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, 12 (7), e0180741

Genetic Mapping of the LOBED LEAF 1 (ClLL1) Gene to a 127.6-kb Region in Watermelon (Citrullus Lanatus L.)


Genetic Mapping of the LOBED LEAF 1 (ClLL1) Gene to a 127.6-kb Region in Watermelon (Citrullus Lanatus L.)

Chunhua Wei et al. PLoS One.


The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Fig 1
Fig 1. Phenotypes of leaf shapes in watermelon.
(a) Lobed and non-lobed leaf watermelon seedlings. (b) Two different leaf shapes in watermelon. Small symmetrical marginal protrusions are marked with red arrows. (c) Comparison of the first ten true leaves from lobed and non-lobed phenotype seedlings.
Fig 2
Fig 2. Genetic mapping of the lobed leaf trait gene ClLL1 in watermelon.
(a) Primary mapping of ClLL1 using 93 F3:4 individuals. Gene ClLL1 was delimited to the region between markers W03041 and W01214. The numbers in brackets after the marker name indicate the numbers of recombinants. (b) Fine mapping of ClLL1. The gene ClLL1 was fine mapped in a l27.6-kb region between markers W08314 and W07061. (c) Marker genotypes of the recombinants near the lobed leaf gene ClLL1 between W08314 and W07061. The alleles are abbreviated according to their origin: A: Lobed leaf; B: Non-lobed leaf; H: Heterozygous.
Fig 3
Fig 3. Prediction and relative expression level of candidate genes in the ClLL1 region.
(a) 23 putative ORFs were predicted in a 127.6-kb region between makers W08314 and W07061. (b) The relative expression level of candidate genes in both lobed and non-lobed leaf plants. The data are presented as average values of three replicates (mean value ± SD). “*, **” represent significant differences at p < 0.05 and p < 0.01, respectively, according to the Student’s t-test. Actin was used as an internal control.
Fig 4
Fig 4. Nucleotide polymorphisms of ORF18 and ORF22 among three watermelon genomes.
No nucleotide polymorphisms were identified in the cDNA sequences of ORF18 among three genomes. Two deletions (27-bp and 24-bp) were found in the second exon of ORF22 among three genomes. The homeodomain (HD) domain and leucine zipper (LZ) motif of ORF22 were predicted by the software Pfam (

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Grant support

This work was supported by Scientific Startup Foundation for Doctors of Northwest A and F University (Z109021604), Basal Research Foundation of Northwest A and F University (Z109021612), and the Modern Agro-industry Technology Research System of China (No. CARS-26-18).