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      High-density linkage mapping and genetic dissection of resistance to broomrape ( Orobanche crenata Forsk.) in pea ( Pisum sativum L.)

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          Abstract

          Pea ( Pisum sativum L.) is a widely cultivated legume of major importance for global food security and agricultural sustainability. Crenate broomrape ( Orobanche crenata Forsk.) (Oc) is a parasitic weed severely affecting legumes, including pea, in the Mediterranean Basin and the Middle East. Previously, the identification of the pea line “ROR12”, displaying resistance to Oc, was reported. Two-year field trials on a segregant population of 148 F 7 recombinant inbred lines (RILs), originating from a cross between “ROR12” and the susceptible cultivar “Sprinter”, revealed high heritability (0.84) of the “ROR12” resistance source. Genotyping-by-sequencing (GBS) on the same RIL population allowed the construction of a high-density pea linkage map, which was compared with the pea reference genome and used for quantitative trait locus (QTL) mapping. Three QTLs associated with the response to Oc infection, named PsOcr-1, PsOcr-2, and PsOcr-3, were identified, with PsOcr-1 explaining 69.3% of the genotypic variance. Evaluation of the effects of different genotypic combinations indicated additivity between PsOcr-1 and PsOcr-2, and between PsOcr-1 and PsOcr-3, and epistasis between PsOcr-2 and PsOcr-3. Finally, three Kompetitive Allele Specific PCR (KASP) marker assays were designed on the single-nucleotide polymorphisms (SNPs) associated with the QTL significance peaks. Besides contributing to the development of pea genomic resources, this work lays the foundation for the obtainment of pea cultivars resistant to Oc and the identification of genes involved in resistance to parasitic Orobanchaceae.

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          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                10 July 2023
                2023
                : 14
                : 1216297
                Affiliations
                [1] 1 Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro , Bari, Italy
                [2] 2 Institute of Biosciences and Bioresources, National Research Council (CNR) , Bari, Italy
                [3] 3 Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam , Amsterdam, Netherlands
                [4] 4 Department of Agricultural, Food and Environmental Sciences, University of Foggia , Foggia, Italy
                Author notes

                Edited by: Tom Warkentin, University of Saskatchewan, Canada

                Reviewed by: Hamid Khazaei, Natural Resources Institute Finland (Luke), Finland; Sara Fondevilla, Spanish National Research Council (CSIC), Spain

                *Correspondence: Stefano Pavan, stefano.pavan@ 123456uniba.it
                Article
                10.3389/fpls.2023.1216297
                10364127
                89efd3dc-f886-4712-803d-df59dd517272
                Copyright © 2023 Delvento, Arcieri, Marcotrigiano, Guerriero, Fanelli, Dellino, Curci, Bouwmeester, Lotti, Ricciardi and Pavan

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 03 May 2023
                : 21 June 2023
                Page count
                Figures: 5, Tables: 2, Equations: 2, References: 77, Pages: 10, Words: 4835
                Funding
                This study was partially carried out within the framework of the Agritech National Research Center, receiving funding from the European Union Next-Generation EU [PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 – D.D. 1032 17/06/2022, CN00000022]. The work from Valentina Fanelli was supported by MIUR-PON Ricerca e Innovazione 2014–2020 (project AIM1809249-attività 2, linea 1).
                Categories
                Plant Science
                Original Research
                Custom metadata
                Plant Breeding

                Plant science & Botany
                pea,broomrape,resistance,mapping,breeding
                Plant science & Botany
                pea, broomrape, resistance, mapping, breeding

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