Dataset Information

Mutant Transcriptome Sequencing Provides Insights into Pod Development in Peanut (Arachis hypogaea L.).

ABSTRACT: Pod size is the major yield component and a key target trait that is selected for in peanut breeding. However, although numerous quantitative trait loci (QTLs) for peanut pod size have been described, the molecular mechanisms underlying the development of this characteristic remain elusive. A peanut mutant with a narrower pod was developed in this study using ethyl methanesulfonate (EMS) mutagenesis and designated as the "pod width" mutant line (pw). The fresh pod weight of pw was only about 40% of that seen in the wild-type (WT) Zhonghua16, while the hull and seed filling of the mutant both also developed at earlier stages. Pods from both pw and WT lines were sampled 20, 40, and 60 days after flowering (DAF) and used for RNA-Seq analysis; the results revealed highly differentially expressed lignin metabolic pathway genes at all three stages, but especially at DAF 20 and DAF 40. At the same time, expression of genes related to auxin signal transduction was found to be significantly repressed during the pw early pod developmental stage. A genome-wide comparative analysis of expression profiles revealed 260 differentially expressed genes (DEGs) across all three stages, and two candidate genes, c26901_g1 (CAD) and c37339_g1 (ACS), responsible for pod width were identified by integrating expression patterns and function annotation of the common DEGs within the three stages. Taken together, the information provided in this study illuminates the processes underlying peanut pod development, and will facilitate further identification of causal genes and the development of improved peanut varieties with higher yields.

SUBMITTER: Wan L

PROVIDER: S-EPMC5684126 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Mutant Transcriptome Sequencing Provides Insights into Pod Development in Peanut (Arachis hypogaea L.).

Wan Liyun L Li Bei B Lei Yong Y Yan Liying L Ren Xiaoping X Chen Yuning Y Dai Xiaofeng X Jiang Huifang H Zhang Juncheng J Guo Wei W Chen Ao A Liao Boshou B

Frontiers in plant science 20171109

Pod size is the major yield component and a key target trait that is selected for in peanut breeding. However, although numerous quantitative trait loci (QTLs) for peanut pod size have been described, the molecular mechanisms underlying the development of this characteristic remain elusive. A peanut mutant with a narrower pod was developed in this study using ethyl methanesulfonate (EMS) mutagenesis and designated as the "pod width" mutant line (pw). The fresh pod weight of pw was ...[more]

PMID: 29170673

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Project description:Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful information for the understanding of the complex mechanisms of plant hormones in controlling pod size by regulating the cell size in peanuts and will facilitate the improvement of peanut breeding.

Project description:In acidic soils, high concentrations of aluminum ions (Al3+) in dissolved form reduce root growth and development of most crops. In addition, Al3+ is also a beneficial element in some plant species in low concentrations. However, the regulatory mechanism of the growth and development of peanut (Arachis hypogaea L.) treated with different concentrations of Al3+ has been rarely studied. In this study, peanut seedlings were treated with AlCl3.18H2O in Hoagland nutrient solution at four different concentrations of Al3+, i.e., 0 (pH 6.85), 1.25 (pH 4.03), 2.5 (pH 3.85), and 5 (pH 3.69) mmol/L, which are regarded as Al0, Al1, Al2, and Al3. The results showed that low concentrations of Al treatment (Al1) promoted peanut growth, while high concentrations of Al treatments (Al2 and Al3) significantly inhibited peanut growth. Compared with the control (Al0), transcriptome analysis showed that the differentially expressed genes (DEGs) of starch and sucrose metabolic pathways were significantly enriched at low concentrations, i.e., Al1 treatment, whereas the expression of AhERD6 (sugar transporter) was significantly up-regulated, and the soluble sugar content was significantly increased. The DEGs of the plant hormone signaling transduction pathway were significantly enriched at high concentrations of Al2 and Al3 treatments, whereas the expression of AhNCED1 (9-cis-epoxycarotenoid dioxygenase) was significantly up-regulated, and the content of ABA was significantly increased. Moreover, the expression of transcription factors (TFs) in peanut was affected by different concentrations of Al. Overall, low concentrations of Al1 promoted peanut growth by increasing soluble sugar content, while high concentrations of Al2 and Al3 inhibited the growth of peanut, induced AhNCED1 gene expression, and increased endogenous ABA content. For peanut, the exposure of Al at low concentrations not only derived an adaptive mechanism to cope with Al stress, but also acted as a stimulator to promote its growth and development.

Dataset Information

Mutant Transcriptome Sequencing Provides Insights into Pod Development in Peanut (Arachis hypogaea L.).

Publications

Mutant Transcriptome Sequencing Provides Insights into Pod Development in Peanut (<i>Arachis hypogaea</i> L.).

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