Transcriptome-wide mining of the differentially expressed transcripts for natural variation of floral organ size in Physalis philadelphica

Abstract

Natural phenotypic variation, a result of genetic variation, developed during evolution in response to environmental selections. Physalis philadelphica, known as tomatillo in the Solanaceae, is rich in floral and post-floral organ size diversity. However, its genetic variation is unknown. Here P. philadelphica was classified into three groups with large, intermediate, and small reproductive organ size, and a positive correlation was observed between floral organ and berry sizes. Through cDNA-amplified fragment length polymorphism (AFLP) analyses, 263 differentially expressed transcript-derived fragments (TDFs) were isolated from two accessions with different floral organ sizes. The genes encode various transcription factors, protein kinases, and enzymes, and they displayed multiple expression patterns during floral development, indicating a complexity in the genetic basis of phenotypic variation. Detailed expression analyses revealed that they were differentially expressed during floral and post-floral development, implying that they have roles in the development of flowers and fruits. Expression of three genes was further monitored in 26 accessions, and in particular the expression variation of Pp30, encoding an AP2-like transcription factor, correlates well with the observed phenotypic variations, which strongly supports an essential role for the gene in the natural variation of floral and post-floral organ size in Physalis. The results suggest that alteration in the expression pattern of a few key regulatory genes in the developmental process may be an important source of genetic variations that lead to natural variation in morphological traits.

Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size

“…1; Supplementary Table 2). Higher expression of POS1 corresponded to a bigger organ size while a lower expression entailed a smaller organ size 20 . Thus, POS1 may positively regulate reproductive organ size of tomatillo in a dosage-dependent manner.…”

“…POS1 was predominantly expressed in the reproductive organs, preferentially in ovaries and developing berries in P. philadelphica (P58, P64 and P59 accessions) and P. floridana P106 (Fig. 3a), and its expression was upregulated during berry development 20 ( Supplementary Fig. 3a).…”

“…5 0 -and 3 0 -rapid amplification of cDNA ends (RACE, Roche) were performed based on the Pp30 fragment obtained previously 20 . PfCRF7 and PfCRF8 in P. floridana, which shared the most similarity with Pp30 (or POS1), were isolated based on their putative orthologues of SlCRF7 and SlCRF8 in Solanum.…”

“…Physalis has emerged as a new leading Solanaceous horticultural crop and as a new plant model for ecology, evolution and development 19,20 . The genus Physalis features a fruiting calyx shaped like a Chinese lantern, also called the inflated calyx syndrome (ICS), a novelty of the floral calyx formed after fertilization that is controlled by several MADS-box transcription factors 19,21,22 .…”

“…Transcriptome-wide screens showed that the expression of Pp30, putatively encoding an APETALA2 (AP2)-like transcription factor is associated with flower and berry size in tomatillo. Furthermore, this gene was proposed to be a valuable candidate gene for the evolution of natural variation of the reproductive organ size in Physalis 20 .…”