A Rare SNP Identified A TCP Transcription Factor Essential For Tendril Developmentin Cucumber

Tendrils are one of the most important aspects in Cucurbitaceae plant type, which are also important model organs to study the movement of plants thigmotropism. Cucumber (Cucumis sativus L.) genome, transcriptome and variation group sequencing work provides a Big Data platform support for the systematic study of cucumber. In a collection of 3,342 cucumber lines, we discovered a unique tendril-less line CG9192 that forms branches instead of tendrils and therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation. On the basis of genomics, genome variation map and transcriptomics, we exploited a strategy of rare variation mapping to discover the cucumber tendril identity gene CsTEN. We presented evidence that cucumber tendrils and branches are homologous structures, which was once the Darwin’s troubled mystery. The main results of this paper are as follows:1. To investigate the morphological differentiation between normal tendril and modified tendril, we perfofrmed phenotypic observation and scanning electron microscopy analysis between line CG9192 and line 404, and found that branches and tendrils are homologous organs. Genetics dada indicated that the trait was conferred by a single recessive Mendelian gene (CsTEN).2. The distribution of rare SNPs in the four groups of cucumber is uneven:the Indian group contains the largest number of rare SNPs (81.0%), which is consistent with the fact that the Indian group is ancestral. We exploited a strategy of rare variation mapping to discover arare SNP (rSNP1), and the affected gene Csa5G644520 is expressed specially in cucumber tendrils, and we inferred that it is the tendril organ identity gene.3. We constructed a larger F2 population to locate CsTEN to a 16 kb interval, and the interval spans only one gene Csa5G644520. Compared with the re-sequencing genome of 115 core accessions, we found that only the rSNP1 could explain the tendril-less trait. Furthermore, we developed rSNP1 into a dCAPS marker and genotyped an additional 1,386 cucumber accessions worldwide that all bear normal tendrils, and the genotype of rSNP1 only existed in CG9192. In summary, both genomic and genetic analyses pinpoint that Csa5G644520 corresponds to the CsTEN gene and that rSNP1 is the genetic basis of the rare tendril-less phenotype.4. CsTEN belongs to the CYC/TB1 clade of TCP transcription factor family. The variation occurs within a protein motif unique to the cucurbits, and the motif is absent from all known plant TCP proteins. The transactivation activity assay in tobacco and yeast indicated that the rSNP1 impaired the function of CsTEN as a transcriptional activator. The results of in situ hybridization showed that CsTEN was specifically expressed in the tendrils at all developmental stages and could be regarded as a novel organ identity gene.5. Ecballium elaterium is the only one species without tendrils in Cucurbitaceae. We screened TEN gene carefully in Ecballium elaterium, in which we found that there are at least two early termination of variation in TEN gene of Ecballium elaterium, resulting in loss of function.6. We constructed near isogenic lines 404 (TENTEN) and 404-tendrilless (tenten), and analyzed the differential transcriptome of normal tendrils and modified tendrils collected from the two lines, respectively. Gene ontology (GO) analysis of the genes with significantly differential expression presented that CsTEN represses branch development and promotes thigmotropism in cucumber tendrils.