Abstract
Background
Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding.
Methods and results
In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-F2 derived plant populations were genotyped for linkage mapping and composite interval mapping based QTL mapping exposed 6 genetic loci, positioned over distinct chromosomes (02, 04, 08, 09, and 12) between the flanking intervals of CAPS markers, which explained an unlinked polygenic architecture in genome. Three minor QTLs of fruit weight (FWt2.1, FWt4.1, FWt9.1), one major QTL of fruit firmness (FrFir8.1), one major QTL of fruit length (FL12.1), and one major QTL of fruit shape (FS12.1) were determined and collectively explained the phenotypic variance from 5.64 to 15.64%. Fruit phenotypic correlation exhibited the significant relationship and principal component analysis also identified the potential variability. Multiple sequence alignments also indicated the significant base-mutations in the detected genetic loci, respectively.
Conclusion
In short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.
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Data availability
The possible datasets generated for this study can be found in the manuscript and attached supplementary material.
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Acknowledgements
Authors are grateful for the financial funding of postdoctoral research project of Northeast Agricultural University, Harbin, China.
Funding
This research was financially supported by National Natural Science Foundation of China (No. 31772331), Taishan Industrial Leading Talents Project (No. LJNY202112), and China Agriculture Research System (CARS-25).
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SA planned and performed the molecular genetic experiment, data curation, formal analysis, manuscript draft, reviewed & edited the manuscript. BAO and YTT helped in field experiment. FA helped in formal analysis. SL, HL, and XW provided the field research resources. PG and FL supervised the entire project, reviewed & edited the manuscript. All authors approved the final version of manuscript.
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Amanullah, S., Osae, B.A., Yang, T. et al. Mapping of genetic loci controlling fruit linked morphological traits of melon using developed CAPS markers. Mol Biol Rep 49, 5459–5472 (2022). https://doi.org/10.1007/s11033-022-07263-x
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DOI: https://doi.org/10.1007/s11033-022-07263-x