The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing

Abstract

A number of linkage maps have been previously developed in olive; however, these are mostly composed of markers that have not been characterized at the sequence level, supplemented with smaller numbers of microsatellite markers. In this investigation, we sought to develop a saturated linkage mapping resource for olive composed entirely of sequence characterized markers. We employed genotyping by sequencing to develop a map of a F 2 population derived from the selfing of the cultivar Koroneiki. The linkage map contained a total of 23 linkage groups comprised of 1,597 tagged SNP markers in 636 mapping bins spanning a genetic distance of 1189.7 cM. An additional 6,658 segregating SNPs were associated with the 23 linkage groups identified but their marker order was not determined in this investigation. The SNP markers sequences were submitted to NCBI database. The linkage map produced will be an invaluable resource for the study of tree habit and vigour traits segregating in the progeny, and will assist to anchor and orientate sequencing scaffolds from future genome sequencing efforts.

Elucidation of the genetic architecture of self‐incompatibility in olive: Evolutionary consequences and perspectives for orchard management

“…They are in agreement with conclusions of studies that tested SI in O. europaea at the postzygotic level, by measuring seed production after controlled crosses or open pollination, together with paternity analysis of the progeny (De la Rosa et al., ; Díaz et al., ; Marchese, Marra, Caruso, et al. ; Marchese, Marra, Costa, et al., ; Mookerjee et al., ). Just as in our study, many studies observed seeds produced by selfing either from controlled crosses with pollen from incompatible genotypes (see Oit28, Oit55, and Oit57 in Tables S3 and S4) or in controlled selfing (Farinelli et al., ) or open pollination (Marchese, Marra, Costa, et al., ).…”

“…The leaky SI observed in olive has provided material for genetic mapping and sequencing (Marchese, Marra, Caruso, et al. ) and allows an opportunity to measure inbreeding depression. For example, in the wild relative P. angustifolia , 2% of 2,000 surveyed seedlings produced from controlled crosses were found to have been selfed (Billiard et al., ).…”

Recent developments in olive (Olea europaea L.) genetics and genomics: applications in taxonomy, varietal identification, traceability and breeding

“…These data were further considered to construct a set of core collections of the olive accessions maintained in the germplasm. The SNPs were further used for: (1) the analysis of genetic identity among five putative clones of the olive cultivar Souri (Ben-Ari et al 2014); (2) the traceability of olive oil (Kalogianni et al 2015) also by developing peptide nucleic acid (PNA) and modified-PNA microarrays (Rossi et al 2012); (3) genetic mapping (Marchese et al 2016a;Ipek et al 2016;.…”

“…Ipek et al (2016) and Marchese et al (2016a) used GBS (Genotyping by Sequencing) to generate a high number of SNPs to obtain highly saturated genetic maps with a higher resolution capacity than those of the existing genetic maps. Ipek et al (2016) identified 10,941 new SNPs by applying GBS.…”

“…The map was constituted of 25 linkage groups, spanning 3049 cM of the genome. Marchese et al (2016a) developed a saturated map with 1597-tagged SNPs on the segregating progeny from the selfing of the cultivar Koroneiki. Twenty-three linkage groups composed the map, covering 11,897 cM.…”