Dataset Information

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.

SUBMITTER: Wei C

PROVIDER: S-EPMC5509165 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Wei Chunhua C Chen Xiner X Wang Zhongyuan Z Liu Qiyan Q Li Hao H Zhang Yong Y Ma Jianxiang J Yang Jianqiang J Zhang Xian X

PloS one 20170713 7

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 th ...[more]

PMID: 28704497

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Project description:Watermelon fruit texture and quality are determined by flesh firmness. As a quality trait, flesh firmness is controlled by multigenes. Defining the key regulatory factors of watermelon flesh firmness is of great significance for watermelon genetic breeding. In this study, the hard-flesh egusi seed watermelon PI186490 was used as the male parent, the soft-flesh cultivated watermelon W1-1 was used as the female parent, and 175 F2 generations were obtained from selfing F1. Primary mapping of the major genes controlling center flesh firmness was achieved by bulked-segregant analysis (BSA)-Seq analysis and molecular marker technology. Finally, major genes were delimited in the physical interval between 6,210,787 and 7,742,559 bp on chromosome 2 and between 207,553 and 403,137 bp on chromosome 8. The content of each cell wall component and hormone was measured, and comparative transcriptome analysis was performed during fruit development in watermelon. The protopectin, cellulose, hemicellulose, indole-3-acetic acid (IAA) and abscisic acid (ABA) contents were measured, and paraffin sections were made during the three fruit developmental stages. The results revealed that protopectin, celluloses, and hemicelluloses exhibited similar trends for flesh firmness, while the IAA and ABA concentrations continued to decrease with fruit ripening. Paraffin sections showed that PI186490 cells were more numerous, were more tightly packed, had clearer cell wall edges and had thicker cell walls than W1-1 cells at every developmental stage. Comparative transcriptome analysis was conducted on RNA samples of flesh during fruit development and ripening in W1-1 and PI186490. The results from the localization interval transcriptome analysis showed that Cla016033 (DUF579 family member), which may influence the cell wall component contents to adjust the flesh firmness in watermelon fruit, was different in W1-1 and PI186490 and that Cla012507 (MADS-box transcription factor) may be involved in the regulation of fruit ripening and affect the hardness of watermelon fruit.

Project description:BACKGROUND: Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. RESULTS: Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. CONCLUSIONS: The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A large proportion of the markers in the integrated map are SSRs, InDels and SNPs, which are easily transferable across laboratories. Moreover, the populations used to construct the integrated map include all three watermelon subspecies, making this integrated map useful for the selection of breeding traits, identification of QTL, MAS, analysis of germplasm and commercial hybrid seed detection.

Dataset Information

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

Publications

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

Similar Datasets

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