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A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash

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Abstract

Key message

Two QTL mapping approaches were used to identify a total of six QTL associated with Phytophthora root and crown rot resistance in a biparental squash population.

Abstract

Phytophthora root and crown rot, caused by the soilborne oomycete pathogen Phytophthora capsici, leads to severe yield losses in squash (Cucurbita pepo). To identify quantitative trait loci (QTL) involved in resistance to this disease, we crossed a partially resistant squash breeding line with a susceptible zucchini cultivar and evaluated over 13,000 F2 seedlings in a greenhouse screen. Bulked segregant analysis with whole genome resequencing (BSA-Seq) resulted in the identification of five genomic regions—on chromosomes 4, 5, 8, 12, and 16—featuring significant allele frequency differentiation between susceptible and resistant bulks in each of two independent replicates. In addition, we conducted linkage mapping using a population of 176 F3 families derived from individually genotyped F2 individuals. Variation in disease severity among these families was best explained by a four-QTL model, comprising the same loci identified via BSA-Seq on chromosomes 4, 5, and 8 as well as an additional locus on chromosome 19, for a combined total of six QTL identified between both methods. Loci, whether those identified by BSA-Seq or linkage mapping, were of small-to-moderate effect, collectively accounting for 28–35% and individually for 2–10% of the phenotypic variance explained. However, a multiple linear regression model using one marker in each BSA-Seq QTL could predict F2:3 disease severity with only a slight drop in cross-validation accuracy compared to genomic prediction models using genome-wide markers. These results suggest that marker-assisted selection could be a suitable approach for improving Phytophthora crown and root rot resistance in squash.

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Data availability

Whole genome resequencing reads used in BSA-Seq and genotyping-by-sequencing reads used in linkage mapping have been deposited in the National Center of Biotechnology Information Sequence Read Archive (SRA) under BioProject accession number PRJNA662576. Files containing allele counts used in BSA-Seq, genotype and phenotype data used in linkage mapping, and annotated variant calls used for candidate gene identification are available at CyVerse (https://datacommons.cyverse.org/browse/iplant/home/shared/GoreLab/dataFromPubs/Vogel_SquashQTL_2020). All scripts used for data analysis are available on Github (http://github.com/gmv23/Pcap-QTL-Mapping).

Availability of data and materials

All data generated in this project have been made publicly available, as described in the Materials and Methods. Seed for germplasm described in this study, as available, may be obtained upon reasonable request.

Code availability

All scripts used for data analysis are available on Github (http://github.com/gmv23/Pcap-QTL-Mapping).

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Acknowledgements

We are grateful for technical assistance from Andrew Aldcroft, Mariami Bekauri, Colin Day, Garrett Giles, Holly Lange, Nicholas King, Carolina Puentes Silva, and Carolina Vogel, as well as statistical advice from Chris Hernandez and Ryokei Tanaka. We would also like to thank Jeff Glaubitz, Peter Schweitzer, and Jing Wu from the Cornell Institute of Biotechnology for consultation regarding library preparation for whole genome sequencing; Mainor Najera, Fernando Villalta Mata, and Andrés Villalta Pereira from VillaPlants for provision of seed increase services; and Mary Kreitinger for assistance in obtaining permits for shipping of seed, tissue, and supplies.

Funding

Funding for this project was provided by the Cucurbit Coordinated Agricultural Project (CucCAP; USDA National Institute of Food and Agriculture Specialty Crop Research Initiative Grant No. 2015-51181-24285) and the New York State Department of Agriculture and Markets.

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Authors and Affiliations

  1. Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA

    Gregory Vogel, Kyle E. LaPlant, Michael Mazourek & Michael A. Gore

  2. Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA

    Gregory Vogel & Christine D. Smart

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  1. Gregory Vogel
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  2. Kyle E. LaPlant
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Contributions

GMV, MM, MAG, and CDS conceived and designed the experiments. GMV and KEL performed the experiments. GMV conducted the data analysis and wrote the manuscript under the guidance of MAG and CDS. All authors edited the manuscript and read and approved the final version.

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Correspondence to Christine D. Smart.

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MM is a cofounder of Row 7 Seeds but has no financial stake in the company.

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Communicated by Amnon Levi.

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Vogel, G., LaPlant, K.E., Mazourek, M. et al. A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash. Theor Appl Genet 134, 1015–1031 (2021). https://doi.org/10.1007/s00122-020-03747-1

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