf Color ◽  
Chlorophyll Metabolism ◽  
Leaf Coloration ◽  
New Varieties ◽  
Ornamental Kale

Abstract Background Anthocyanin, chlorophyll, and carotenoid pigments are widely distributed in plants, producing various colors. Ornamental kale (Brassica oleracea var. acephala DC) which has colorful inner leaves is an ideal plant to explore how these three pigments contribute to leaf color. The molecular mechanisms of the coloration in ornamental kale could provide reference for exploring the mechanisms of pigmentation in other plants. Results In this study, we sequenced the transcriptome and determined the pigment contents of an unusual cultivar of ornamental kale with three different types of leaf coloration: pink (C3), light pink (C2), and variegated pink–green (C1). A total of 23,965 differentially expressed genes were detected in pairwise comparisons among the three types of leaves. The results indicate that Bo9g058630 coding dihydroflavonol 4–reductase (DFR) and Bo3g019080 coding shikimate O–hydroxycinnamoyltransferase (HCT) acted in anthocyanin biosynthesis in pink leaves. Bo1g053420 coding pheophorbidase (PPD) and Bo3g012430 coding 15–cis–phytoene synthase (crtB) were identified as candidate genes for chlorophyll metabolism and carotenoid biosynthesis, respectively. The transcription factors TT8, MYBL2, GATA21, GLK2, and RR1 might participate in triggering the leaf color change in ornamental kale. Anthocyanin content was highest in C3 and lowest in C1. Chlorophyll and carotenoid contents were lowest in C2 and highest in C1. Conclusions Based on these findings, we suspected that the decrease in anthocyanin biosynthesis and the increase in chlorophyll and carotenoid biosynthesis might be the reason for the leaf changing from pink to variegate pink–green in this unusual cultivar. Our research provides insight into the molecular mechanisms of leaf coloration in ornamental kale, contributing to a theoretical foundation for breeding new varieties.

An ABA-flavonoid relationship contributes to the differences in drought resistance between different sea buckthorn subspecies

2020 ◽  
Author(s):  
Guori Gao ◽  
Zhongrui Lv ◽  
Guoyun Zhang ◽  
Jiayi Li ◽  
Jianguo Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Normal Growth ◽  
Carotenoid Biosynthesis ◽  
Sea Buckthorn ◽  
Mutual Regulation ◽  
The Difference

Abstract Drought is the most severe abiotic stress and hinders the normal growth and development of plants. Sea buckthorn (Hippophae rhamnoides Linn.) is a typical drought-resistant tree species. In this study, the leaves of the H. rhamnoides ssp. sinensis (“FN”) and H. rhamnoides ssp. mongolica (“XY”) were selected during drought-recovery cycles for RNA sequencing, and physiological and biochemical analyses. The results revealed that drought stress significantly decreased leaf water potential, net photosynthetic rate, and stomatal conductance in both sea buckthorn subspecies. Similarly, the contents of flavone, flavonol, isoflavone and flavanone significantly decreased under drought stress in “XY.” Conversely, in “FN,” the flavone and abscisic acid (ABA) contents were significantly higher under drought stress and recovered after rehydration. Meanwhile, 4,618 and 6,100 differentially expressed genes (DEGs) were identified under drought stress in “FN” and “XY,” respectively. In total, 5,164 DEGs were observed in the comparison between “FN” and “XY” under drought stress. This was more than the 3,821 and 3,387 DEGs found when comparing the subspecies under control and rehydration conditions, respectively. These DEGs were mainly associated with carotenoid biosynthesis, flavonoid biosynthesis, photosynthesis, and plant hormone signal transduction. Six hub DEGs (ABCG5, ABCG22, ABCG32, ABCG36, ABF2 and PYL4) were identified to respond to drought stress based on WGCNA and BLAST analysis using DroughtDB. These six DEGs were annotated to play roles in the ABA-dependent signaling pathway. Sixteen RNA sequencing results involving eight genes and similar expression patterns (12/16) were validated using quantitative real-time PCR. The biochemical and molecular mechanisms underlying the regulation of drought responses by ABA and flavonoids in sea buckthorn were clarified. In this study, gene co-expression networks were constructed, and the results suggested that the mutual regulation of ABA and flavonoid signaling contributed to the difference in drought resistance between the different sea buckthorn subspecies.

scholarly journals RNA-Seq-Based Profiling of pl Mutant Reveals Transcriptional Regulation of Anthocyanin Biosynthesis in Rice (Oryza sativa L.)

