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

Abstract

In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of haploid inducer DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three haploid inducers: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n=2x-1=23 to 2n=2x+3=27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the haploid inducer parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual haploid inducer DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.

Establishment and inheritance of minichromosomes from Arabidopsis haploid induction

“…Potentially, formation of telomeres may also stabilize certain centromeric fragments. Instability is commonly associated with haploid induction (Maheshwari et al 2015;Tan et al 2015;Kuppu et al 2015;Amundson et al 2021;Sun et al 2022) and with wide crosses (Madlung et al 2005;Shibata et al 2013), and minis are likely to arise in these crosses (Seymour et al 2012;Tan et al 2015;Kuppu et al 2015). One question is whether minichromosomes require mutations in specialized loci of DNA metabolism for their formation and maintenance.…”

PL-4 (CIP596131.4): an Improved Potato Haploid Inducer

“…Abnormal dihaploids were also noted (1.4% for PL-4, 10.1% and 6.3% for IvP101 and IvP35, respectively). These could represent extreme aneuploidy cases (Tan et al 2015;Amundson et al 2021).…”

“…Three hypotheses have been proposed for the mechanism of haploid induction in potatoes: parthenogenesis, parentspecific chromosome elimination and egg-pseudo fertilization (Wangenheim et al 1960;Clulow et al 1991;Amundson et al 2021). The exact mechanism at play has not yet been elucidated.…”

LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

“…We asked if the method could be useful in eight comparable, but unrelated dihaploid families generated through haploid induction crosses. Seven of these dihaploid families (Amundson et al 2020b) revealed the presence of translocated or misplaced heterochromatic and pericentromeric blocks, but no arm translocations (Suppl. Fig.…”