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Yan Wang - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of Taproot thickening in radish (Raphanus sativus L.).
BMC plant biology, 2020Co-Authors: Yang Xie, Yan Wang, Yinglong Chen, Mingjia Tang, Jiali Ying, Junhui Dong, Everlyne M’mbone Muleke, Liwang LiuAbstract:Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying Taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish Taproot thickening from three advanced inbred lines with different root size. A total of 2606 differentially expressed genes (DEGs) were shared between ‘NAU-DY’ (large acicular) and ‘NAU-YB’ (medium obovate), which were significantly enriched in ‘phenylpropanoid biosynthesis’, ‘glucosinolate biosynthesis’, and ‘starch and sucrose metabolism’ pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between ‘NAU-DY’ and ‘NAU-YH’ (small circular), whereas 12 miRNAs exhibited specific differential expression in ‘NAU-DY’. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of Taproot type variation, and a putative regulatory model of Taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis. This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying Taproot thickening in root vegetable crops.
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Comparative proteomic analysis provides insight into a complex regulatory network of Taproot formation in radish (Raphanus sativus L.).
Horticulture research, 2018Co-Authors: Yang Xie, Yan Wang, Lianxue Fan, Yinglong Chen, Mingjia Tang, Xiaobo Luo, Liwang LiuAbstract:The fleshy Taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level. In this study, a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of Taproot thickening using iTRAQ approach. In total, 1862 differentially expressed proteins (DEPs) were identified from 6342 high-confidence proteins, among which 256 up-regulated proteins displayed overlapped accumulation in S1 (pre-cortex splitting stage) vs. S2 (cortex splitting stage) and S1 vs. S3 (expanding stage) pairs, whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs. S3 and S2 vs. S3 pairs. Gene Ontology (GO) and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as "starch and sucrose metabolism", "plant hormone signal transduction", and "biosynthesis of secondary metabolites". A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels. Furthermore, association analysis showed that 187, 181, and 96 DEPs were matched with their corresponding differentially expressed genes (DEGs) in S1 vs. S2, S1 vs. S3, and S2 vs. S3 comparison, respectively. Notably, several functional proteins including cell division cycle 5-like protein (CDC5), expansin B1 (EXPB1), and xyloglucan endotransglucosylase/hydrolase protein 24 (XTH24) were responsible for cell division and expansion during radish Taproot thickening process. These results could facilitate a better understanding of the molecular mechanism underlying Taproot thickening, and provide valuable information for the identification of critical genes/proteins responsible for Taproot thickening in root vegetable crops.
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Comparative proteomic analysis provides insight into a complex regulatory network of Taproot formation in radish (Raphanus sativus L.)
Nature Publishing Group, 2018Co-Authors: Yang Xie, Yan Wang, Lianxue Fan, Yinglong Chen, Mingjia Tang, Xiaobo Luo, Liwang LiuAbstract:Root vegetables: tapping into root thickening for improved yields An investigation into the proteins and genes responsible for Taproot thickening in radish could help improve yields of root vegetables. The fleshy Taproot of vegetables like radish are vital to food supplies worldwide, but the precise mechanisms behind healthy, high quality Taproot formation, and thickening are unclear. Liwang Liu at Nanjing Agricultural University in Nanjing, China, and co-workers have identified several functional proteins and corresponding genes responsible for cell division in Taproot growth and thickening. The team analyzed changes in protein expression at three different developmental stages of radish Taproot. They identified 1862 differentially expressed proteins involved in several processes including sugar and starch metabolism, hormone signaling, and biosynthesis of metabolites. Their results provide fundamental insights into the regulation of Taproot thickening in radish and could be expanded to other root vegetables
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Transcriptome Profiling of Taproot Reveals Complex Regulatory Networks during Taproot Thickening in Radish (Raphanus sativus L.).
