High-throughput RNA-Seq data analysis of SNPs in a model plant

Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, researchers at Sun Yat-sen University generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes. A total of 9044 high-quality SNPs were obtained among the three accessions, and a consensus map was constructed. The researchers further discovered several dorsoventral asymmetrically expressed genes that were confirmed by qRT-PCR among different petals, including previously reported three CYC-like proliferating cell factor (TCP) genes. One MADS-box gene was highly expressed in dorsal petals, and several MYB factors were predominantly expressed among dorsal, lateral, and/or ventral petals, together with a ventrally expressed TCP gene. In sum, our comprehensive database complements the existing resources for comparative genetic mapping and facilitates future investigations in legume zygomorphic flower development.

A Neighbor-joining consensus tree and the expression patterns of TCP genes in pea

(a) An unrooted protein tree for the TCP proteins using MEGA 5.0.1. The tree summarizes the evolutionary relationships among the 24 AtTCPs and 22 PsTCPs. Bootstrap values are denoted above the nodes. (b) The expression patterns of the TCP genes among different organs in pea. VA, Vegetative shoot apices; RA, Reproductive shoot apices; Small, 2-mm small buds; Big, 5-mm big buds; Dp, Dorsal petals; Lp, Lateral petals; Vp, Ventral petals.