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Fine mapping of the locus controlling self-incompatibility in European hazelnut

Abstract

Incompatibility in European hazelnut (Corylus avellana L.) is sporophytic and under the control of a single locus on linkage group 5 between markers G05-510 and AU02-1350. In this study, two rounds of marker development and a population of 192 seedlings with known S-alleles that showed recombination between the flanking markers were used for fine mapping. Using the sequences of random amplified polymorphic DNA and simple sequence repeat (SSR) markers and bacterial artificial chromosome end sequences, 36 contigs from the genome sequence of “Jefferson” hazelnut were identified for pursuit. Di-nucleotide SSR markers in those contigs were developed, characterized, and mapped. This reduced the size to a region of 500 kb that contained the S-locus and 50 predicted genes, in which single-nucleotide polymorphism and additional SSR markers were developed. When the new markers were used in fine mapping, they fully exploited all recombination in the fine mapping population and reduced the region to 193.5 kb containing 18 genes. This 193.5-kb region most likely contains the S1 haplotype. A second region, 2 Mbp away from the first in the “Jefferson” genome (V3), is predicted to represent the S3 haplotype based on SSR marker allele sizes and the ratio of parental reads that align to them. Although they appear side-by-side in the “Jefferson” genome (V3), the mapped markers appear in both sequences in the same order. Gene annotations in the S1 and S3 haplotypes are highly similar and include five probable leucine-rich repeat receptor-like protein kinases with homology to Arabidopsis thaliana genes At1g35710 and three probable receptor-like serine/threonine protein kinases with homology to At5g15080 (PIX7).

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Data availability

Marker sequences were deposited in GenBank. Additional data is available upon request.

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Funding

This study was supported by the Oregon Hazelnut Commission, United States Department of Agriculture–National Institute of Food and Agriculture-Specialty Crops Research Initiative Grant 2016-51181-25412, a Specific Cooperative Agreement with the United States Department of Agriculture for eastern filbert blight research, and the Oregon Agricultural Experiment Station.

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Authors

Contributions

Data collection and analyses were performed by Ryan J. Hill and Claudia Baldassi. Research materials, experimental design, funding, and supervision were supplied by Shawn A. Mehlenbacher. Shawn A. Mehlenbacher also identified the S-alleles of 192 recombinant seedlings. Kelly J. Vining annotated genome sequences. Jacob W. Snelling aligned BAC end and genome sequences to identify contigs associated with the S-locus. Jacob W. Snelling also aligned the “Jefferson” S1 and S3 haplotype sequences with Illumina reads of parents OSU 252.146 and OSU 414.062. Ryan J. Hill wrote the first draft of the manuscript with input from the other authors. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Shawn A. Mehlenbacher.

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Data archiving statement

Sequences from which HRM and SSR markers were developed are deposited in GenBank as accession numbers MT181674 through MT181749.

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Communicated by C. Chen

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Hill, R.J., Baldassi, C., Snelling, J.W. et al. Fine mapping of the locus controlling self-incompatibility in European hazelnut. Tree Genetics & Genomes 17, 6 (2021). https://doi.org/10.1007/s11295-020-01485-5

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Keywords

  • Corylus avellana
  • Filbert
  • Linkage mapping
  • High-resolution melting
  • Simple sequence repeat
  • Microsatellite
  • Pollen
  • Stigma
  • S-locus