Frontiers in plant science, 2016Co-Authors: Jing Wang, Ronghua Wang, Yan Wang, Xianwen Zhu, Yang Xie, Xiaobo Luo, Xiaochuan Sun, Muleke M. EverlyneAbstract:Radish (Raphanus sativus L.,) is one of the most important vegetable crops worldwide. Taproot thickening represents a critical developmental period that determines yield and quality in radish life cycle. To isolate differentially expressed genes (DGEs) involved in radish Taproot thickening process and explored the molecular mechanism in underlying Taproot development, three cDNA libraries from radish Taproot collected at pre-cortex splitting stage (L1), cortex splitting stage (L2) and expanding stage (L3) were constructed and sequenced by RNA-Seq technology. More than seven million clean reads were obtained from the three libraries, respectively, from which 4,717,617 (L1, 65.35%), 4,809,588 (L2, 68.24%) and 4,973,745 (L3, 69.45%) reads were matched to the radish reference genes. A total of 85,939 transcripts were generated from three libraries, from which 10,450, 12,325 and 7,392 differentially expressed transcripts (DETs) were detected in L1 vs. L2, L1 vs. L3, and L2 vs. L3 comparisons, respectively. Gene Ontology and pathway analysis showed that many DEGs, including EXPA9, Cyclin, CaM, Syntaxin, MADS-box, SAUR and CalS were involved in cell events, cell wall modification, regulation of plant hormone levels, signal transduction and metabolisms, which may relate to Taproot thickening. Furthermore, the integrated analysis of mRNA-miRNA revealed that 43 miRNAs and 92 genes that formed 114 miRNA-target mRNA pairs were co-expressed, and three miRNA-target regulatory networks of Taproot were constructed from different libraries. Finally, the expression patterns of 16 selected genes were confirmed using RT-qPCR analysis. A hypothetical model of genetic regulatory network associated with Taproot thickening in radish was put forward. The Taproot formation of radish is mainly contributed to cell differentiation, division and expansion, which are regulated and promoted by certain specific signal transduction pathways and metabolism possesses. These results could provide new insights into the complex molecular mechanism underlying Taproot thickening and facilitate genetic improvement of Taproot in radish.
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de novo Taproot transcriptome sequencing and analysis of major genes involved in sucrose metabolism in radish raphanus sativus l
Frontiers in Plant Science, 2016Co-Authors: Rugang Yu, Ronghua Wang, Liang Xu, Yan Wang, Wei Zhang, Benard KaranjaAbstract:Radish (Raphanus sativus L.) is an important annual or biennial root vegetable crop. The fleshy Taproot comprises the main edible portion of the plant with high nutrition and medical value. Molecular biology study of radish begun rather later, and lacks sufficient transcriptomic and genomic data in pubic databases for understanding of the molecular mechanism during the radish Taproot formation. To develop a comprehensive overview of the ‘NAU-YH’ root transcriptome, a cDNA library, prepared from three equally mixed RNA of Taproots at different developmental stages including pre-cortex splitting stage, cortex splitting stage and expanding stages was sequenced using high-throughput Illumina RNA sequencing. From approximately 51 million clean reads, a total of 70,168 unigene with a total length of 50.28 Mb, an average length of 717 bp and a N50 of 994 bp were obtained. In total, 63,991 (about 91.20% of the assembled unigenes) unigenes were successfully annotated in five public databases including NR, GO, COG, KEGG and Nt. GO term analysis revealed that the majority of these unigenes were predominately involved in basic physiological and metabolic processes, catalytic, binding and cellular process．In addition, a total of 103 unigenes encoding eight enzymes in the sucrose metabolism related pathways were also identified by KEGG pathways analysis. Sucrose synthase (29 unigenes), invertase (17 unigenes), sucrose-phosphate synthase (16 unigenes), fructokinase (16 unigenes) and hexokinase (11 unigenes) ranked top five enzymes in these eight key enzymes. From which, two genes (RsSuSy1, RsSPS1) were validated by T-A cloning and sequenced in radish, while six unigenes were validated by RT-qPCR analysis. These results would be served as an important public reference platform to identify the related key genes during Taproot thickening and facilitate the revealing of molecular mechanisms underlying Taproot thickening in radish.
Jeffrey J Volenec - One of the best experts on this subject based on the ideXlab platform.
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Phosphorus and potassium effects on Taproot C and N reserve pools and long-term persistence of alfalfa (Medicago sativa L.).
