Abstract
Understanding the molecular mechanisms regulating pea seed developmental process is extremely important for pea breeding. In this study, we used high-throughput RNA-Seq and bioinformatics analyses to examine the changes in gene expression during seed development in vegetable pea and grain pea, and compare the gene expression profiles of these two pea types. RNA-Seq generated 18.7 G of raw data, which were then de novo assembled into 77,273 unigenes with a mean length of 930 bp. Our results illustrate that transcriptional control during pea seed development is a highly coordinated process. There were 459 and 801 genes differentially expressed at early and late seed maturation stages between vegetable pea and grain pea, respectively. Soluble sugar and starch metabolism related genes were significantly activated during the development of pea seeds coinciding with the onset of accumulation of sugar and starch in the seeds. A comparative analysis of genes involved in sugar and starch biosynthesis in vegetable pea (high seed soluble sugar and low starch) and grain pea (high seed starch and low soluble sugar) revealed that differential expression of related genes at late development stages results in a negative correlation between soluble sugar and starch biosynthetic flux in vegetable and grain pea seeds. RNA-Seq data was validated by using real-time quantitative RT-PCR analysis for 30 randomly selected genes. To our knowledge, this work represents the first report of seed development transcriptomics in pea. The obtained results provide a foundation to support future efforts to unravel the underlying mechanisms that control the developmental biology of pea seeds, and serve as a valuable resource for improving pea breeding.
Highlights
Pea (Pisum sativum L.) is one of the most widely grown grain legumes in the world, and its seeds are an important source of protein for human diets as well as for animal feed (Bastianelli et al, 1998)
Because we are interested in understanding the transcriptional changes that may be involved in regulating pea seed development and the differences between grain pea and vegetable pea, we performed RNA sequencing (RNA-Seq) analyses of early and late developing seeds of Zhewan 1 and Zhongwan 6
Our results indicate that the sugar metabolism process is coordinated by several genes, and that differences in the level of seed sugar content between vegetable pea and grain pea could be the result of differential expression of these genes during the filling stage of seed development
Summary
Pea (Pisum sativum L.) is one of the most widely grown grain legumes in the world, and its seeds are an important source of protein for human diets as well as for animal feed (Bastianelli et al, 1998). Various studies on legume seed development show that the process is genetically programmed and correlated with changes in metabolite levels (Weber et al, 2005; Le et al, 2007) Despite this understanding, little molecular genetics work has been performed on pea, due to both the size of genome (4.5 Gb) as well as its highly repetitive nature (75–97%), causing it to be considered as a “genomic orphan” species (Macas et al, 2007; Smýkal et al, 2012). Little molecular genetics work has been performed on pea, due to both the size of genome (4.5 Gb) as well as its highly repetitive nature (75–97%), causing it to be considered as a “genomic orphan” species (Macas et al, 2007; Smýkal et al, 2012) Such genomic information, is essential for deciphering the genetic control of pea seed development
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