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Data from: Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

Citation

Amundson, Kirk (2021), Data from: Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability, Dryad, Dataset, https://doi.org/10.25338/B8JS8D

Abstract

In cultivated tetraploid potato, reduction to diploidy (dihaploidy) allows hybridization to diploid germplasm, introgression breeding, and may facilitate the production of inbreds. Pollination with haploid inducers yields maternal dihaploids, as well as triploid and tetraploid hybrids. It is not known if dihaploids result from parthenogenesis, entailing development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of haploid inducer DNA in some of the dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three haploid inducers, IVP35, IVP101, and PL4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids with karyotypes ranging from 2n=2x-1=23 to 2n=2x+3=27. Of 74 aneuploids with additional chromosomes, 66 contained chromosomes from the non-inducer parent and 8 showed chromosomes from the inducer parent. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny. Residual haploid inducer DNA is consistent with genome elimination as the mechanism of haploid induction. Further, the fact that paternal chromosome breaks are specific to dihaploids and tetraploid progeny suggests that they may be specific to 2x sperms, and supports the hypothesis that 2x sperms facilitate genome elimination.

Methods

19 tetraploid potato clones were pollinated with one of three haploid inducer clones (IVP101, IVP35, or PL4) and germinated on soil. Presence or absence of the pollinator-specific "embryo-spot" phenotype was recorded. Genomic DNA was extracted from homogenized leaf tissue and used to construct short-read sequencing libraries. Sequencing data was analyzed using the methods described in Amundson et al., 2020 Genetics (https://doi.org/10.1534/genetics.119.302843) to detect whole chromosome aneuploidy and determine parental origin of aneuploidy when present.

Usage Notes

Supplemental Dataset S1: Description of parents and offspring type of progeny of potato dihaploid induction crosses. Each offspring is a row in the table. For each offspring, we list the following:

  • CIP_ID: Unique identifier number assigned by the International Potato Center (CIP). Identifier numbers can be queried at http://genebank.cipotato.org/gringlobal/search.aspx to obtain more information about each sample.
  • UCD_ID: Internal UC Davis identifier number referred to throughout analysis at https://github.com/kramundson/MM_manuscript.
  • pistil_parent: Breeder code for pistillate parent of each progeny.
  • pistil_parent_CIP: CIP identifier number of pistillate parent.
  • pollen_parent: Breeder code for pollinator parent (haploid inducer) of each progeny.
  • pollen_parent_CIP: CIP identifier number of pollinator parent.
  • Phureja_marker_phenotype: Presence or absence of pollinator-specific "embryo spot" and nodal banding phenotype. DH = no spot or banding, PM = spot and/or banding. Prefix "ati" if phenotype atypical
  • aneuploidy_origin: Aneuploidy status of each progeny. Set to "euploid" if no aneuploidy detected in progeny, "non-inducer" if aneuploidy of pistillate parent chromosomes detected, and "inducer" if aneuploidy of pollinator chromosomes detected.
  • ploidy_eval: Ploidy of each offspring inferred from flow cytometry or guard cell chloroplast counting.
  • snp_ploidy: Ploidy of each offspring inferred from whole-genome sequencing
  • genomic_hi_perc: Average depth of pollinator allele at SNP loci fixed for different alleles in either parent.
  • chrXX: Aneuploidy call for a given chromosome. Calls pertain to whole-chromosome or segmental gains or losses with parental origin annotated where possible.

Supplemental Dataset S2: Attributes of sequencing libraries generated in this study. For each unique combination of biological sample, library preparation, sequencing run and sequencing lane, we list the following:

  • UCD_ID: Internal UC Davis identifier number referred to throughout analysis at https://github.com/kramundson/MM_manuscript.
  • parent_breeder_code: If parent, the breeder code of that parent. Set to NA for progeny.
  • pistil_parent: Breeder code for pistillate parent of each progeny.
  • pollen_parent: Breeder code for pollinator parent (haploid inducer) of each progeny.
  • B1/I1: Forward index sequence of library
  • B2/I2: Reverse index sequence of library
  • illumina_id: Illumina instrument, run, chip and lane identifier
  • read_type: Type of sequencing
  • in_dihaploid_pool: Indicates whether library was used in pooling low-coverage dihaploid data. See https://github.com/kramundson/MM_manuscript.
  • Library: Unique library identifier
  • sequencing_platform: Type of instrument sequencing was conducted on.
  • spot_count: Raw read count from each sequencing run.

Supplemental Dataset S3: IGV screenshots of short read alignments of putative HI introgression segments in dihaploids MM246, MM247 and MM1114, showing an overview of the region, apperance of HI-derived haplotypes in the regions, and flanking regions left and right of the segment.

Funding

National Science Foundation, Award: IOS-1444612