Plant science : an international journal of experimental plant biology, 2018Co-Authors: William Kess Berg, S M Cunningham, Sofia Lissbrant, Sylvie M. Brouder, Jeffrey J VolenecAbstract:Abstract Improved P and K nutrition can enhance yield and persistence of alfalfa (Medicago sativa L.) grown on low fertility soils, but it is unknown if the improved agronomic performance is associated with greater Taproot N and C reserves. Our objective was to use cluster analysis to determine how alfalfa plant persistence is altered by P and K fertilization, and determine if changes in specific Taproot C and/or N reserves were associated with alfalfa plant death. Taproots were dug and plants counted in May and December of each year and Taproots analyzed for P, K, starch, sugar, amino-N, and soluble protein. K-means clustering was used to create six clusters that were subsequently compared using two-sample t-tests. Low K in herbage and Taproots was associated with low yield and poor persistence of the Low and Very Low clusters and Taproots of these plants generally had low starch, protein, and amino-N concentrations. Plants died primarily between May and December. Plant persistence of the low yielding, P-deficient Medium cluster was high and associated with high starch concentrations. Low amino-N concentrations in Taproots may provide an early indication of potential plant death because these were evident in poor-persisting Low and Very Low clusters early in the study.
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effect of summer irrigation on seasonal changes in Taproot reserves and the expression of winter dormancy activity in four contrasting lucerne cultivars
Crop & Pasture Science, 2010Co-Authors: Keith G. Pembleton, S M Cunningham, Jeffrey J VolenecAbstract:In the summer dry environment of cool temperate Tasmania, summer irrigation is used to maximise forage production. For lucerne (Medicago sativa L.) this irrigation is likely to interact with winter-dormancy genotypes to influence seasonal changes in Taproot reserves and thus, the process of cold acclimation. To test this hypothesis four lucerne cultivars with contrasting levels of winter dormancy (DuPuits: winter-dormant; Grasslands Kaituna: semi winter-dormant; SARDI 7: winter-active: SARDI 10, highly winter-active) were grown in small plots at Elliott, Tasmania, under irrigated or dryland conditions. At each defoliation Taproots were sampled and assayed for the concentration of soluble sugars, starch, amino acids, soluble protein, the abundance of vegetative storage proteins (VSP), and the abundance of mRNA transcripts associated with cold acclimation and VSP. Taproot-soluble protein concentrations in DuPuits significantly increased from summer to autumn when plants were grown under dryland conditions. When grown under irrigated conditions, Taproot-soluble protein concentrations decreased over summer and increased in autumn for all cultivars. The abundance of VSP increased in summer in all cultivars grown under dryland conditions. Taproot-soluble sugar concentrations increased and starch decreased in autumn for all cultivars grown under both water regimes. Plants grown under dryland conditions showed little change in RNA transcript abundance of cold acclimation genes across all cultivars and sampling dates, while in those plants grown under irrigated conditions, transcript abundance was influenced by sampling date, and for some genes, by cultivar. There was a clear carry-over effect from the exposure of summer drought on the winter-dormancy response. The expression of winter dormancy at an agronomic and molecular level was greater under dryland conditions.
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Effect of summer irrigation on seasonal changes in Taproot reserves and the expression of winter dormancy/activity in four contrasting lucerne cultivars
Crop & Pasture Science, 2010Co-Authors: Keith G. Pembleton, S M Cunningham, Jeffrey J VolenecAbstract:In the summer dry environment of cool temperate Tasmania, summer irrigation is used to maximise forage production. For lucerne (Medicago sativa L.) this irrigation is likely to interact with winter-dormancy genotypes to influence seasonal changes in Taproot reserves and thus, the process of cold acclimation. To test this hypothesis four lucerne cultivars with contrasting levels of winter dormancy (DuPuits: winter-dormant; Grasslands Kaituna: semi winter-dormant; SARDI 7: winter-active: SARDI 10, highly winter-active) were grown in small plots at Elliott, Tasmania, under irrigated or dryland conditions. At each defoliation Taproots were sampled and assayed for the concentration of soluble sugars, starch, amino acids, soluble protein, the abundance of vegetative storage proteins (VSP), and the abundance of mRNA transcripts associated with cold acclimation and VSP. Taproot-soluble protein concentrations in DuPuits significantly increased from summer to autumn when plants were grown under dryland conditions. When grown under irrigated conditions, Taproot-soluble protein concentrations decreased over summer and increased in autumn for all cultivars. The abundance of VSP increased in summer in all cultivars grown under dryland conditions. Taproot-soluble sugar concentrations increased and starch decreased in autumn for all cultivars grown under both water regimes. Plants grown under dryland conditions showed little change in RNA transcript abundance of cold acclimation genes across all cultivars and sampling dates, while in those plants grown under irrigated conditions, transcript abundance was influenced by sampling date, and for some genes, by cultivar. There was a clear carry-over effect from the exposure of summer drought on the winter-dormancy response. The expression of winter dormancy at an agronomic and molecular level was greater under dryland conditions.
