Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker Roberto Mariotti, Alice Fornasiero, Soraya Mousavi, Nicolò G.M. Cultrera, Federico Brizioli, Saverio Pandolfi, Valentina Passeri, Martina Rossi, Gabriele Magris, Simone Scalabrin, et al. To cite this version: Roberto Mariotti, Alice Fornasiero, Soraya Mousavi, Nicolò G.M. Cultrera, Federico Brizioli, et al.. Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker. Frontiers in Plant Science, Frontiers, 2020, 10, 10.3389/fpls.2019.01760. hal-02997321 HAL Id: hal-02997321 https://hal.archives-ouvertes.fr/hal-02997321 Submitted on 25 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License ORIGINAL RESEARCH published: 28 January 2020 doi: 10.3389/fpls.2019.01760 Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence- Tagged Site Marker † † Roberto Mariotti 1 , Alice Fornasiero 2,3 , Soraya Mousavi 1, Nicolò G.M. Cultrera 1, 1 fi1 1 1 2,3 Edited by: Federico Brizioli , Saverio Pandol , Valentina Passeri , Martina Rossi ,GabrieleMagris , 4 4 2 5 Inaki Hormaza, Simone Scalabrin , Davide Scaglione , Gabriele Di Gaspero , Pierre Saumitou-Laprade , 5 6 2,3 1* Institute of Subtropical and Philippe Vernet , Fiammetta Alagna , Michele Morgante and Luciana Baldoni Mediterranean Hortofruticultura La 1 CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy, 2 Institute of Applied Genomics, Udine, Italy, Mayora (IHSM), Spain 3 Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy, 4 IGA Technology Reviewed by: Services, Udine, Italy, 5 University of Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France, 6 ENEA - Trisaia Juan De Dios Alché, Research Centre, Rotondella, Italy Experimental Station of Zaidín (EEZ), Spain Carlos Romero, The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Inter- Polytechnic University of Valencia, varietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), Spain suggesting a simple Mendelian inheritance of the trait. A double digest restriction *Correspondence: Luciana Baldoni associated DNA (ddRAD) sequencing of a biparental population segregating for [email protected] incompatibility groups has been performed and high-density linkage maps were †These authors have contributed constructed in order to map the SI locus and identify gene candidates and linked equally to this work markers. The progeny consisted of a full-sib family of 229 individuals derived from the Specialty section: cross ‘Leccino’ (G1) × ‘Dolce Agogia’ (G2) varieties, segregating 1:1 (G1:G2), in This article was submitted to accordance with a diallelic self-incompatibility (DSI) model. A total of 16,743 single Plant Breeding, nucleotide polymorphisms was identified, 7,006 in the female parent ‘Leccino’ and a section of the journal Frontiers in Plant Science 9,737 in the male parent ‘Dolce Agogia.’ Each parental map consisted of 23 linkage Received: 27 August 2019 groups and showed an unusual large size (5,680 cM in ‘Leccino’ and 3,538 cM in ‘Dolce Accepted: 16 December 2019 Agogia’). Recombination was decreased across all linkage groups in pollen mother cells of Published: 28 January 2020 ‘Dolce Agogia,’ the parent with higher heterozygosity, compared to megaspore mother Citation: ‘ ’ Mariotti R, Fornasiero A, Mousavi S, cells of Leccino, in a context of a species that showed exceptionally high recombination Cultrera NGM, Brizioli F, Pandolfi S, rates. A subset of 109 adult plants was assigned to either incompatibility group by a Passeri V, Rossi M, Magris G, stigma test and the diallelic self-incompatibility (DSI) locus was mapped to an interval of Scalabrin S, Scaglione D, Di Gaspero G, Saumitou-Laprade P, 5.4 cM on linkage group 18. This region spanned a size of approximately 300 Kb in the Vernet P, Alagna F, Morgante M and olive genome assembly. We developed a sequence-tagged site marker in the DSI locus Baldoni L (2020) Genetic Mapping of fi fi the Incompatibility Locus in Olive and and identi ed ve haplotypes in 57 cultivars with known incompatibility group assignment. Development of a Linked Sequence- A combination of two single-nucleotide polymorphisms (SNPs) was sufficient to predict Tagged Site Marker. G1 or G2 phenotypes in olive cultivars, enabling early marker-assisted selection of Front. Plant Sci. 10:1760. doi: 10.3389/fpls.2019.01760 compatible genotypes and allowing for a rapid screening of inter-compatibility among Frontiers in Plant