Shenhao Wang 1,2,5, Xueyong Yang 1,5, Mengnan Xu 1,2, Xingzhong Lin 3, Tao Lin 1, Jianjian Qi1,4, Guangjin Shao 1, Nana Tian 3, Qing Yang 3, Zhonghua Zhang 1 and Sanwen Huang 1,2
1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing 100081, China.
2Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
3College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
4Inner Mongolia Potato Engineering and Technology Research Centre, Inner Mongolia University, Hohhot 010021, China
5 These authors contributed equally to this work.
Correspondence to Sanwen Huang (firstname.lastname@example.org)
Key words: rare variant, TCP transcription factor, cucumber tendril, homologous organs
Rare genetic variants are abundant in genomes but less tractable in genome wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential to tendril development in cucumber (Cucumis sativus L.). In a collection of >3,000 lines, we discovered a unique tendril-less line that forms branches instead of tendrils and therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation and subsequently identified the causative single nucleotide polymorphism (SNP). The affected gene TEN is conserved within the cucurbits and is expressed specially in tendrils, representing a new organ identity gene. The variation occurs within a protein motif unique to the cucurbits and apparently impairs its function as a transcriptional activator. Analyses of transcriptomes from near-isogenic lines identified downstream genes required for tendril’s capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes.
molecular plant，available online 24 October 2015