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. 2018 Oct 19;18(1):246.
doi: 10.1186/s12870-018-1475-2.

Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers

Salam Y Abu Zaitoun  1 , Rana M Jamous  1 , Munqez J Shtaya  1   2 , Omar B Mallah  1 , Imad S Eid  1 , Mohammed S Ali-Shtayeh  3
Affiliations

Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers

Salam Y Abu Zaitoun et al. BMC Plant Biol. .

Abstract

Background: Crop landraces embody a source of beneficial genes potentially providing endurance to environmental stress and other agronomic qualities including yield. Our study included 88 snake melon accessions (Cucumis melo var. flexuosus) collected from 9 districts in the Palestinian West-Bank. These accessions represent four landraces of Palestinian snake melon: Green, and White Baladi, and Green, and White Sahouri.

Results: This is the first report on successful application of genotyping by sequencing in snake melon. Nine thousand seven hundred fifty single-nucleotide polymorphism (SNP) and 7400 DArTseq genetic markers were employed to evaluate genetic biodiversity and population structure of Palestinian snake melon germplasm collection. Clustering based on neighbor-joining-analysis, principle coordinate and Bayesian model implemented in Structure showed that patterns of genetic diversity of snake melon landraces depends on their geographical source and unraveled the presence of two major local landraces (Sahouri, and Baladi) with accessions from each group clustering together. A significant correlation was observed between both types of markers in Mantel correlation test. A significant association between genetic and geographic matrices (P < 0.0001) was also detected. AMOVA indicated that majority of variation (90%) was due to the difference within accessions.

Conclusion: The Palestinian landraces seem to have unique genes that may allow the enhancement of the global snake melon gene pool and developments of the plant production worldwide. Our subsequent objective is to detect genotypes with promising qualities and to conduct association mapping studies concentrating on Fusarium-wilt resistance, yield, and environmental stresses.

Keywords: Cucumis melo var. flexuosus; DArT-seq; Genetic diversity; Genotyping by sequencing; Palestinian snake melon landraces; Population structure; SNP.

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Conflict of interest statement

Ethics approval and consent to participate

Permission from the farmers to carry out field experiments was obtained under the direct supervision from BERC/Palestine.

Consent for publication

An earlier version of this work was presented at “The XIV Solanaceae and III Cucurbitaceae Genomics Joint Conference (SOLCUC 2017),” 2017: http://solcuc2017.org/documentos/abstractsBook.pdf.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Population STRUCTURE analysis of 88 snake melon accessions using 7400 DArTseq and 9750 SNP markers. The proportion of membership in each group and subgroups at ΔK = 2 as defined with a model-based clustering method from Pritchard et al. [45] based on DArTseq and SNP markers. The collection sites and local landrace of each group and subgroup were analyzed and found well align which mentioned next to each
Fig. 2
Fig. 2
Principal coordinate analysis of snake melon accessions based on (a) DArTseq and (b) SNP markers
Fig. 3
Fig. 3
Neighbour-joining analysis of 88 snake melon accessions based on (a) DArTseq and (b) SNP markers
Fig. 4
Fig. 4
Association between geographical distance and genetic diversity based on (a) DArTseq and (b) SNP markers
Fig. 5
Fig. 5
Mantel correlation test between DArTseq and SNP markers
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