2021 ◽  
Vol 22 (18) ◽  
pp. 9787
Author(s):  
Ruonan Xu ◽  
Ronghui Pan ◽  
Yuchan Zhang ◽  
Yanlei Feng ◽  
Ujjal Kumar Nath ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Oryza Sativa L ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Regulatory Gene ◽  
Leaf Color ◽  
Phenotypic Marker ◽  
Bhlh Genes ◽  
Purple Leaf

Purple-colored leaves in plants attain much interest for their important biological functions and could be a potential source of phenotypic marker in selecting individuals in breeding. The transcriptional profiling helps to precisely identify mechanisms of leaf pigmentation in crop plants. In this study, two genetically unlike rice genotypes, the mutant purple leaf (pl) and wild (WT) were selected for RNA-sequencing and identifying the differentially expressed genes (DEGs) that are regulating purple leaf color. In total, 609 DEGs were identified, of which 513 and 96 genes were up- and down-regulated, respectively. The identified DEGs are categorized into metabolic process, carboxylic acid biosynthesis, phenylpropanoids, and phenylpropanoid biosynthesis process enrichment by GO analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their association with phenylpropanoid synthesis, flavonoid synthesis, and phenylalanine metabolism. To explore molecular mechanism of purple leaf color, a set of anthocyanin biosynthetic and regulatory gene expression patterns were checked by qPCR. We found that OsPAL (Os02g0626100, Os02g0626400, Os04g0518400, Os05g0427400 and Os02g0627100), OsF3H (Os03g0122300), OsC4HL (Os05g0320700), and Os4CL5 (Os08g0448000) are associated with anthocyanin biosynthesis, and they were up-regulated in pl leaves. Two members of regulatory MYB genes (OsMYB55; Os05g0553400 and Os08g0428200), two bHLH genes (Os01g0196300 and Os04g0300600), and two WD40 genes (Os11g0132700 and Os11g0610700) also showed up-regulation in pl mutant. These genes might have significant and vital roles in pl leaf coloration and could provide reference materials for further experimentation to confirm the molecular mechanisms of anthocyanin biosynthesis in rice.

scholarly journals Genomic architecture of biomass heterosis inArabidopsis

2017 ◽  
Vol 114 (30) ◽  
pp. 8101-8106 ◽  
Author(s):  
Mei Yang ◽  
Xuncheng Wang ◽  
Diqiu Ren ◽  
Hao Huang ◽  
Miqi Xu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Expression Patterns ◽  
Natural Populations ◽  
Genome Wide Association Studies ◽  
Genomic Architecture ◽  
Genome Wide ◽  
Stimulus Responsive ◽  
Abiotic Stimuli

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200Arabidopsishybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates includeWUSCHEL,ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representativeArabidopsishybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis inArabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.

scholarly journals Comprehensive Transcriptomic Analysis of Mouse Gonadal Development Involving Sexual Differentiation, Meiosis and Gametogenesis

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Wang ◽  
Geng G. Tian ◽  
Zhuxia Zheng ◽  
Bo Li ◽  
Qinghe Xing ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Candidate Genes ◽  
Sexual Differentiation ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Gonadal Development ◽  
Transcriptome Database ◽  
Alternatively Spliced ◽  
Expression Module

Abstract Background Mammalian gonadal development is crucial for fertility. Sexual differentiation, meiosis and gametogenesis are critical events in the process of gonadal development. Abnormalities in any of these events may cause infertility. However, owing to the complexity of these developmental events, the underlying molecular mechanisms are not fully understood and require further research. Results In this study, we employed RNA sequencing to examine transcriptome profiles of murine female and male gonads at crucial stages of these developmental events. By bioinformatics analysis, we identified a group of candidate genes that may participate in sexual differentiation, including Erbb3, Erbb4, and Prkg2. One hundred and two and 134 candidate genes that may be important for female and male gonadal development, respectively, were screened by analyzing the global gene expression patterns of developing female and male gonads. Weighted gene co-expression network analysis was performed on developing female gonads, and we identified a gene co-expression module related to meiosis. By alternative splicing analysis, we found that cassette-type exon and alternative start sites were the main forms of alternative splicing in developing gonads. A considerable portion of differentially expressed and alternatively spliced genes were involved in meiosis. Conclusion Taken together, our findings have enriched the gonadal transcriptome database and provided novel candidate genes and avenues to research the molecular mechanisms of sexual differentiation, meiosis, and gametogenesis.

scholarly journals Illumina® Sequencing Reveals Candidate Genes of Carotenoid Metabolism in Three Pummelo Cultivars (Citrus Maxima) with Different Pulp Color

2019 ◽  
Vol 20 (9) ◽  
pp. 2246 ◽  
Author(s):  
Cui-Cui Jiang ◽  
Yan-Fang Zhang ◽  
Yan-Jin Lin ◽  
Yuan Chen ◽  
Xin-Kun Lu
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanism ◽  
Expression Patterns ◽  
Carotenoid Biosynthesis ◽  
Aldehyde Oxidase ◽  
Carotenoid Content ◽  
Rna Seq ◽  
Carotenoid Accumulation ◽  
Carotenoid Metabolism ◽  
Citrus Maxima

