Plant materials and phenotypic data collection
The male parent, ZXG01061 (P1), is a dwarf watermelon variety. The female parent, W1-1 (P2), is a standard watermelon variety. The F1 generation was obtained from a cross between ZXG01061 and W1-1, and the F2 generation was derived from a self-cross of F1 (Fig. 1). In the summer of 2017, individuals of P1 (n = 30), P2 (n = 30), F1 (n = 30), and F2 (n = 213) were all grown in a greenhouse at the Xiang Yang Experimental Agricultural Station of Northeast Agricultural University, Harbin, China, for genetic inheritance analysis and BSA-seq analysis. In the summer of 2018, 1,097 F2 individuals were grown in the greenhouse for genetic inheritance verification and initial mapping of the cladw locus. Each plant of ZXG01061, W1-1, F1, and F2 individuals was photographed and preserved, and watermelon internode length was measured with a ruler at 50 days after sprouting. Segregation analysis was based on chi-square analysis of the expected segregation ratios of a single gene using IBM SPSS Statistics 22.0 software (International Business Machines Corp, New York, United States).
The eighth internode tissues of ZXG01061 and W1-1 were collected in the reproductive growth period. These samples were immediately fixed in a formaldehyde-acetic acid-ethanol (FAA) mixture and stored. From the fixed samples, paraffin sections of the stem tips and flower buds were generated according to standard procedures. First, the samples were dehydrated in an alcohol series, cleared, and subjected to paraffin embedding. Then, the samples were deparaffinized with xylene, cut to a thickness of 6 to 8 microns, dewaxed, fixed with red and green dye, and sealed. Representative specimens with a complete structure according to the staining of the cleared paraffin sections were selected, sealed with neutral gum sealed, and sliced to obtain the final specimens (Li, 2009). The slices were observed and photographed with a Nikon TE2000-U microscope.
DNA extraction and BSA-seq
DNA extraction was performed on undamaged young leaf tissue of ZXG01061, W1-1, F1, and F2 plants, and samples were stored at -80°C. Total genomic DNA was extracted using the modified CTAB (hexadecyl trimethyl ammonium bromide) method. The concentration and quality of DNA were verified by using 1% agarose gels and a DNA ultraviolet spectrophotometer. Two bulked DNA samples were prepared by mixing DNA equally from 30 standard- and 30 short-internode-length F2 plants. DNA from two bulked samples and the parental lines were selected for sequencing and then subjected to ultrasonic fragmentation, purification, end repair, sequencing, and adapter ligation. Next, the samples were filtered by 1% agarose gel electrophoresis to obtain a target insert size of 500 bp for further analysis and purification. PCR amplification was used to construct a paired-read sequencing library. The DNA of parental lines and gene pools was sequenced (20 × sequencing depth) on the Illumina X10 platform at the Beijing Genomics Institute (BGI) (Shenzhen, China).
BSA analysis and primary mapping
The total resequenced reads were analysed by removing low-quality reads, reads containing adaptors, and reads with >10% unknown bases. The cleaned reads were aligned across the watermelon reference genome (97103) (Guo et al., 2013) by using the Burrows–Wheeler Aligner (BWA) software package (Li and Durbin, 2009). The raw reads showing single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) were sorted, and low-quality reads (<20 read depth) were removed with the SAMtools rmdup command (Li et al., 2009). The Unified Genotyper module of GATK was used to detect SNPs in multiple samples (McKenna et al., 2010). The chromosome region related to dwarfism was determined by the Δ(SNP index) value derived from locally estimated scatterplot smoothing (LOESS) regression (P value ≤ 0.01) curves at each SNP position of both bulks according to previously reported equations (Li et al., 2017). Δ(SNP index) analysis of each chromosome was conducted for both types of bulks on the basis of read depth to test the significance of the SNPs according to a P value of ≤ 0.01 and LOESS regression, and the detected region showing a value above the threshold was designated as the main region responsible for controlling dwarfism.