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Partitioning of Taproot constituents and crown bud development are affected by water deficit in regrowing alfalfa (Medicago sativa L.).
Crop Science, 2010Co-Authors: Keith G. Pembleton, Jeffrey J Volenec, Richard P. Rawnsley, Dj DonaghyAbstract:Growth of alfalfa (Medicago sativa L.) following the correction of water deficits will depend, in part, on the amount of plant constituents available to support regrowth and the availability of crown buds for the development of new shoots. To investigate if water deficit affected the accumulation of Taproot constituents and crown bud development of alfalfa, two alfalfa cultivars were exposed to increasing levels of water deficit (100, 75, 50 25 and 0% of the replacement water requirement) during a regrowth period. Shoot growth was reduced in proportion to the level of water deficit. Taproot starch concentrations decreased while Taproot soluble sugar increased in plants exposed to a water deficit. Thirty-five d after initiation of treatments, Taproot protein and amino acid concentrations were similar in all treatments that received water. Water deficit increased the relative concentration of low and middle molecular weight Taproot vegetative storage proteins (VSP) and water deficits reduced the number and mass of green crown buds. Both cultivars had a similar response to water deficit for all Taproot constituents and crown bud development. Further studies are required to determine the influence of increasing VSP abundance and decreasing numbers of crown buds on plant recovery following the removal of a water deficit. © Crop Science Society of America.
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Influence of phosphorus and potassium on alfalfa yield, Taproot C and N pools, and transcript levels of key genes after defoliation.
Crop Science, 2009Co-Authors: W. K. Berg, S M Cunningham, Sylvie M. Brouder, Brad C. Joern, K. D. Johnson, Jeffrey J VolenecAbstract:Fertilization with K and P impacts alfalfa (Medi- cago sativa L.) yield, but how these nutrients influence Taproot reserves and gene expression is unknown. Our objectives were to determine how P and K impact (i) alfalfa yield and yield components, (ii) accumulation and use of Taproot carbon (C) and nitrogen (N) pools, and (iii) transcript levels for β-amylase, sucrose synthase, and the high molecular weight vegetative storage protein in alfalfa Taproots. Yield and yield components were determined at 30-d intervals beginning in late May. Roots were sampled after the late June harvest (Day 0) and 1, 3, 6, 10, 14, 21, and 30 d thereafter. Addition of P and K increased forage yield by enhancing mass per shoot. High P resulted in rapid starch use, while Taproots of plants fertilized with K had low sugar concentrations. Transcripts decline by Day 6 and by Day 10 were below detection limits. Transcripts for β-amylase and sucrose synthase accumulated rapidly after Day 10 in Taproots of plants fertilized with both P and K. Balanced P and K nutrition resulted in the accumulation and effective utilization of C and N reserves and in improved alfalfa adaptation to defoliation.
Rugang Yu - One of the best experts on this subject based on the ideXlab platform.
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de novo Taproot transcriptome sequencing and analysis of major genes involved in sucrose metabolism in radish raphanus sativus l
Frontiers in Plant Science, 2016Co-Authors: Rugang Yu, Ronghua Wang, Liang Xu, Yan Wang, Wei Zhang, Benard KaranjaAbstract:Radish (Raphanus sativus L.) is an important annual or biennial root vegetable crop. The fleshy Taproot comprises the main edible portion of the plant with high nutrition and medical value. Molecular biology study of radish begun rather later, and lacks sufficient transcriptomic and genomic data in pubic databases for understanding of the molecular mechanism during the radish Taproot formation. To develop a comprehensive overview of the ‘NAU-YH’ root transcriptome, a cDNA library, prepared from three equally mixed RNA of Taproots at different developmental stages including pre-cortex splitting stage, cortex splitting stage and expanding stages was sequenced using high-throughput Illumina RNA sequencing. From approximately 51 million clean reads, a total of 70,168 unigene with a total length of 50.28 Mb, an average length of 717 bp and a N50 of 994 bp were obtained. In total, 63,991 (about 91.20% of the assembled unigenes) unigenes were successfully annotated in five public databases including NR, GO, COG, KEGG and Nt. GO term analysis revealed that the majority of these unigenes were predominately involved in basic physiological and metabolic processes, catalytic, binding and cellular process．In addition, a total of 103 unigenes encoding eight enzymes in the sucrose metabolism related pathways were also identified by KEGG pathways analysis. Sucrose synthase (29 unigenes), invertase (17 unigenes), sucrose-phosphate synthase (16 unigenes), fructokinase (16 unigenes) and hexokinase (11 unigenes) ranked top five enzymes in these eight key enzymes. From which, two genes (RsSuSy1, RsSPS1) were validated by T-A cloning and sequenced in radish, while six unigenes were validated by RT-qPCR analysis. These results would be served as an important public reference platform to identify the related key genes during Taproot thickening and facilitate the revealing of molecular mechanisms underlying Taproot thickening in radish.
