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

PLOS ONE, Dec 2019

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 PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0180741&type=printable

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

July Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.) Chunhua Wei 0 1 2 Xiner Chen 0 1 2 Zhongyuan Wang 0 1 2 Qiyan Liu 0 1 2 Hao Li 0 1 2 Yong Zhang 0 1 2 Jianxiang Ma 0 1 2 Jianqiang Yang 0 1 2 Xian Zhang 0 1 2 0 College of Horticulture, Northwest A&F University , Yangling , China 1 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 2 Editor: Hector Candela, Universidad Miguel HernaÂndez de Elche , SPAIN 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 nonlobed 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. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Introduction 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 nonlobed 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 ]. Leaf shape morphogenesis is a complex process and several genes have been identified that mediate its development [ 13 ]. In Cardamine hirsuta, the class I KNOTTED1-like homeobox (KNOX) proteins organize auxin maxima via the PINFORMED1 (PIN1) auxin efflux transporter, thus promoting leaflet initiation [ 14 ]; the transcriptional level of KNOX can be repressed by CLAUSA and TRIPINNATE gene products, thus affecting the leaflet number in tomato [ 15,16 ]. In Arabidopsis, the transcription factor CUP-SHAPED COTYLEDON rendered the genes CUC1, CUC2, and CUC3 redundant, but showed partially distinct functions in embryonic shoot meristem formation and cotyledon boundary specification [17]; gene CUC2 can be targeted by miR164A, and the balance between CUC2 and miR164A determines the extent of leaf serration [ 18 ]. Loss-of-function mutations of the gene Mt-AGO7/LOBED LEAFLET1 result in lobed leaf margins in Medicago truncatula [ 19 ]. The hormone cytokinin (CK) has been reported to mediate the activity of KNOX1 proteins that aid the regulation of leaf shape in tomato [ 20 ]. The homeodomain leucine-zipper transcription factor LMI1 (AT5G03790) is a meristem identity regulator that interacts with LFY to activate CAL expression, providing additional functions in the formation of simple serrated leaves and in suppressing bract formation [ 21 ]. A previous study has demonstrated that the gene RCO (REDUCED COMPLEXITY, a LMI1-like homologue) is also required for leaflet development in C. hirsuta [ 22 ]. To date, several lobed leaf genes have been genetically analyzed and mapped within different species. In rapeseed (Brassica napus L), the LOBED-LEAF 1 (BnL (...truncated)


This is a preview of a remote PDF: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0180741&type=printable

Chunhua Wei, Xiner Chen, Zhongyuan Wang, Qiyan Liu, Hao Li, Yong Zhang, Jianxiang Ma, Jianqiang Yang, Xian Zhang. Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.), PLOS ONE, 2017, Volume 12, Issue 7, DOI: 10.1371/journal.pone.0180741