title: A fragment substitution in the promoter of CsHDZIV11/CsGL3 is responsible for fruit spine density in cucumber (Cucumis sativus L.).
abstract: The indel in the promoter of CsHDZIV11 co-segregates with fruit spine density and could be used for molecular breeding in cucumber. Fruit spine density is an important quality trait for marketing in cucumber (Cucumis sativus L.). However, the molecular basis of fruit spine density in cucumber remains unclear. In this study, we isolated a mutant, few spines 1 (fs1), from CNS2 (wild type, WT), a North China-type cucumber with a high density of fruit spines. Genetic analysis showed that fs1 was controlled by a single recessive Mendelian factor. Bulked segregant analysis combined with genome resequencing were used for mapping fs1 in the F2 population derived from a cross between the fs1 mutant and WT, and it was located on chromosome 6 through association analysis. To develop more polymorphic markers to locate fs1, another F2 population was constructed from the cross between fs1 and 'Chinese long' 9930. Then, fs1 was narrowed down to a 110.4-kb genomic region containing 25 annotated genes. A fragment substitution was identified in the promoter region of Csa6M514870 between fs1 and WT. This fragment in fs1 was also present in wild cucumber. Csa6M514870 encodes a PDF2-related protein, a homeodomain-leucine zipper IV transcription factor (CsHDZIV11/CsGL3) sharing high identity and similarity with proteins related to trichome formation or epidermal cell differentiation. Quantitative reverse-transcription PCR revealed a higher expression level of CsHDZIV11 in young fruits from fs1 compared to WT. A molecular marker based on this indel co-segregated with the spine density. This work provides a solid foundation not only for understanding the molecular mechanism of fruit spine density, but also for molecular breeding in cucumber.
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Lina
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Shuangshuang
authors.initials: S
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Zezhou
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Zhihui
authors.initials: Z
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Chenxing
authors.initials: C
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Li
authors.affiliation: State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China. zhren@sdau.edu.cn.
authors.forename: Zhonghai
authors.initials: Z
authors.lastname: Ren
mesh_terms: D018553:Cucumis sativus / Q000235:genetics* / Q000254:growth & development; D018744:DNA, Plant / Q000235:genetics; D005638:Fruit / Q000254:growth & development*; D017343:Genes, Plant; D005808:Genes, Recessive; D005819:Genetic Markers; D018398:Homeodomain Proteins / Q000235:genetics*; D054643:INDEL Mutation; D016350:Leucine Zippers / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers; D018398:Homeodomain Proteins; D010940:Plant Proteins