Abstract
Almond (Prunus dulcis (Mill) D.A. Webb) is the only nut tree species in Rosaceae family and it is one of the most important nut crops all over the world. Cultivar breeding programs in almond take a long time due to its relatively long juvenile period. In the present study, we aimed (1) to construct high-density genetic linkage maps in two intra-specific almond populations, (2) to detect syntenic rates of the markers derived from ‘Gulcan-2 × Lauranne’ and ‘Guara × Nurlu’ F1 populations and (3) to identify synteny of the almond genome with peach, Japanese apricot and sweet cherry genomes. In this study, diversity arrays technology (DArT) and single nucleotide polymorphisms (SNP) markers were used for high-density genetic linkage map construction. In ‘Gulcan-2 × Lauranne’ population, the ‘Gulcan-2’ maternal linkage map included 3206 markers, and the total map length was 436.8 cM with 7.34 marker density (marker/cM), whereas the ‘Lauranne’ paternal genetic map contained 3308 markers, and the total map length was 486.4 cM with 6.80 marker density. In ‘Guara × Nurlu’ population, the ‘Guara’ maternal linkage map included 2430 markers, and total map length was 378.6 cM with 6.42 marker density (marker/cM), whereas the ‘Nurlu’ paternal genetic map contained 3,005 markers, and the total map length was 497.0 cM with 6.05 marker density. The highest synteny ratio was detected between almond and peach with 69.22%, while the lowest synteny ratio was detected between almond and sweet cherry with 54.75%. Synteny analysis revealed that high levels of the collinear gene pairs were detected with peach and sweet cherry genomes as pseudochromosomes in the same chromosome pairs. However, Japanese apricot had high synteny percentage with almond genome in different chromosomes. The genetic linkage maps based on DArT and SNP loci generated in this study will be very useful for future quantitative trait loci (QTL) analysis, synteny analysis of the almond genome with other Prunus species can be used for molecular breeding, and genetic studies in Prunus species.
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Data availability
All analyzed data during this study are included in this published article [and its supplementary information files]. LGs, loci, positions, significance, and segregations belonging to ‘Gulcan-2 × Lauranne’ and ‘Guara × Nurlu’ F1 almond populations are given in Supplementary File-1. The results of the blast of the loci in these populations to the almond genome have been shared in Supplementary File-2.
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This research was financially supported by the Turkish General Directorate of Agricultural Research and Policies (TAGEM/14/ARGE/01) for financial support.
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HT and SK conceived and designed the experiments. HT, HK and JW performed most of the experiments and analyzed the data. HT, HK and SK wrote the manuscript. The authors read and approved the final manuscript.
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Tevfik, H., Karcı, H., Wai, J. et al. Construction of high density linkage maps in almond and synteny analysis with peach, Japanese apricot and sweet cherry genomes. Euphytica 219, 82 (2023). https://doi.org/10.1007/s10681-023-03210-4
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DOI: https://doi.org/10.1007/s10681-023-03210-4