Pummelo (Citrus maxima) is one of important fruit trees, which belongs to Citrus species. The fruits of different pummelo cultivars have different colors and differ in the contents of carotenoid. Our results clearly showed that ‘Huangjinmiyou’ (HJMY) has the highest content of β-carotene, followed by ‘Hongroumiyou’ (HRMY) and ‘Guanximiyou’ (GXMY). Lycopene is dominantly accumulated in HRMY. However, the molecular mechanism underlying the carotenoid accumulation in pummelo flesh is not fully understood. In this study, we used the RNA-Seq technique to investigate the candidate genes of carotenoid metabolism in the flesh of pummelo cv. GXMY and its mutants HRMY and HJMY in three development periods of fruit. After data assembly and bioinformatic analysis, a total of 357 genes involved in biosynthesis of secondary metabolites were isolated, of which 12 differentially expressed genes (DEGs) are involved in carotenoid biosynthesis. Among these 12 DEGs, phytoene synthase (PSY2), lycopene β-cyclase (LYCB2), lycopene Ɛ-cyclase (LYCE), carotenoid cleavage dioxygenases (CCD4), 9-cis-epoxycarotenoid dioxygenase (NCED2), aldehyde oxidase 3 (AAO3), and ABA 8′-hydroxylases (CYP707A1) are the most distinct DEGs in three pummelo cultivars. The co-expression analysis revealed that the expression patterns of several transcription factors such as bHLH, MYB, ERF, NAC and WRKY are highly correlated with DEGs, which are involved in carotenoid biosynthesis. In addition, the expression patterns of 22 DEGs were validated by real-time quantitative PCR (RT-qPCR) and the results are highly concordant with the RNA-Seq results. Our results provide a global vision of transcriptomic profile among three pummelo cultivars with different pulp colors. These results would be beneficial to further study the molecular mechanism of carotenoid accumulation in pummelo flesh and help the breeding of citrus with high carotenoid content.

scholarly journals Identification of mRNAs Related to Tibial Cartilage Development of Yorkshire Piglets

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shuaifei Feng ◽  
Xiaoyong Du ◽  
Chao Wang ◽  
Dengdeng Ye ◽  
Guanjun Ma ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Comparison Group ◽  
Bone Development ◽  
Expression Patterns ◽  
Osteoclast Differentiation ◽  
Economic Losses ◽  
Mineral Absorption ◽  
Cartilage Development

Cartilage dysplasia is one of the important reasons for the weakness of pig limbs and hooves. Porcine rickets with weak limbs and hooves bring huge economic losses to the pig industry. However, research on the development of pig cartilage is lacking. This study investigated the key genes and molecular mechanisms involved in cartilage development via an RNA-seq technique. Samples of proximal tibia cartilage were collected from three normal piglets with 1 day, 14 days, and 28 days of age, respectively, and then these samples were divided into two comparison groups (1-day vs. 14-day group, 14-day vs. 28-day group). Through the transcriptome analysis, 108 differentially expressed genes (DEGs), such as FORL2, were obtained from 1-day vs. 14-day comparison group, and 3602 DEGs were obtained from 14-day vs. 28-day comparison group, including SOX9, BMP6, and MMP13. The gene ontology (GO) functional and KEGG pathway enrichment revealed that many functions of DEGs were related to bone development. The pathways of DEGs from Day 1 vs. Day 14 were mainly enriched in mineral absorption, but the DEGs of Day 14 vs. Day 28 were enriched in osteoclast differentiation. Then, the expression patterns of six candidate genes were verified via qPCR. In conclusion, candidate genes affecting cartilage development in Yorkshire pigs were obtained by transcriptome analysis, and the clues showed that Day 14 to Day 28 is a more active and extensive period in cartilage developments, which played a key role in revealing the molecular mechanism of pig cartilage development basis, also compensating for vacancies in cartilage research.

Mediterranean fruit fly genes exhibit different expression patterns between heat and cold treatments

2021 ◽  
pp. 1-7
Author(s):  
Kay Anantanawat ◽  
Alexie Papanicolaou ◽  
Kelly Hill ◽  
Wei Xu
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Insect Pest ◽  
Expression Patterns ◽  
Critical Role ◽  
Cold Treatment ◽  
Fruit Fly ◽  
Mediterranean Fruit Fly ◽  
Molecular Response

Abstract Invasive Tephritid fruit flies are a global threat to both agriculture and horticulture industries. Biosecurity has played a critical role in reducing their damage but becomes more and more challenging after several key chemical pesticides were banned or withdrawn for health or environmental reasons. This has led to non-chemical approaches including heat and cold treatments being broadly utilized to get rid of fruit fly infestation. However, the molecular mechanisms to kill the flies underlying these stressors are not clear yet. This knowledge will certainly help refine current post-harvest treatment strategies and develop more efficient, cost-effective and environmentally friendly approaches for fruit fly management. Previously, the molecular response of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) to heat was examined thoroughly, in which 31 key genes were identified with significant changes in expression levels and their high-resolution expression timeline was constructed across 11 timepoints. However, whether these candidate genes respond to cold in the same way was unknown. Here, a temperature bioassay was conducted and the expression profiles of these genes were investigated across the same 11 timepoints using cold treatment. The results showed that most of candidate genes exhibited divergent expression profiles compared to heat treatment, suggesting that the fly molecular response to cold may be different from those to heat. This study provides new knowledge of Tephritid fruit fly response to cold at a molecular level, which could aid in improving current fruit fly management and facilitate the development of new strategies to control this serious horticultural insect pest.

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