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transcriptome profiling of root micrornas reveals novel insights into Taproot thickening in radish raphanus sativus l
BMC Plant Biology, 2015Co-Authors: Rugang Yu, Yiqin Gong, Ronghua Wang, Liang Xu, Yan Wang, Cecilia LimeraAbstract:Background Radish (Raphanus sativus L.) is an economically important root vegetable crop, and the Taproot-thickening process is the most critical period for the final productivity and quality formation. MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory function in plant growth and development. However, the characterization of miRNAs and their roles in regulating radish Taproot growth and thickening remain largely unexplored. A Solexa high-throughput sequencing technology was used to identify key miRNAs involved in Taproot thickening in radish.
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de novo transcriptome sequencing of radish raphanus sativus l and analysis of major genes involved in glucosinolate metabolism
BMC Genomics, 2013Co-Authors: Rugang Yu, Liang Xu, Yan Wang, Lulu Zhai, Yiqin GongAbstract:Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy Taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish Taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish. In this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish Taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling. The ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during Taproot formation in radish.
Valérie Serra - One of the best experts on this subject based on the ideXlab platform.
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growth and branching of the Taproot of young oak trees a dynamic study
Journal of Experimental Botany, 1994Co-Authors: Loyic Pagès, Valérie SerraAbstract:The growth and branching of the Taproot of young oak trees were studied on seedlings grown in root observation boxes over a period of 30-45 d. The development of shoots and roots were recorded daily on a set of eight plants, and additional observations on the initiation of primordia were made on another set of 18 plants. Taproot growth was typically indeterminate and linear, with growth rates in the range of 1.5-2.5 cm d -1 . In some cases, however, growth slowed down or stopped, and resumed a few days later. The growth of shoots and roots were not synchronized. Taproots branched in two ways: acropetal branches emerged from 4-8-d-old Taproot tissues, and late branches emerged from older tissues (up to 30 d in our experiment)
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Growth and branching of the Taproot of young oak trees—a dynamic study
Journal of Experimental Botany, 1994Co-Authors: Loyic Pagès, Valérie SerraAbstract:The growth and branching of the Taproot of young oak trees were studied on seedlings grown in root observation boxes over a period of 30-45 d. The development of shoots and roots were recorded daily on a set of eight plants, and additional observations on the initiation of primordia were made on another set of 18 plants. Taproot growth was typically indeterminate and linear, with growth rates in the range of 1.5-2.5 cm d -1 . In some cases, however, growth slowed down or stopped, and resumed a few days later. The growth of shoots and roots were not synchronized. Taproots branched in two ways: acropetal branches emerged from 4-8-d-old Taproot tissues, and late branches emerged from older tissues (up to 30 d in our experiment)
Liwang Liu - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of Taproot thickening in radish (Raphanus sativus L.).
BMC plant biology, 2020Co-Authors: Yang Xie, Yan Wang, Yinglong Chen, Mingjia Tang, Jiali Ying, Junhui Dong, Everlyne M’mbone Muleke, Liwang LiuAbstract:Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying Taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish Taproot thickening from three advanced inbred lines with different root size. A total of 2606 differentially expressed genes (DEGs) were shared between ‘NAU-DY’ (large acicular) and ‘NAU-YB’ (medium obovate), which were significantly enriched in ‘phenylpropanoid biosynthesis’, ‘glucosinolate biosynthesis’, and ‘starch and sucrose metabolism’ pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between ‘NAU-DY’ and ‘NAU-YH’ (small circular), whereas 12 miRNAs exhibited specific differential expression in ‘NAU-DY’. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of Taproot type variation, and a putative regulatory model of Taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis. This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying Taproot thickening in root vegetable crops.
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Comparative proteomic analysis provides insight into a complex regulatory network of Taproot formation in radish (Raphanus sativus L.).
