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

Liyun Wan,Bei Li,Bei Li,Huifang Jiang,Huifang Jiang,Liying Yan,Liying Yan,Yong Lei,Yong Lei,Juncheng Zhang,Juncheng Zhang,Boshou Liao,Boshou Liao,Xiaofeng Dai,Xiaofeng Dai,Yuning Chen,Yuning Chen,Ao Chen,Xiaoping Ren,Xiaoping Ren,Wei Guo

doi:10.3389/fpls.2017.01900

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.

Highlights

Peanut (Arachis hypogaea L.) is one of the most important oil crops in the world
Understanding of the molecular mechanisms that underlie pod size and shape remains limited; RNA-Seq was applied in this study to investigate transcriptome differences at three different developmental stages between pw and WT lines and thousands of differentially expressed genes (DEGs) were identified
Lignification can be held responsible for differences in hull phenotypes between the pw and WT lines, FIGURE 7 | The auxin transduction pathway is depressed in the early developmental stages and activated at the late stage in the pw mutant. (A) Heatmaps represent the expression of the 20 DEGs in auxin pathway in the pw and WT lines at days after flowering (DAF) 20. (B) Heatmaps represent the expression of the nine DEGs in auxin pathway in the pw and WT lines at DAF40. (C) Heatmaps represent the expression of the 14 DEGs in auxin pathway in the pw and WT lines at DAF 60

Summary

Introduction

As the demand for oil is ever-increasing, there is an urgent need to breed new peanut varieties with high yields, a characteristic that is dependent on pod size. Previous research has shown that pod size is mainly determined by quantitative trait loci (QTL), and several of these have been identified (Fonceka et al, 2012; Chen et al, 2016, 2017; Wang et al, 2016; Luo et al, 2017). Narrow Pod Peanut Mutant Transcriptome has shown that peanut genotypes from different backgrounds harbor distinct QTLs; the primary characteristics of peanut which distinguish this plant from others include aerial flowering, a gynophore (peg) that elongates gravitropically, and subterranean fruiting. Research on pod development lags far behind that of other cereal crops (Chen et al, 2013, 2016a). The hull of a peanut is composed of 46.8% holocellulose, 43.4% Klason lignin, 5.8% ash, and 4.0% organic solvent extracts (OSE) (Wang et al, 2016)

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Conclusion