Global gene expression profiles in developing soybean seeds

Asakura, Tomiko; Tamura, Tomoko; Terauchi, Kaede; Narikawa, Tomoyo; Yagasaki, Kazuhiro; Ishimaru, Yoshiro; Abe, Keiko

doi:10.1016/j.plaphy.2011.12.007

Cited by 36 publications

(34 citation statements)

References 30 publications

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“…While a certain percentage of genes expressed in seeds are housekeeping genes and/or are transcribed in multiple tissues, our data appear consistent with previously published expression profiles on seed development [14,50], as many of the here-in-identified genes are strictly related to seed development and are exclusively expressed in seeds. A number of those genes are transcribed at high levels and play major roles for enhancing agronomic traits.…”

Section: Discussionsupporting

confidence: 92%

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

et al. 2014

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BackgroundVariation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement.ResultsIn an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively.ConclusionsAs a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.

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Section: Discussionsupporting

confidence: 92%

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

et al. 2014

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“…Rankings arise from consistencies in fold change differences between samples; as such, a series of pairwise comparisons for each individual tissue against the rest of the sequenced tissues in our study identifies high-ranking transcripts that are preferentially expressed in a tissue compared to the rest. The RP method has been used recently to help develop expression profiles for plants such as soybean [19], aspen trees [20], and the study of hormonal responses in Arabidopsis [21]. We employed RP to identify genes preferentially expressed in one particular tissue compared to the other sampled tissues, i.e.…”

Section: Resultsmentioning

confidence: 99%

A detailed gene expression study of the Miscanthusgenus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

et al. 2013

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BackgroundThe Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and future genetic improvement. A comprehensive catalog of expressed sequences were generated from a variety of Miscanthus species and tissue types, with an emphasis on characterizing gene expression changes in spring compared to fall rhizomes.ResultsIllumina short read sequencing technology was used to produce transcriptome sequences from different tissues and organs during distinct developmental stages for multiple Miscanthus species, including Miscanthus sinensis, Miscanthus sacchariflorus, and their interspecific hybrid Miscanthus × giganteus. More than fifty billion base-pairs of Miscanthus transcript sequence were produced. Overall, 26,230 Sorghum gene models (i.e., ~ 96% of predicted Sorghum genes) had at least five Miscanthus reads mapped to them, suggesting that a large portion of the Miscanthus transcriptome is represented in this dataset. The Miscanthus × giganteus data was used to identify genes preferentially expressed in a single tissue, such as the spring rhizome, using Sorghum bicolor as a reference. Quantitative real-time PCR was used to verify examples of preferential expression predicted via RNA-Seq. Contiguous consensus transcript sequences were assembled for each species and annotated using InterProScan. Sequences from the assembled transcriptome were used to amplify genomic segments from a doubled haploid Miscanthus sinensis and from Miscanthus × giganteus to further disentangle the allelic and paralogous variations in genes.ConclusionsThis large expressed sequence tag collection creates a valuable resource for the study of Miscanthus biology by providing detailed gene sequence information and tissue preferred expression patterns. We have successfully generated a database of transcriptome assemblies and demonstrated its use in the study of genes of interest. Analysis of gene expression profiles revealed biological pathways that exhibit altered regulation in spring compared to fall rhizomes, which are consistent with their different physiological functions. The expression profiles of the subterranean rhizome provides a better understanding of the biological activities of the underground stem structures that are essentials for perenniality and the storage or remobilization of carbon and nutrient resources.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-864) contains supplementary material, which is available to authorized users.

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“…Compared with Arabidopsis and rice, only limited transcriptome data are reported on seed development in soybean (Asakura et al , 2012; Jones and Vodkin, 2013; Lu et al , 2016; Sha et al , 2012). In this context, Jones et al (2010) identified a number of seed-specific genes in soybean using microarray chips consisting of 27000 cDNAs (Vodkin et al , 2004).…”

Section: Introductionmentioning

confidence: 99%

Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis

Wang

et al. 2017

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Global gene expression profiles in developing soybean seeds

Cited by 36 publications

References 30 publications

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

A detailed gene expression study of the Miscanthusgenus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis

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