Research Article: Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)

Date Published: July 13, 2017

Publisher: Public Library of Science

Author(s): Chunhua Wei, Xiner Chen, Zhongyuan Wang, Qiyan Liu, Hao Li, Yong Zhang, Jianxiang Ma, Jianqiang Yang, Xian Zhang, Hector Candela.


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.

Partial Text

Leaves are vitally important photosynthetic organs of flowering plants, determining the distribution of nutrients, gas exchange, and water transport. Leaves furthermore exhibit a remarkable variety in size, shape, and position on the stem [1–3]. Leaf shapes reveal a clearly visible diversity among different species and even within the same species [4–8]. In addition to molecular genetic regulators, leaf shapes can also be influenced by various environmental factors, such as severe fluctuations in temperature and light regimens [9,10]. Leaf margin is an important trait of leaf shape and can be serrated, lobed, or entire (the latter phenotype is named non-lobed throughout this study) [3,11]. In general, the leaf shape character can be easily identified at the seedling stage and thus, it can be used as an efficient morphological marker to distinguish hybrids from parental lines, consequently ensuring the purity of hybrid seeds [3,12].

The watermelon is an important cucurbit crop planted widely throughout the world [27]. Currently, lobed leaf shape watermelon varieties dominate the market. However, both genetic control and underlying mechanisms that lead to the formation of lobed leaf shape in watermelon are still poorly understood. In this study, we revealed that the lobed leaf trait in watermelon was controlled by a single dominant allele, named ClLL1. Environmental factors, such as strong fluctuations in temperature or light regimens, were reported to adversely affect both leaf growth processes and leaf shape [10]. For example, the palmately lobed leaf trait in melon, another important cucurbit crop, was controlled by the single recessive gene pll, which is only expressed in individuals grown in the field [2]. However, the lobed leaf phenotype in watermelon can steadily be observed after the emergence of the sixth true leaf in plants either grown in the field or in artificial climate chambers and greenhouse conditions, indicating that the expression of gene ClLL1 is not or only slightly affected by environmental factors. It has been reported that the cucurbit genome speciation event occurred 15–23 million years ago [27]. Therefore, it will be interesting to further investigate the underlying mechanism of leaf shape formation in these two cucurbit relatives.




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