An event of alternative splicing affects the expression of two BnCYCD3-1-like genes in Brassica napus

Guo, Yuanyuan; Li, Jie; Yan, Fang; Wan, Yunbao; Tang, Jiajia; Wei, Tao; Jiang, Xuefei; Wang, Rui; Wang, Maolin

doi:10.1016/j.gene.2018.12.085

Cited by 3 publications

(5 citation statements)

References 36 publications

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“…Few studies have investigated this multi-silique trait in rapeseed; however, there have been similar reports of multi-pistil traits in other crops, particularly in wheat (Triticum aestivum): Duan et al (2015) discovered a male-sterile wheat mutant, dms, with a dwarf status and multi-pistils, a pleiotropic phenotype found to be controlled by a single recessive gene, which was not identified. Guo et al (2019a) and Guo et al (2019b) reported another multi-ovary trait in the wheat line DUOII, which was controlled by a dominant gene, and used a proteomics approach to propose some candidate proteins. Yang et al (2017) mapped a gene promoting the formation of three pistils (Pis1) to chromosome 2D and identified some candidate genes according to their annotations, while Zhu et al (2019) discovered a wheat multi-pistil mutant, 12TP, which was found to contain a semidominant mutation located on chromosome arm 2DL.…”

Section: Discussionmentioning

confidence: 99%

“… Guo et al. (2019a) and Guo et al. (2019b) reported another multi-ovary trait in the wheat line DUOII, which was controlled by a dominant gene, and used a proteomics approach to propose some candidate proteins.…”

Section: Discussionmentioning

confidence: 99%

“…AS not only provides an important source of transcriptomic and proteomic diversity and plasticity for use in natural selection (Labadorf et al, 2010), but it also plays specific roles in the response (Chauhan et al, 2019) or adaptation to environmental stresses (Filichkin et al, 2015). Guo et al (2019a) and Guo et al (2019b) identified four splicing variants of two BnCYCD3-1-LIKE genes in B. napus and found evidence that their AS may play an important role in the response to environmental stresses. Xia et al (2017) discovered that the AS with intron retention of EARLY MATURITY8 (EAM8) led to early flowering in a barley (Hordeum vulgare) landrace; while in shepherd's purse (Capsella bursa-pastoris), flowering time varied with changes in the splicing of a FLOWERING LOCUS C (FLC) homolog (Slotte et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“… Guo et al. (2019a) and Guo et al. (2019b) identified four splicing variants of two BnCYCD3-1-LIKE genes in B. napus and found evidence that their AS may play an important role in the response to environmental stresses.…”

Section: Introductionmentioning

confidence: 99%

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Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis

Chai

Zhang

et al. 2020

PeerJ

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Background Flower and fruit development are vital stages of the angiosperm lifecycle. We previously investigated the multi-silique trait in the rapeseed (Brassica napus) line zws-ms on a genomic and transcriptomic level, leading to the identification of two genomic regions and several candidate genes associated with this trait. However, some events on the transcriptome level, like alternative splicing, were poorly understood. Methods Plants from zws-ms and its near-isogenic line (NIL) zws-217 were both grown in Xindu with normal conditions and a colder area Ma’erkang. Buds from the two lines were sampled and RNA was isolated to perform the transcriptomic sequencing. The numbers and types of alternative splicing (AS) events from the two lines were counted and classified. Genes with AS events and expressed differentially between the two lines, as well as genes with AS events which occurred in only one line were emphasized. Their annotations were further studied. Results From the plants in Xindu District, an average of 205,496 AS events, which could be sorted into five AS types, were identified. zws-ms and zws-217 shared highly similar ratios of each AS type: The alternative 5′ and 3′ splice site types were the most common, while the exon skipping type was observed least often. Eleven differentially expressed AS genes were identified, of which four were upregulated and seven were downregulated in zws-ms. Their annotations implied that five of these genes were directly associated with the multi-silique trait. While samples from colder area Ma’erkang generated generally reduced number of each type of AS events except for Intron Retention; but the number of differentially expressed AS genes increased significantly. Further analysis found that among the 11 differentially expressed AS genes from Xindu, three of them maintained the same expression models, while the other eight genes did not show significant difference between the two lines in expression level. Additionally, the 205 line-specific expressed AS genes were analyzed, of which 187 could be annotated, and two were considered to be important. Discussion This study provides new insights into the molecular mechanism of the agronomically important multi-silique trait in rapeseed on the transcriptome level and screens out some environment-responding candidate genes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis

Chai

Zhang

et al. 2020

PeerJ

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“…Meanwhile, other types of genes were also reported recently. For example, the cyclin-D3-1-like gene may respond to environmental stresses via alternative splicing in Brassica napus ( Guo et al., 2019 ), and the gene encoding cyclophilin 38 was induced to increase IR events nearly 30-fold under heat stress in P. patens ( Chang et al., 2014 ). In the past, the AS events of most genes in response to stresses were identified by wet-lab experiments, while recent studies have developed the methodology for genome-wide identification of AS events and AS networks by transcriptomics, so that more splicing variations can be detected.…”

Section: Introductionmentioning

confidence: 99%

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses

Yang

Zhao

et al. 2022

Front. Plant Sci.

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Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.

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Response of Auxin, Carbohydrate and Lignin Metabolism to Habitat during the Development of Ginseng Taproot

Zhang,

Sun,

Lin

et al. 2024

Agronomy

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Panax ginseng taproot serves as a crucial storage organ and constitutes a significant component of Chinese herbal medicine. In China, ginseng is cultivated using two primary methods: under-forest planting and farmland planting. These methods create distinct habitats that notably influence the morphology of ginseng taproots. However, the precise regulatory mechanisms governing ginseng taproot expansion remain to be fully elucidated. This study aimed to delineate the patterns of ginseng taproot expansion by examining taproots transplanted into farmland (TCG) and forest environments (TLCG and TQCG). Our findings indicate that light intensity and soil available potassium levels in TCG plots significantly exceed those in TLCG and TQCG plots. Compared with TLCG and TQCG, the taproot diameter of TCG increased by 11.54% and 27.73%, respectively. At the same time, combined with the microstructure of the transverse section of the taproot, it showed that the expansion of the TCG taproot was closely related to cell expansion. During TCG taproot expansion, there was an increase in indole-3-acetic acid (IAA) content, significant starch accumulation, and a decrease in lignin content. By analyzing the expression of key genes, we found that compared with TLCG and TQCG, the expression of genes PgTPS1 and PgALDH1 was upregulated, and the expression of genes PgHCT1, PgPAL3, PgPER3, and PgPER51 were downregulated in TCG taproot. Additionally, the transcription factors PgARF18.1 and PgbHLH42 were identified as responsive to habitat changes, playing pivotal roles in taproot expansion. In conclusion, this study provides foundational insights into the regulatory mechanisms of ginseng taproot expansion, offering significant implications for enhancing the quality and value of ginseng.

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An event of alternative splicing affects the expression of two BnCYCD3-1-like genes in Brassica napus

Cited by 3 publications

References 36 publications

Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis

Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses

Response of Auxin, Carbohydrate and Lignin Metabolism to Habitat during the Development of Ginseng Taproot

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