Genomic Outcomes of Haploid Induction Crosses in Potato (Solanum tuberosum L.)

Abstract

The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.

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

“…S3). Taken together, and consistent with previous reports (Amundson et al, 2020; Pham et al, 2019; Samitsu and Hosaka, 2002; Wagenvoort and Lange, 1975), our data show that approximately 8.7% of presumed dihaploids are aneuploid, without detectable aneuploidy bias for parental genotype or homologous chromosome in this material.…”

“…All of the haploid inducer genotypes contributed genetic material to at least one dihaploid, and the frequencies at which they did so were not significantly different ( p =0.7747; Fisher Exact test). The low overall frequency (8/923; 0.87%) of HI chromosome retention is consistent with previous results in which chromosomes from the inducer parent were not detected in cohorts of less than 200 individuals (Amundson et al, 2020; Samitsu and Hosaka, 2002; Pham et al, 2019).…”

“…To generate dihaploid and hybrids, we pollinated 19 tetraploid clones with haploid inducers IVP35, IVP101 or PL4, recorded presence or absence of inducer-specific anthocyanin pigmentation at the nodes of the plantlets, and evaluated the ploidy of each plantlet by chloroplast counting or flow cytometry (Supplementary Dataset S1). Next, 1,001 individuals from the putatively dihaploid progeny were selected for chromosome dosage analysis by low coverage whole genome sequencing, as previously described (Amundson et al, 2020). Briefly, for each dihaploid, read depth per chromosome is standardized to that dihaploid’s tetraploid parent such that values near 1, 2 or 3 correspond to monosomy, disomy or trisomy, respectively.…”

“…Given the role of dihaploids in efforts to convert potatoes to a diploid inbred crop, the incidental transfer of HI DNA remains a concern, as it has been reported to influence the phenotype of dihaploids (Allainguillaume et al, 1997). The relatively small sample sizes of previous studies, including our previous evaluation of 167 dihaploids that did not identify instances of HI DNA transfer (Amundson et al, 2020), warrant a robust characterization of the frequency and molecular state of incidental HI DNA transfer in primary dihaploids. Furthermore, to our knowledge, no study has investigated the genomic integrity of triploid and tetraploid hybrids obtained from potato haploid induction crosses.…”

“…From these results, it was concluded that the 2x sperm fertilizes the central cell, leaving no sperm to fertilize the egg, which then develops parthenogenetically. However, HI-specific DNA markers in dihaploids or near-dihaploid aneuploids were reported in some studies (Clulow et al, 1991; Waugh et al, 1992; Clulow et al, 1993; Wilkinson et al, 1995; Clulow and Rousselle-Bourgeois, 1997; Pham et al, 2019; Bartkiewicz et al, 2018; Ercolano et al, 2004; Straadt and Rasmussen, 2003; Allainguillaume et al, 1997), but not others (Samitsu and Hosaka, 2002; Amundson et al, 2020). This suggests retention of HI DNA either as chromosomes or segments thereof in an otherwise haploid plant, a diagnostic feature of uniparental chromosome elimination in plants (Zhao et al, 2013; Tan et al, 2015; Kuppu et al, 2015; Gernand et al, 2005; Riera-Lizarazu et al, 1996; Laurie and Bennett, 1986; Kynast et al, 2001; Li et al, 2017; Ishii et al, 2010; Maheshwari et al, 2015).…”