Segregation and efficacy of the cry1Ia1 gene for control of potato tuberworm in four populations of cultivated potato.

The potato (Solanum tuberosum L.) cultivar 'SpuntaG2' contains a single copy of the Bacillus thuringiensis (Bt) cry1Ia1 gene and controls potato tuberworm (Phthorimaea operculella Zeller, Lepidoptera: Gelechiidae). Two potato cultivars and two breeding lines were crossed with SpuntaG2 creating four populations used to study cry1Ia1 segregation and efficacy. The cry1Ia1 gene segregated in each of the four populations with a 1:1 ratio. All progeny that were polymerase chain reaction positive for the cry1Ia1 gene had no surviving larvae and no leaf mining in detached leaf assays after 72 h. These results support previous evidence that SpuntaG2 carries a single copy of the cry1Ia1 gene and that transmission of the transgene from parent to progeny is not restricted and follows expected Mendelian segregation ratios. Based on detached leaf assays, the efficacy of the cry1Ia1 gene is retained through sexual transmission. If the SpuntaG2 cry1Ia1 insertion event is deregulated for commercial use, SpuntaG2 could be used for conventional breeding and the progeny carrying the SpuntaG2 event would also be available for commercial use.

Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries.

Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.

Integration of two diploid potato linkage maps with the potato genome sequence.

To facilitate genome-guided breeding in potato, we developed an 8303 Single Nucleotide Polymorphism (SNP) marker array using potato genome and transcriptome resources. To validate the Infinium 8303 Potato Array, we developed linkage maps from two diploid populations (DRH and D84) and compared these maps with the assembled potato genome sequence. Both populations used the doubled monoploid reference genotype DM1-3 516 R44 as the female parent but had different heterozygous diploid male parents (RH89-039-16 and 84SD22). Over 4,400 markers were mapped (1,960 in DRH and 2,454 in D84, 787 in common) resulting in map sizes of 965 (DRH) and 792 (D84) cM, covering 87% (DRH) and 88% (D84) of genome sequence length. Of the mapped markers, 33.5% were in candidate genes selected for the array, 4.5% were markers from existing genetic maps, and 61% were selected based on distribution across the genome. Markers with distorted segregation ratios occurred in blocks in both linkage maps, accounting for 4% (DRH) and 9% (D84) of mapped markers. Markers with distorted segregation ratios were unique to each population with blocks on chromosomes 9 and 12 in DRH and 3, 4, 6 and 8 in D84. Chromosome assignment of markers based on linkage mapping differed from sequence alignment with the Potato Genome Sequencing Consortium (PGSC) pseudomolecules for 1% of the mapped markers with some disconcordant markers attributable to paralogs. In total, 126 (DRH) and 226 (D84) mapped markers were not anchored to the pseudomolecules and provide new scaffold anchoring data to improve the potato genome assembly. The high degree of concordance between the linkage maps and the pseudomolecules demonstrates both the quality of the potato genome sequence and the functionality of the Infinium 8303 Potato Array. The broad genome coverage of the Infinium 8303 Potato Array compared to other marker sets will enable numerous downstream applications.