Horticulture research, 2018Co-Authors: Yang Xie, Yan Wang, Lianxue Fan, Yinglong Chen, Mingjia Tang, Xiaobo Luo, Liwang LiuAbstract:The fleshy Taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level. In this study, a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of Taproot thickening using iTRAQ approach. In total, 1862 differentially expressed proteins (DEPs) were identified from 6342 high-confidence proteins, among which 256 up-regulated proteins displayed overlapped accumulation in S1 (pre-cortex splitting stage) vs. S2 (cortex splitting stage) and S1 vs. S3 (expanding stage) pairs, whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs. S3 and S2 vs. S3 pairs. Gene Ontology (GO) and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as "starch and sucrose metabolism", "plant hormone signal transduction", and "biosynthesis of secondary metabolites". A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels. Furthermore, association analysis showed that 187, 181, and 96 DEPs were matched with their corresponding differentially expressed genes (DEGs) in S1 vs. S2, S1 vs. S3, and S2 vs. S3 comparison, respectively. Notably, several functional proteins including cell division cycle 5-like protein (CDC5), expansin B1 (EXPB1), and xyloglucan endotransglucosylase/hydrolase protein 24 (XTH24) were responsible for cell division and expansion during radish Taproot thickening process. These results could facilitate a better understanding of the molecular mechanism underlying Taproot thickening, and provide valuable information for the identification of critical genes/proteins responsible for Taproot thickening in root vegetable crops.
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Comparative proteomic analysis provides insight into a complex regulatory network of Taproot formation in radish (Raphanus sativus L.)
Nature Publishing Group, 2018Co-Authors: Yang Xie, Yan Wang, Lianxue Fan, Yinglong Chen, Mingjia Tang, Xiaobo Luo, Liwang LiuAbstract:Root vegetables: tapping into root thickening for improved yields An investigation into the proteins and genes responsible for Taproot thickening in radish could help improve yields of root vegetables. The fleshy Taproot of vegetables like radish are vital to food supplies worldwide, but the precise mechanisms behind healthy, high quality Taproot formation, and thickening are unclear. Liwang Liu at Nanjing Agricultural University in Nanjing, China, and co-workers have identified several functional proteins and corresponding genes responsible for cell division in Taproot growth and thickening. The team analyzed changes in protein expression at three different developmental stages of radish Taproot. They identified 1862 differentially expressed proteins involved in several processes including sugar and starch metabolism, hormone signaling, and biosynthesis of metabolites. Their results provide fundamental insights into the regulation of Taproot thickening in radish and could be expanded to other root vegetables
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Transcriptome profiling of root microRNAs reveals novel insights into Taproot thickening in radish ( Raphanus sativus L.)
BMC plant biology, 2015Co-Authors: Yan Wang, Yiqin Gong, Ronghua Wang, Cecilia Limera, Wei Zhang, Xianwen Zhu, Liwang LiuAbstract:Radish (Raphanus sativus L.) is an economically important root vegetable crop, and the Taproot-thickening process is the most critical period for the final productivity and quality formation. MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory function in plant growth and development. However, the characterization of miRNAs and their roles in regulating radish Taproot growth and thickening remain largely unexplored. A Solexa high-throughput sequencing technology was used to identify key miRNAs involved in Taproot thickening in radish. Three small RNA libraries from ‘NAU-YH’ Taproot collected at pre-cortex splitting stage, cortex splitting stage and expanding stage were constructed. In all, 175 known and 107 potential novel miRNAs were discovered, from which 85 known and 13 novel miRNAs were found to be significantly differentially expressed during Taproot thickening. Furthermore, totally 191 target genes were identified for the differentially expressed miRNAs. These target genes were annotated as transcription factors and other functional proteins, which were involved in various biological functions including plant growth and development, metabolism, cell organization and biogenesis, signal sensing and transduction, and plant defense response. RT-qPCR analysis validated miRNA expression patterns for five miRNAs and their corresponding target genes. The small RNA populations of radish Taproot at different thickening stages were firstly identified by Solexa sequencing. Totally 98 differentially expressed miRNAs identified from three Taproot libraries might play important regulatory roles in Taproot thickening. Their targets encoding transcription factors and other functional proteins including NF-YA2, ILR1, bHLH74, XTH16, CEL41 and EXPA9 were involved in radish Taproot thickening. These results could provide new insights into the regulatory roles of miRNAs during the Taproot thickening and facilitate genetic improvement of Taproot in radish.
