Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion

Abstract

SummaryThe failure of peg penetration into the soil leads to seed abortion in peanut. Knowledge of genes involved in these processes is comparatively deficient. Here, we used RNA-seq to gain insights into transcriptomes of aerial and subterranean pods. More than 2 million transcript reads with an average length of 396 bp were generated from one aerial (AP) and two subterranean (SP1 and SP2) pod libraries using pyrosequencing technology. After assembly, sets of 49 632, 49 952 and 50 494 from a total of 74 974 transcript assembly contigs (TACs) were identified in AP, SP1 and SP2, respectively. A clear linear relationship in the gene expression level was observed between these data sets. In brief, 2194 differentially expressed TACs with a 99.0% true-positive rate were identified, among which 859 and 1068 TACs were up-regulated in aerial and subterranean pods, respectively. Functional analysis showed that putative function based on similarity with proteins catalogued in UniProt and gene ontology term classification could be determined for 59 342 (79.2%) and 42 955 (57.3%) TACs, respectively. A total of 2968 TACs were mapped to 174 KEGG pathways, of which 168 were shared by aerial and subterranean transcriptomes. TACs involved in photosynthesis were significantly up-regulated and enriched in the aerial pod. In addition, two senescence-associated genes were identified as significantly up-regulated in the aerial pod, which potentially contribute to embryo abortion in aerial pods, and in turn, to cessation of swelling. The data set generated in this study provides evidence for some functional genes as robust candidates underlying aerial and subterranean pod development and contributes to an elucidation of the evolutionary implications resulting from fruit development under light and dark conditions.

Comparative transcriptome analysis of aerial and subterranean pods development provides insights into seed abortion in peanut

“…As shown in the previous study, the seed in aerial pods aborted at the 6 days after marked (DAM) (Chen et al 2013). To identify differentially expressed genes (DEGs) relating to seed abortion during peanut aerial and subterranean pods development, we used a customized NimblerGen onligonucleotide microarrays at the 1, 2, 4, 8 DAM.…”

“…However, only until the peg carries the ovule into the soil where can the pod normally swell to allow room for the embryo to grow and eventually become subterranean pod (Feng et al 1995; Moctezuma and Feldman 1999, 2003). The failure of peg penetration into the soil leads to suppression of pod swelling initiation and form aerial pod, finally causing seed abortion and seriously impacting on the peanut production (Chen et al 2013). For instance, when gynophore penetration into the soil is prevented by any means of a physical barrier but still under a light treatment, the pod will not form normally (Zamski and Ziv 1976; Thompson et al 1985; Moctezuma 2003).…”

“…For instance, they are explored to investigate how the transcriptome is deployed in aerial and subterranean pods (Chen et al 2013), and how gene expression varies in response to disease infection (Guo et al 2008; Wang et al 2012). Furthermore, in our previous studies (Chen et al 2013; Zhu et al 2013), both RNA-seq and proteomics analysis shed light on the potential candidate genes and proteins that regulated aerial and subterranean pods development.…”

“…For instance, they are explored to investigate how the transcriptome is deployed in aerial and subterranean pods (Chen et al 2013), and how gene expression varies in response to disease infection (Guo et al 2008; Wang et al 2012). Furthermore, in our previous studies (Chen et al 2013; Zhu et al 2013), both RNA-seq and proteomics analysis shed light on the potential candidate genes and proteins that regulated aerial and subterranean pods development. These studies not only revealed that the embryo of the aerial pod ceased growth at early stages and finally aborted, but also underlined two senescence associated genes and one late embryogenesis-abundant gene as candidates to embryo abortion of aerial pod; additionally, proteins involved in lignin synthesis and ubiquitin proteasome system might regulate pods swelling to allow room for embryo development.…”

Gynophore miRNA analysis at different developmental stages in Arachis duranensis

“…Many studies have focused on furthering our understanding of the gynophore development. Chen et al (2013) took advantage of available transcriptome data to detect two cell-aging transcripts that significantly increased in the late stage of unburied gynophores and may participate in the abortion of gynophores on the ground. Xia et al (2013) found that a series of transcripts, including endogenous hormones, respond to optical signals, and that morphogenesis and cell division pathway transcripts showed distinct changes before and after the burying of the gynophore.…”