Self‐Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single‐Nucleotide Polymorphism Array

Abstract

Within a population of F 1 hybrids between two genotypes (S. tuberosum L. Group Phureja DM 1-3 516 R44 [DM] and S. tuberosum L. Group Tuberosum RH89-039-16 [RH]) used in the potato genome sequencing project, we observed fruit set after self-pollination on many plants. Examination of pollen tube growth in self-fertile and self-unfruitful F 1 plants after controlled selfpollinations revealed no difference in the ability of pollen tubes to reach the ovary. To identify genomic regions linked with selffertility, we genotyped the F 1 population using a genome-wide single-nucleotide polymorphism (SNP) array. Polymorphic and robust SNPs were analyzed to identify allelic states segregating with the self-fertile phenotype. All 88 highly significant SNPs occurred on chromosome 12. Seeds obtained after self-pollination of self-fertile individuals were used to advance the population for four generations. Genotyping 46 self-fruitful and 46 self-unfruitful S 3 plants on the Infinium 8303 Potato SNP array revealed eight SNPs segregating with self-fertility on chromosomes 4, 9, 11, and 12. Three times more heterozygosity than expected was found in the S 3 generation. Estimates of heterozygosity were influenced by copy number variation (CNV) in the potato genome leading to spurious heterozygous genotyping calls. Some spurious heterozygosity could be removed by application of a CNV filter developed from alignment of additional monoploid potato genomic sequence to the DM reference genome. The genes responsible for fruit set in self-fertile plants in the F 1 generation were restricted to chromosome 12, whereas new genomic regions contributed to the ability of S 3 plants to set fruit after self-pollination.

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation

“…tuberosum Group Phureja DM1-3 516 R44, and a heterozygous diploid breeding line, S . tuberosum Group Tuberosum RH89-039-16, was used in this study for transformation [ 23 ]. Tissue culture plants were propagated from shoot tip and axillary bud explants and grown in Murashige and Skoog (MS) medium (PhytoTechnology Laboratories, Shawnee Mission, KS) and 3% sucrose (Sigma-Aldrich, St. Louis, MO) in Magenta G3 boxes (Magenta Corp., Chicago, IL) on fluorescent light racks set to 16 h light:8 h dark with a temperature of 25°C (light) and 18°C (dark) and a light intensity of 300 μmol m −2 s −1 .…”

Development of pre-breeding diploid potato germplasm displaying wide phenotypic variations as induced by ethyl methane sulfonate mutagenesis

“…In contrast to tetraploid cultivated potatoes (2n = 4x = 48), diploid potato species (2n = 2x = 24) have small and less complex genomes, making their genetic studies more attractive. Thus, although self-incompatibility and inbreeding depression are common issues encountered in diploids (Peterson et al 2016), the use of diploids in potato breeding has become a promising alternative and undesirable traits, if present, can be easily removed through the selfpollination of self-compatible germplasm, unlike tetraploids (Li et al 2013). Therefore, the development and maintenance of a diverse pre-breeding diploid potato germplasm is seen as a vital resource for fast and effective potato breeding.…”

Characterization of the F Locus Responsible for Floral Anthocyanin Production in Potato

“…The approximate 1:1 ratio and complete penetrance of the flower color phenotype indicated a single gene segregating from the heterozygous purpleflowered RH was the likely cause. Analysis of previously generated genotype data for this population (Peterson et al 2016) identified SNPs significantly linked to the phenotype on the distal end of chromosome 10 ( Figure 2). This finding is consistent with previous literature regarding the F locus for flower color (van Eck et al 1993) which mapped the locus to the same approximate position using restriction fragment length polymorphism analysis.…”