title: A Rare SNP Identified a TCP Transcription Factor Essential for Tendril Development in Cucumber.
abstract: 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 for tendril development in cucumber (Cucumis sativus L.). In a collection of >3000 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. The affected gene TEN encodes a TCP transcription factor conserved within the cucurbits and is expressed specifically in tendrils, representing a new organ identity gene. The variation occurs within a protein motif unique to the cucurbits and impairs its function as a transcriptional activator. Analyses of transcriptomes from near-isogenic lines identified downstream genes required for the tendril's capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes.
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
authors.forename: Shenhao
authors.initials: S
authors.lastname: Wang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Xueyong
authors.initials: X
authors.lastname: Yang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
authors.forename: Mengnan
authors.initials: M
authors.lastname: Xu
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Xingzhong
authors.initials: X
authors.lastname: Lin
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Lin
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Inner Mongolia Potato Engineering and Technology Research Centre, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Jianjian
authors.initials: J
authors.lastname: Qi
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Guangjin
authors.initials: G
authors.lastname: Shao
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Nana
authors.initials: N
authors.lastname: Tian
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Yang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China. Electronic address: huangsanwen@caas.cn.
authors.forename: Sanwen
authors.initials: S
authors.lastname: Huang
mesh_terms: D000595:Amino Acid Sequence; D018553:Cucumis sativus / Q000737:chemistry / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism*; D018547:Plant Stems / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors
keywords: TCP transcription factor; cucumber tendril; homologous organs; rare variant