Identification of genomic regions associated with multi-silique trait in Brassica napus

Chai, Linna; Zhang, Jinfang; Lu, Kun; Li, Haojie; Wu, Lintao; Wan, Hongshen; Zheng, Beibei; Cui, Cheng; Jiang, Jun; Jiang, Long

doi:10.1186/s12864-019-5675-4

Cited by 14 publications

(42 citation statements)

References 53 publications

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“…napus (Jiang et al, 1998), investigating the associated regions of chromosomes at the genomic level and transcriptomically exploring the DEGs in multi-silique and single-silique plants (Chai et al, 2019). The multi-silique trait was found to be controlled by three recessive alleles and was significantly affected by environment; however, the mechanisms by which environmental factors affect this trait remained unknown, even if we knew that temperature could switch on/off the multi-silique trait (Chai et al, 2019). As mentioned above, AS is a pathway by which the environment could regulate plant physiology, therefore in this study, we analyzed AS events in order to investigate the mechanism by which plants perceive temperature fluctuations.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, real-time quantitative PCR (qPCR) was performed to validate the transcriptome sequencing. Since the validation for transcriptome sequencing data from plants in Xindu had been confirmed previously (Chai et al, 2019), we only validated the data from plants in colder Ma'erkang herein. Amplification reactions were performed on iQ™5 Real-Time PCR System (Biorad) as follows: an initial denaturation step at 95 °C for 3 min, 39 cycles at 95 153°C for 10 s, 60 °C for 30 s, and 72 °C for 30 s. After each run, a melt curve was acquired to check for amplification specificity by heating the samples from 60 °C to 95 °C.…”

Section: Sequencing and Expression Analysismentioning

confidence: 95%

“…The rapeseed line zws-ms and its NIL, zws-217 (Chai et al, 2019), were kept in the Crop Research Institute, Sichuan Academy of Agricultural Sciences, China. Both zws-ms and zws-217 were homozygous for almost all genes, differing from each other only in the multi-silique trait of zws-ms ( Figure 1).…”

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

“…Three zws-ms plants (samples T01, T02, and T03) and three zws-217 plants (T04, T05, and T06) were selected for RNA isolation, as described previously (Chai et al, 2019). Flower buds were detached from each plant at the budding stage (BBCH 57), and their total RNA was PeerJ reviewing PDF | (2019:12:44287:4:0:NEW 6 Sep 2020)…”

Section: Total Rna Extraction and Sequencing Library Constructionmentioning

confidence: 99%

“…The agronomic traits related to rapeseed yield include the pod (silique) number per plant, branch number, and seed weight (Liu et al, 2015;Zhang et al, 2006;. We previously reported that zws-ms, a multisilique rapeseed line (Chai et al, 2019), produces three independent pistils and 9 to 10 stamens on the same receptacle in a flower, which consequently leads to the formation of three independent siliques on a carpopodium rather than the single siliques typically observed.…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #1 of "Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis (v0.1)"

Liu¹

2020

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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 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 5 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 the 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 8 genes did not show significant difference between the two lines in expression level. Additionally, the 205 line-specifically 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 transcriptome level and screens out some environmentresponding candidate genes.

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Section: Discussionmentioning

confidence: 99%

Section: Sequencing and Expression Analysismentioning

confidence: 95%

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

Section: Total Rna Extraction and Sequencing Library Constructionmentioning

confidence: 99%