Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance

Vidal, Ramón; Nascimento, Leandro Costa do; Mondego, Jorge Maurı́cio Costa; Pereira, Gonçalo Amarante Guimarães; Carazzolle, Marcelo Falsarella

doi:10.1590/s1415-47572012000200014

Cited by 42 publications

(28 citation statements)

References 24 publications

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“…This result is consistent with previous studies that showed that the soybean genome is palaeopolyploid and contains an abundance of homolog regions that are derived from the genome duplication. Nearly 75 % of the genes in the soybean genome are multiple copies (Doyle and Egan 2010;Schmutz et al 2010). Thus, the dendrogram analysis was crucial in matching the putative soybean TFRDs with the previously characterized homolog genes of Arabidopsis (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…The BR 16 cultivar is sensitive to water stress, while the Embrapa 48 cultivar shows a higher capacity to tolerate periods of drought (Casagrande et al 2001;Oya et al 2004;Texeira et al 2008;Vidal et al 2012). The drought assays were conducted in both a PSys in which the plants were grown in sand and a HSys in which the plants were grown in a nutrient solution (Martins et al 2008;Kulcheski et al 2010).…”

Section: Methods Plant Material and Drought Stress Treatmentsmentioning

confidence: 99%

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Differential Impact of Acclimation and Acute Water Deprivation in the Expression of Key Transcription Factors in Soybean Roots

et al. 2016

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Soybean (Glycine max) is one of the major world commodities. In order to increase the soybean yields, it has been searched drought-tolerant cultivars, once the drought is the major constraint to soybean grown. Therefore, it is crucial to elucidate the molecular mechanisms associated with drought tolerance. Here, the in silico approach allowed us to identify 12 genes belonging to six different transcription factor families in soybean that have been associated with key events on drought response. The expression pattern of each gene was investigated by qPCR in root samples of drought-sensitive and drought-tolerant cultivars undergoing drought stress in potbased (PSys) and hydroponic (HSys) cultivation systems. GmaxMYC2-like 2 was induced under abrupt drought conditions in HSys in both cultivars, whereas GmaxAREB1-like 1 Fábia Guimarães-Dias and Anna C. Neves-Borges contributed equally to this work. Electronic supplementary materialThe online version of this article (

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Section: Discussionmentioning

confidence: 99%

Section: Methods Plant Material and Drought Stress Treatmentsmentioning

confidence: 99%

Differential Impact of Acclimation and Acute Water Deprivation in the Expression of Key Transcription Factors in Soybean Roots

et al. 2016

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“…There are only very few studies published utilizing NGS to study abiotic stress responses in plants (Deyholos, 2010). These include studies on salt stress (Molina et al, 2008; Fan et al, 2013), cold stress (Tamura and Yonemaru, 2010) and drought stress (Dugas et al, 2011; Dong et al, 2012; Vidal et al, 2012). …”

Section: Advancements In Functional Genomics Techniques For Spatial Rmentioning

confidence: 99%

Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals

Shelden¹,

Roessner²

2013

Front. Plant Sci.

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Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice) and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive), yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics, and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript/metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance.

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“…Although RNA-seq has recently been utilized in plant species for SNP discovery [23-28], a comprehensive and in-depth characterization and functional annotation of transcript sequence and expression polymorphisms is not yet available for any plant species. As a proof-of-concept, we sequenced seed transcriptomes at a mid-maturation stage of nine soybean lines varying in oil composition and content.…”

Section: Introductionmentioning

confidence: 99%

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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Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance

Cited by 42 publications

References 24 publications

Differential Impact of Acclimation and Acute Water Deprivation in the Expression of Key Transcription Factors in Soybean Roots

Differential Impact of Acclimation and Acute Water Deprivation in the Expression of Key Transcription Factors in Soybean Roots

Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals

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

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