SWATH-MS-facilitated proteomic profiling of fruit skin between Fuji apple and a red skin bud sport mutant

Chen, Mo Xian; Sun, Chao; Zhang, Kai Lu; Song, Yu; Tian, Yuan; Chen, Xi; Liu, Ying Gao; Ye, Nenghui; Zhang, Jianhua; Qu, Shenchun; Zhu, Fu Yuan

doi:10.1186/s12870-019-2018-1

Cited by 24 publications

(5 citation statements)

References 58 publications

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“…ABA was also involved in the regulation of self-protection processes (Ahmadi, Agharezaee, Kamgar-Haghighi, & Sepaskhah, 2014). Omics research is widely used to find the underlying molecular mechanism behind observed physiological changes (Chen et al, 2019;Zhu et al, 2017Zhu et al, , 2018. Root proteomic analysis showed that proteins involved in ABA signaling, amino acid synthesis, and N remobilization were up-regulated in the soil drying phase of AWD irrigation, when compared with CF irrigation (Li, Nong, et al, 2016;Li, Azeem, et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of photosynthesis‐related genes regulated by alternate wetting and drying irrigation in flag leaves of rice

Song

Feng

Das

et al. 2020

Food and Energy Security

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Alternate wetting and drying (AWD) irrigation has been widely used to replace continuous flooding (CF), which does not result in yield loss while improving water productivity. However, it is still unexplored as to how this agricultural practice would affect gene expression to control plant physiology. In this study, we found that photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), chlorophyll (Chl) content, and leaf water potential (Lwp) significantly decreased while abscisic acid (ABA) content and water use efficiency (WUE) increased when soil water potential reached to −15 kPa in the AWD irrigation regime. We then analyzed the differences between AWD and CF irrigation practices in transcriptomic profiles for flag leaves. Genes were found to be differentially expressed in photosynthesis related pathways namely, Chl biosynthesis, photosynthesis‐antenna proteins pathway, photosynthesis process, and ABA signal transduction pathway. The study provides important information on the morphological adaptations observed in the flag leaves in response to AWD irrigation, which will act as a basic framework to conduct molecular studies for improving rice cultivation.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of photosynthesis‐related genes regulated by alternate wetting and drying irrigation in flag leaves of rice

Song

Feng

Das

et al. 2020

Food and Energy Security

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“…The different colors of apple fruits were mainly caused by the difference of anthocyanin accumulation. Abundant apple germplasm resources and color mutants provide excellent materials for the study of plant anthocyanin metabolism [ 28 ]. In addition, the shape of the branches usually affects the yield and quality of the fruit.…”

Section: Discussionmentioning

confidence: 99%

Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious)

Ren,

Li,

Guo

et al. 2023

BMC Plant Biol

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Background Bud sport is a kind of somatic mutation that usually occurred in apple. ‘Red Delicious’ is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the ‘Red Delicious’ (G0) and its four generation mutants including ‘Starking Red’ (G1), ‘Starkrimson’ (G2), ‘Campbell Redchief’ (G3) and ‘Vallee Spur’ (G4). Results The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively. Conclusions Our study identified potential genes associated with spur-type and skin-color differences in ‘Red Delicious’ and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport.

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“…The present results also provide a fast and efficient means of alleviating the damage caused by HT stress during the meiosis stage of young spikes of rice, which may contribute to the regulation of rice cultivation. Furthermore, corporation of innovative multi-omics technology may help us unravel the molecular dynamics of this interesting research topic 45,46 .…”

Section: Discussionmentioning

confidence: 99%

Spermidine Enhanced Free Polyamine Levels and Expression of Polyamine Biosynthesis Enzyme Gene in Rice Spikelets under Heat Tolerance before Heading

Zhou

Pu³

et al. 2020

Sci Rep

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High temperatures (Ht) before heading strongly inhibit the development of spikelets in rice. Spermidine (Spd) can improve rice's resistance to HT stress; however, the mechanism underlying this effect has not been elucidated. This study investigated several parameters, including yield, superoxide anion (o 2 .-), protective enzyme activities, and polyamine content, in a heat-sensitive genotype, Shuanggui 1. The yield and yield components decreased dramatically when subjected to HT stress, while this reduction could be partially recovered by exogenous Spd. Spd also slowed the generation rate of o 2 .and increased protective enzyme, superoxide dismutase (SOD) and catalase (CAT) activities both under normal and high temperatures, which suggested that Spd may participate in the antioxidant system. Furthermore, genes involved in polyamine synthesis were analyzed. The results show that HT before heading significantly increased the expression of arginine decarboxylase OsADC1, Spd synthase OsSPDS1 and OsSPDS3 and had little effect on the expression of the S-adenosylmethionine decarboxylase OsSAMDC2 and ornithine decarboxylase OsODC1. In addition, exogenous Spd considerably reduced the expression of OsSAMDC2, OsSPDS1 and OsSPDS3 under Ht but not the expression of OsADC1. the above mentioned results indicate that the exogenous Spd could help young rice spikelets to resist Ht stress by reducing the expression of OsSAMDC2, OsSPDS1 and OsSPDS3, resulting in higher levels of endogenous Spd and Spm, which were also positively correlated with yield. In conclusion, the adverse effect of HT stress on young spikelets seems to be alleviated by increasing the amounts of Spd and Spm, which provides guidance for adaptation to heat stress during rice production. High temperature is considered to be one of the primary environmental stress factors that affect crop growth and development. Surface air temperature is predicted to be approximately 2∼4.5 °C higher at the end of the century 1. In addition, extreme temperature events, including high-temperature (HT) stress, will occur more frequently worldwide 2. When subjected to HT over normal temperature (NT), the life processes of crop will be severely affected, leading to reduced yields 3,4. Rice (Oryza sativa L.) is one of the most important staple food crops and feeds approximately 65% of the population in China 5,6. HT stress hinders its growth at any time during the crop life cycle but particularly during

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SWATH-MS-facilitated proteomic profiling of fruit skin between Fuji apple and a red skin bud sport mutant

Cited by 24 publications

References 58 publications

Transcriptomic analysis of photosynthesis‐related genes regulated by alternate wetting and drying irrigation in flag leaves of rice

Transcriptomic analysis of photosynthesis‐related genes regulated by alternate wetting and drying irrigation in flag leaves of rice

Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious)

Spermidine Enhanced Free Polyamine Levels and Expression of Polyamine Biosynthesis Enzyme Gene in Rice Spikelets under Heat Tolerance before Heading

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