Cleaved amplified polymorphism sequence (CAPS) marker development and genetic mapping
CAPS markers were developed based on resequencing data of the two parents (ZXG01061 and W1-1). The reads were filtered to remove all unusable regions by applying an in-house Perl program and were mapped to the watermelon reference genome (http://www.icugi.org/, 97103 v1) using BWA with the default parameters (Li and Durbin 2009). We used SAMtools software to sort and index map reads with mapping scores >20 (Li et al. 2009) and obtained 500 bp of flanking sequences on both sides of each candidate SNP locus identified between ZXG01061 and W1-1 with SAMtools software. The candidate SNP loci were transformed into CAPS markers using SNP2CAPS (Thiel et al. 2004). Ten restriction endonucleases (EcoRI, MboI, HindIII, PstI, MspI, BclI, TaqI, MboII, ScaI, and XhoI) were used to detect the restriction enzyme cutting site and design PCR primers based on the target chromosome using the results of BSA-seq. Primers were designed with Primer Premier 6.0 (http://www.premierbiosoft.com/) and synthesized by Sangon Biotech (Table 1). The PCR amplification procedure and system were described by Amanullah et al., 2018. The enzyme digestion experiment was performed according to the instructions for each restriction enzyme. Other SNP sites that could not be converted into CAPS markers were designated as Kompetitive Allele-Specific PCR (KASP) markers and genotyped at the Vegetable Research Center of the Beijing Academy of Agricultural and Forestry Sciences. The codominant polymorphic markers were selected for genotyping, with the individuals exhibiting recessive traits.
Exogenous gibberellin (GA3) treatment
The two parental lines, ZXG01061 and W1-1, were exogenously treated with GA3 in the greenhouse. The GA3 used for exogenous treatment was obtained from Solarbio Science and Technology Ltd. (Beijing, China). The GA3 powder was dissolved in a small quantity of ethanol and diluted in distilled water (ddH2O) to obtain the final solution. All plants were exogenously treated with various GA3 concentrations (0.3 mmol/L, 0.9 mmol/L, and 1.5 mmol/L), while control plants were treated by the simple spray application of an ethanol and ddH2O mixture. Plant height was subsequently measured once a week after seed germination.
GA extraction and content determination
When the parental lines reached their reproductive growth stage (50 days after sprouting), the eighth internodes were collected from three individuals for each line, and all plants showed the same growth rate according to visual observation. Fresh internode tissues were ground to a powder in liquid nitrogen. A 50 mg ground sample was weighed, and an appropriate amount of internal standard was added, followed by extraction with methanol:water:formic acid at a ratio of 15:4:1. After concentration, the extract was redissolved in 100 μL of an 80% methanol water solution, passed through a 0.22 μm PTFE filter membrane, and place in an injection bottle for LC–MS/MS analysis. Then, the same sample was analysed by qRT–PCR.
Gene expression analysis and candidate gene cloning
The eighth internodes of W1-1 and ZXG01061 were collected, and total RNA was extracted from 500 mg frozen tissue samples by using an EasyPure Plant RNA Kit (TransGen Biotech, China) according to the manufacturer’s instructions. The total RNA was evaluated by running a 2 µL sample in a 1% formamide denaturing gel. The total RNA sample obtained from a pool composed of material from 6 representative plants was used for cDNA synthesis. A 1 µg total RNA sample was initially used for first-strand synthesis, and double-stranded cDNA was synthesized by using the SMARTTM cDNA Library Construction Kit for the determination of total RNA and cDNA.
Gene expression levels were identified by quantitative real-time polymerase chain reaction (qRT–PCR) using a real-time PCR system (Analytik Jena AG, Germany) with SYBR Green Master Mix reagent (Novogene, Beijing, China) according to the manufacturer’s instructions. Each sample was analysed with three biological replicates. Cla020175 was used as the internal control (Wang et al. 2016). Specific transcript amplification was verified by the observation of a single peak in the melting curve analysis after completion of the amplification reaction. Negative controls without any cDNA template were included in each run to test for potential impurities. The relative gene expression levels were determined by the 2ΔΔCT method (Livak and Schmittgen. 2001). The cloning of the candidate gene sequence was performed in W1-1 and ZXG01061 with the primers in Table 1. The amplified targeted fragments were then inserted into the pMD18-T vector and sent to Sangon Biotech (Shanghai, China) for sequencing.