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

Abstract

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.

A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.)

“…In recent years, the combination of a bulked segregant analysis (BSA) and next-generation sequencing technology (BSA-Seq) has been widely applied to identify candidate genes controlling important agronomic traits in watermelon, such as dwarf phenotype 37 – 40 , lobed leaves 41 , yellow skin 42 , fruit shape 43 , fruit pigment accumulation 44 and anthracnose resistance 45 . In this study, we investigated the inheritance of watermelon dwarf genes in the F 2 population of ‘w106’ (dwarf) × ‘Charleston Gray’ (CG; vine), which indicated that the dwarf phenotype was controlled by a single recessive gene.…”

Ethylene‐responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon

“…With the advancement of next‐generation sequencing (NGS) technology, sequencing‐based gene mining strategies, such as bulk segregant analysis (BSA), genetic mapping and genome‐wide association study (GWAS), have been widely used as affordable, efficient and routine approaches to dissect crop traits in rice (Wang et al , ) tomato (Chapman et al , ; Soyk et al , ), cucumber(Li et al , ; Xu et al , ), peanut(Luo et al , ), chickpea(Deokar et al , ),spinach(She et al , ), apple(Jia et al , ) and melon (Hu et al , ). Recently, genes or QTLs related to sugar transporter (Ren et al , ), dwarfism (Dong et al , ) and lobed leaves (Wei et al , ) have been reported in watermelon. However, the genetic dissection of rind hardness has not been reported and remains a knowledge gap in fresh fruits such as watermelon.…”

Understanding genetic diversity, population structure and development of a core collection of Indian accessions of watermelon (Citrullus lanatus(Thunb.) Matsum. and Nakai)

“…The non-lobed leaf trait can be used as a morphological marker for maintenance of parental lines of hybrids as the character is recessive to normal lobed leaf. This is governed by a single dominant gene ( ClLL1 ) situated on chromosome 4 (Wei et al ., 2017). Though sweetness and flesh colour are the two most important traits that strongly influence consumer preference (Kyriacou et al ., 2017); fruit shape, stripe pattern and as well as seed colour also stands as one of the key acceptance determining traits.…”