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BSA-seq mapping reveals major QTL for broomrape resistance in four sunflower lines

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Abstract

Broomrape (Orobanche cumana) is a parasitic weed that causes substantial yield losses in sunflower. In this study, four biparental genetic populations comprised of between 96 and 150 F3 families were phenotyped for resistance to broomrape race G. Bulk segregant analyses (BSA) combined with genotyping-by-sequencing (GBS) technology was used to verify previously identified genes and map new resistance QTLs. Resistance had a polygenic basis, and numerous QTLs were found in all mapping populations. Contributing components to resistance that were common to all populations mapped to two major QTLs on chromosome 3, which were designated or3.1 and or3.2. QTL or3.1 was positioned in a genomic region where a previous broomrape resistance gene Or5 has been mapped, while QTL or3.2 was identified for the first time in the lower region of the same chromosome. Following the identification of major QTLs for resistance using the BSA-seq approach, all plants from three F2 populations were genotyped using newly developed CAPS markers nearest to the QTL peak for or3.2, which confirmed the association of these markers with broomrape race G resistance. The results of this study will bring us a step closer to understanding the mechanisms underlying resistance of sunflower to highly virulent broomrape races, and the molecular markers developed herein will be highly useful for sunflower breeding programs.

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Funding

This work was in part supported by project TR31025 financed by the Ministry of Education, Science and Development, Republic of Serbia and funding from Genome BC and Genome Canada to LHR.

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Authors and Affiliations

  1. Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, B.C., V6T 1Z4, Canada

    Ivana Imerovski, Gregory L. Owens & Loren H. Rieseberg

  2. Institute of Field and Vegetable Crops, Maksima Gorkog 30, Novi Sad, 21000, Serbia

    Boško Dedić, Sandra Cvejić, Dragana Miladinović & Siniša Jocić

  3. Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA

    Gregory L. Owens

  4. Faculty of Sciences, University of Novi Sad, Novi Sad, 21 000, Serbia

    Nataša Kočiš Tubić

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  1. Ivana Imerovski
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  2. Boško Dedić
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  3. Sandra Cvejić
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  4. Dragana Miladinović
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  5. Siniša Jocić
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Table S1

Description of the environments (combination of location and season) of the trials for the multi-environment study (DOCX 21 kb)

Table S2

Relative broomrape incidence (in %) of four selected sunflower inbred lines, their F1s and differential line set in the eight different environments. Relative values expressed as percentage of the susceptible control Labud (DOCX 25 kb)

Table S3

Accession numbers of biosamples deposited in SRA (DOCX 20 kb)

Table S4

Initial dataset size and number of SNPs per population after filtering within “QTLseqr” (DOCX 20 kb)

Table S5

CAPS markers developed from SNPs obtained by genotype-by-sequencing (DOCX 20 kb)

Fig. S1

(a) Testing sites used for germplasm screening in year 2011 and for multi-environmental trials on selected lines during 2016 and 2017. (b) Within the selected sites, broomrape incidence rate on the differential line LC1093 (carrying gene Or6) is shown with the pie-charts. The size of the pie-charts is scaled to reflect the infestation rate on LC1093 (i.e. number of broomrape plant on the host plant). The map was generated using averages from data collected during 2011–2016 (JPG 696 kb)

Fig. S2

Frequency distribution of broomrape resistance within 300 sunflower lines evaluated in the field in Serbia (a), Spain (b), Constanta, Romania (c) and Tulcea, Romania(d) during summer of 2011. (e) Venn diagram representation of number of resistant lines in the four environments. Lines with a score of 0 or 1 were considered as resistant, whereas all other lines were considered susceptible. Seven lines were resistant in all four environments (PNG 1005 kb)

Fig. S3

Frequency distribution of broomrape resistance scores of the F3 families in the populations (a) HA-267/OD-DI-82, (b) LIV-10/HA-26-PR, (c) LIV-17/HA-26-PR and (d) AB-VL-8/L-OS-1. (PDF 1650 kb)

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Imerovski, I., Dedić, B., Cvejić, S. et al. BSA-seq mapping reveals major QTL for broomrape resistance in four sunflower lines. Mol Breeding 39, 41 (2019). https://doi.org/10.1007/s11032-019-0948-9

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