Wei Chunhua, Chen Xiner, Wang Zhongyuan, Liu Qiyan, Li Hao, Zhang Yong, Ma Jianxiang, Yang Jianqiang, Zhang Xian
College of Horticulture, Northwest A&F University, Yangling, China.
PLoS One. 2017 Jul 13;12(7):e0180741. doi: 10.1371/journal.pone.0180741. eCollection 2017.
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.
裂叶性状是作物中一种独特的形态特征，对农业生产力具有许多潜在优势。尽管大多数西瓜品种具有裂叶，但导致裂叶形成的遗传因素仍不清楚。F2:3叶形分离群体为研究西瓜裂叶形成的潜在机制提供了机会。遗传分析表明，一个显性等位基因（命名为ClLL1）控制裂叶性状。利用从F2:3个体衍生而来的大型F3:4群体对ClLL1进行定位。通过结合BSA和RNA-seq在全基因组范围内共鉴定出5966个可靠的SNP和Indel。利用经过验证的SNP和Indel标记，将ClLL1的位置缩小到标记W08314和W07061之间的127.6 kb区域，该区域包含23个推定的开放阅读框（ORF）。通过qRT-PCR进行的表达分析揭示了三个ORF（ORF3、ORF11和ORF18）在裂叶和非裂叶植株之间的差异表达模式（倍数变化大于2倍或小于0.5倍）。基于基因注释和表达分析，ORF18（编码一种未表征的蛋白质）和ORF22（编码一种类同源框-亮氨酸拉链蛋白）被认为是最有可能的候选基因。此外，序列分析显示ORF18的cDNA序列没有多态性；然而，在ORF22中鉴定出两个明显的缺失。本研究是首次报道西瓜叶形基因的定位，将有助于未来研究中ClLL1的克隆和功能表征。
