Genome-wide transcriptome profiling indicates the putative mechanism underlying enhanced grain size in a wheat mutant

Zhong, Xiao‐bo; Lin, Na; Ding, Jinjin; Lan, Jingyu; Tang, Huaping; Qi, Pengfei; Deng, Mei; Ma, Jian; Wang, Jirui; Chen, Guoyue; Lan, Xiujin; Wei, Yuming; Zheng, Youliang; Jiang, Qiantao

doi:10.1007/s13205-020-02579-6

Cited by 6 publications

(5 citation statements)

References 81 publications

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“…A study of sbeIIb mutants in rice showed that many starch synthesis enzyme genes were upregulated, except for genes encoding granule-bound starch synthase, branching enzyme, pullulanase, and starch phosphorylase, which were downregulated. This increased amylose and resistant starch content, in addition to an increase in many other substances such as sugar, fatty acids, amino acids, and plant sterols in the endosperm ( Baysal et al., 2020 ), and the wheat mutant SM482gs , with increased grain size, TKW, and protein content with BR biosynthesis and signal transduction, were significantly upregulated, but AGP-S1 , AGP-L2 , SSI , SSIIa , SSIIIa , SBEIIa , SBEIIb , and GBSSIa show the lower expression on SM482gs ( Zhong et al., 2021 ), which indicated that plant sterols might be involved in the synthesis of amylose in plant grains. In rice, overexpression of HMGS significantly increased fatty acids, abscisic acid, gibberellins, and lutein in transgenic rice ( Pérez et al., 2022 ), while overexpression of HMGS in mustard significantly increased grain weight ( Liao et al., 2014b ).…”

Section: Discussionmentioning

confidence: 99%

Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat

et al. 2023

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Wheat is a significant source of protein and starch worldwide. The defective kernel (Dek) mutant AK-3537, displaying a large hollow area in the endosperm and shrunken grain, was obtained through ethyl methane sulfonate (EMS) treatment of the wheat cultivar Aikang 58 (AK58). The mode of inheritance of the AK-3537 grain Dek phenotype was determined to be recessive with a specific statistical significance level. We used bulked segregant RNA-seq (BSR-seq), BSA-based exome capture sequencing (BSE-seq), and the ΔSNP-index algorithm to identify candidate regions for the grain Dek phenotype. Two major candidate regions, DCR1 (Dek candidate region 1) and DCR2, were identified on chromosome 7A between 279.98 and 287.93 Mb and 565.34 and 568.59 Mb, respectively. Based on transcriptome analysis and previous reports, we designed KASP genotyping assays based on SNP variations in the candidate regions and speculated that the candidate gene is TraesCS7A03G0625900 (HMGS-7A), which encodes a 3-hydroxy-3-methylglutaryl-CoA synthase. One SNP variation located at position 1,049 in the coding sequence (G>A) causes an amino acid change from Gly to Asp. The research suggests that functional changes in HMGS-7A may affect the expression of key enzyme genes involved in wheat starch syntheses, such as GBSSII and SSIIIa.

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Section: Discussionmentioning

confidence: 99%

Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat

et al. 2023

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“…We selected three datasets from the GEO and SRA databases [6,26,27], comprising 100 samples across seven distinct stages of grain development (Table 1). Over 2.1 billion raw reads from these datasets were pseudoaligned to the reference transcriptome of Triticum aestivum cv.…”

Section: Data Collection and Identification Of Degs During Wheat Grai...mentioning

confidence: 99%

“…These findings suggest that the selected genes are strongly associated with grain development, including genes involved in cell wall biosynthesis. [26], dataset B was derived from [6], and dataset C was derived from [27]. DEGs were identified using the DESeq2 [29] software, with an adjusted p-value less than 0.05 and a two-fold change.…”

Section: Robust Identification Of Degs During Grain Developmentmentioning

confidence: 99%

“…Crucially, to enable a detailed examination of gene expression dynamics throughout grain development, the chosen data sets included at least three distinct temporal stages. The datasets utilized in this study were SRA accession numbers PRJNA278920 [26], PRJNA525250 [6], and PRJNA471426 [27].…”

Section: Rna-seq Data Collection and Analysismentioning

confidence: 99%

“…(C) Histogram depicting the total number of unique and shared DEGs across two or three datasets. Dataset A was derived from[26], dataset B was derived from[6], and dataset C was derived from[27]. DEGs were identified using the DESeq2[29] software, with an adjusted p-value less than 0.05 and a two-fold change.…”

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Integrated Transcriptome Analysis Identified Key Expansin Genes Associated with Wheat Cell Wall, Grain Weight and Yield

Mira

Arenas‐M

Calderini

et al. 2023

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This research elucidates the dynamic expression of expansin genes during the wheat grain (Triticum aestivum L.) development process using comprehensive meta-analysis and experimental validation. We leveraged RNA-seq data from multiple public databases, applying stringent criteria for selection, and identified 60,852 differentially expressed genes across developmental stages. From this pool, 28,558 DEGs were found to exhibit significant temporal regulation in at least two different datasets and were enriched for processes integral to grain development such as carbohydrate metabolism and cell wall organization. Notably, 30% of the 241 known expansin genes showed differential expression during grain growth. Hierarchical clustering and expression level analysis revealed temporal regulation and distinct contributions of expansin subfamilies during the early stages of grain development. Further analysis using co-expression networks underscored the significance of expansin genes, revealing their substantial co-expression with genes involved in cell wall modification. Finally, qPCR validation and grain morphological analysis under field conditions indicated a significant negative correlation between the expression of select expansin genes, and grain size and weight. This study illuminates the potential role of expansin genes in wheat grain development and provides new avenues for targeted genetic improvements in wheat.

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Elucidating the Defence Response of Wheat Mutants Developed for augmenting Terminal Heat Stress Tolerance and Improved Grain-Quality

Kumar,

Bakshi,

Goswami

et al. 2024

J Plant Growth Regul

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Genome-wide transcriptome profiling indicates the putative mechanism underlying enhanced grain size in a wheat mutant

Cited by 6 publications

References 81 publications

Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat

Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat

Integrated Transcriptome Analysis Identified Key Expansin Genes Associated with Wheat Cell Wall, Grain Weight and Yield

Elucidating the Defence Response of Wheat Mutants Developed for augmenting Terminal Heat Stress Tolerance and Improved Grain-Quality

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