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Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

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Abstract

The olive (Olea europaea L.) was domesticated in the Mediterranean area over 6000 years ago and is currently one of the area’s most important oleaginous crops. Due to its economic, cultural and ecological importance, breeding programs aimed at obtaining new olive cultivars have been developed in most olive-producing countries. An efficient breeding program requires a large and genetically variable germplasm collection. In this study, we used next-generation sequencing technology for the identification of 145,974 single nucleotide polymorphism (SNPs) loci. A subset of 138 SNPs was then used to analyze the genetic relationships between 119 cultivars making up most of the Israeli germplasm collection. The various cultivars did not cluster according to their geographic origin but rather showed a high correlation with their function (oil, table or dual purpose). Comparison of genetic diversity between 15 cultivars using SSRs and SNPs revealed that for the purposes of analyzing genetic variation between olive cultivars, the SSR marker seems more suitable. However, based on the analysis of several trees of the same cultivar sampled from different nurseries, the SNP marker proved to be a more reliable criterion for cultivar identification. This study presents the most comprehensive SNP analysis of olive phylogeny to date. Based on the rapid development of SNP genotyping methods over the last few years, we believe that in the near future, we will be able to genotype many sample genomes using the appropriate SNPs at a reasonably low cost. Therefore, we can expect that in the future, SNPs will definitely be the marker of choice for biodiversity analysis as well as for gene cloning and QTL identification in olives.

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Authors and Affiliations

  1. Institute of Plant Science, Volcani Center, Agricultural Research Organization (ARO), P.O. Box 6, Bet-Dagan, 50250, Israel

    Iris Biton, Adi Doron-Faigenboim, Mahital Jamwal, Yair Mani, Ravit Eshed, Ada Rosen, Amir Sherman, Ron Ophir, Shimon Lavee, Benjamin Avidan & Giora Ben-Ari

  2. Institute of Plant Science, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel

    Shimon Lavee

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  1. Iris Biton
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  2. Adi Doron-Faigenboim
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  3. Mahital Jamwal
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  4. Yair Mani
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  5. Ravit Eshed
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  6. Ada Rosen
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  7. Amir Sherman
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  8. Ron Ophir
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  9. Shimon Lavee
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  10. Benjamin Avidan
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  11. Giora Ben-Ari
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Correspondence to Giora Ben-Ari.

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Table S1: List of all analyzed cultivars - the Israeli germplasm collection. (XLSX 13 kb)

11032_2015_304_MOESM2_ESM.xlsx

Table S2: List of the 138 SNPs used in this study. For each SNP we specified the flanking sequences as well as its two alleles, PIC and Ho values, the contig (oleaestdb) where the SNP is located as well as its position within this contig and the quality score. (XLSX 23 kb)

11032_2015_304_MOESM3_ESM.pdf

Fig. S1: Morphological variation among fruits of all cultivars from the Israeli germplasm collection. Fruits of all analyzed cultivars are presented. Each cultivar is represented by one fruit and the variation of fruit size and shape between cultivars can be assessed. (PDF 405 kb)

11032_2015_304_MOESM4_ESM.pdf

Fig. S2: A flow chart of the study including the various steps carried out for SNPs identification (blue rectangles), SNPs genotyping (red rectangles) and SNP analysis (green rectangles). (PDF 46 kb)

11032_2015_304_MOESM5_ESM.pdf

Fig. S3: Multiple alignments of the deep sequencing results. The output of the Genome Analysis Toolkit (GATK) software version 2.5.2 (McKenna et al. 2010) that was used for the detection of SNPs between ‘Barnea’ and ‘Manzanillo.’ Each raw presented one sequence read of ‘Barnea’ (green) or ‘Manzanillo’ (yellow). Two SNP loci in the presented sequences are shown (A/T and T/C). (PDF 273 kb)

Fig. S4: Distribution of cleaned sequence lengths over all sequences. (PDF 78 kb)

11032_2015_304_MOESM7_ESM.pdf

Fig. S5: Distribution of various types of identified SNPs. SNPs were characterized by their genotypes in the sequenced cultivars, ‘Barnea’ and ‘Manzanillo’ and divided into four groups: Heterozygote only in ‘Barnea,’ heterozygote only in ‘Manzanillo,’ heterozygote in both cultivars and homozygote to different alleles in each of the two cultivars. (PDF 65 kb)

11032_2015_304_MOESM8_ESM.pdf

Fig. S6: Delta K value for K = 3–14. The true number of subpopulation of all cultivars making up the Israeli germplasm collection using STRUCTURE and STRUCTURE HARVESTER. The peak at K = 3 indicates the most likely value of K. (PDF 16 kb)

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Biton, I., Doron-Faigenboim, A., Jamwal, M. et al. Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection. Mol Breeding 35, 107 (2015). https://doi.org/10.1007/s11032-015-0304-7

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