Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

Abstract

Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits.

Improved genetic resolution for linkage mapping of resistance to potato wart in monoparental dihaploids with potential diagnostic value in tetraploid potato varieties

“…In addition, 50 tetraploid potato cultivars were used to determine the diagnostic value of selected molecular markers developed in this study. The pollinations with the dihaploid inducers were performed in a greenhouse on emasculated `Karolin´ flowers (Bartkiewicz et al 2018 ). The seeds of the cross of `Karolin´ and S. phureja IVP35 were preselected based on the occurrence of an embryo spot.…”

“…The parental genotypes were genotyped with two repeats. Custom genotyping was performed by Neogene Genomics (Neogene Genomics, Lincoln, Nebraska, USA) and has been described previously in Bartkiewicz et al ( 2018 ). The SNP array results were validated using the following Kompetitive Allele Specific PCR (KASP) markers of the SNP markers that were most significantly linked to potato wart resistance: solcap_snp_c2_33740, solcap_snp_c2_33712, solcap_snp_c1_4319, solcap_snp_c1_4322, solcap_snp_c2_6082, solcap_snp_c2_6287, solcap_snp_c1_2275, solcap_snp_c2_6309 and solcap_snp_c2_6285.…”

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

“…Assessment of small introgressions is more challenging. Recent genotyping (Bartkiewicz et al 2018) or sequencing (Pham et al 2019) of other dihaploid potato populations found that ~1% of SNP loci displayed presence of HI DNA in very small tracts and with lower than expected allelic ratio. As in these reports, we detected many, widely dispersed SNP represented by proportionally fewer aligned reads than expected for addition of a haploid inducer DNA segment, or alternatively, replacement of a non-HI haplotype by homologous recombination.…”

“…In potato ( Solanum tuberosum L.), the world's fourth most important crop in terms of calories consumed per person per day ( http://www.fao.org/faostat/en/#compare ), haploid seed can be routinely obtained via pollination with select haploid inducer varieties from the diploid S. tuberosum Andigenum Group (formerly S. tuberosum Phureja Group or S. phureja (Spooner et al 2014) . Such crosses with tetraploid potato (2n=4x=48) produce 2 n =2 x =24 dihaploids that can be used for genetic mapping (Kotch et al 1992;Pineda et al 1993;Ercolano et al 2004;Velásquez et al 2007;Mihovilovich et al 2014;Bartkiewicz et al 2018) . Additionally, these crosses produce hybrids that can be either triploid or tetraploid (Wagenvoort and Lange 1975;Hanneman and Ruhde 1978) , and can be identified as seed because they express a purple embryo spot, a dominant anthocyanin marker encoded by the haploid inducers that is expected to be absent in the dihaploids (Fig.1) (Hermsen and Verdenius 1973a) .…”

“…Recently, widespread and ubiquitous introgression of very short DNA regions (>100bp) from the haploid inducer genome into potato dihaploids has been reported by SNP genotyping (Bartkiewicz et al 2018) and by whole genome sequencing (Pham et al 2019) . In the latter case, depending on the progeny, 25,000 to 300,000 translocation events were inferred, suggesting a massive contribution from the transient haploid inducer genome to the maternally contributed genome.…”