Science | www.frontiersin.org 1 January 2020 | Volume 10 | Article 1760 Mariotti et al. The Incompatibility Locus in Olive cultivars in order to guarantee effective fertilization and increase olive production. The construction of high-density linkage maps has led to the development of the first functional marker in olive and provided positional candidate genes in the SI locus. Keywords: genetic map, Olea europaea, double digest restriction associated deoxyribonucleic acid sequencing, self-incompatibility, functional markers INTRODUCTION of the incompatibility locus on the genome, the identification of candidate genes controlling this trait, and markers closely linked In cultivated olive (Olea europaea subsp. europaea var. to incompatibility. The availability of such information will allow europaea), the cross breeding activities have been delayed by for a systematic screening of olive cultivars to identify their group the particularly long generation time (Santos-Antunes et al., of incompatibility through genotyping with linked markers. 2005), the extended juvenile phase, the high demanding Olive is a diploid species (2n = 2x = 46) with a genome size of nursery practices, such as the forcing of seedling growth approximately 1.4 Gb (Cruz et al., 2016), with a mean C-value of (Rugini et al., 2016) and the time and space needed for plant 1.59 pg (1.56 Gb), where more than 30% sequences are growing (Picheny et al., 2017). In olive, breeding programs last represented by tandem repeats (Barghini et al., 2014). Up to about 30 years on average (Lavee et al., 2014; Rallo et al., 2016) now, only intraspecific crosses have been used for olive mapping, and have been limited to the empirical selection of a few sporadic and very early studies were performed with dominant markers intraspecific crosses (Rallo et al., 2008), or to clonal selection (de la Rosa et al., 2003; Wu et al., 2004; Aabidine et al., 2010; (Manaï et al., 2007; Gomes et al., 2008; Trapero et al., 2013; Khadari et al., 2010). Recently, more dense maps have been Mousavi et al., 2019), while the timing for the selection of new produced by the use of codominant markers, such as diversity cultivars in other fruit crops has been greatly reduced, also by the arrays technology (DArT) (Domínguez-García et al., 2012; application of new efficient genomic tools (Biscarini et al., 2017; Atienza et al., 2014), simple-sequence repeat (SSR) (Sadok et al., Laurens et al., 2018; Cai et al., 2019). However, the importance of 2013), and single-nucleotide polymorphism (SNP) markers olive cultivation at worldwide level and the new challenges posed (Marchese et al., 2016; İpek et al., 2017; Unver et al., 2017). by the ongoing climate change, are leading to an ever increasing SNPs are sequence-tagged markers widely used for demand for new cultivars (Gutierrez et al., 2009; Urban, 2015; association and genetic mapping due to their wide distribution Bosso et al., 2016). along the genome, high-throughput genotyping, and ease to One of the current limitations to olive productivity is score (Vezzulli et al., 2008; Deulvot et al., 2010; Lou et al., represented by its complex self- and inter-incompatibility 2017). Molecular markers linked to the traits of interest can be system (Saumitou-Laprade et al., 2017a; Alagna et al., 2019), a identified through different strategies, such as genetic linkage barrier that may seriously curb yield and restrict the varietal mapping based on biparental populations (Curtolo et al., 2017; Ji choice for planting to only a few inter-compatible or self-fertile et al., 2018; Zheng et al., 2018; Sapkota et al., 2019), or through varieties. Fruit set deficiencies due to ineffective pollination are genome-wide association studies (GWAS), based on unrelated generally underestimated by the farmers, however, it has been individuals (Khan et al., 2013; Nicolas et al., 2016; Elsadr et al., demonstrated that supplemental pollination may significantly 2019). The generation of high-resolution linkage maps, a increase olive production (Ayerza and Coates, 2004), indicating prerequisite for gene positional cloning, allows the genetic the importance of an effective pollination design of dissection of quantitative trait loci, assists in comparisons of olive orchards. synteny, and provides marker order for anchoring sequence In olive as well as in other species of the