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

DNA methylation in diploid inbred lines of potatoes and its possible role in the regulation of heterosis

Self-incompatible diploid potatoes were altered to self-compatible ones by a function of S-locus inhibitor gene and continued selfing generated highly homozygous inbreds. In this study, this process was investigated for the status of DNA methylation by a simple method using genomic DNA digested by methylation-sensitive restriction enzymes prior to RAPD analysis. We detected 31 methylation-sensitive RAPD bands, of which 11 were newly appeared in the selfed progenies, and 6 of them stably inherited to subsequent generations. Aberrant segregations and paternal- or atavism-like transmission were also found. Segregating methylation-sensitive bands in initial populations became fixed in the advanced selfed progenies by 75.0–93.8%, of which 41.7% were fixed to all present and 58.3% to all absent. Because DNA methylation is generally recognized to suppress gene expression as regulatory factors, homozygosity/heterozygosity of methylated DNA may be involved in inbreeding depression/heterosis

Genetic similarity analysis and identification of Indian potato cultivars by random amplified polymorphic DNAs*

1123-1128Random amplified polymorphic DNAs (RAPDs) were used to fingerprint eighteen commercial Indian potato cultivars. A total of seventy-four distinct DNA fragments (bands), ranging from 124 to 4074 bp, were amplified by using twelve random primers. Fifty-seven of these bands were polymorphic. Cuitivar specific DNA fingerprints were generated by two random decamer primers (OPA-03 and OPC-04). Pair-wise genetic similarity analysis on the basis of presence or absence of bands revealed a wide range of variability among the cultivars, thereby, suggesting a wide genetic base of Indian potato cultivars. Kinship relationship was not correlated with the similarity values. Kufri swam a, which has the wild species Solanum vernei in its pedigree, showed maximum genetic divergence from other cultivars. Similarly, kufri badshah and kufri alankar were also genetically distinct from other cultivars studied. Remaining fifteen cultivars were grouped in to two closely related clusters. Usefulness of RAPD analysis in identification of cultivars and genetic divergence among Indian cuitivars has been discussed

Genetics and cytogenetics of the potato

Tetraploid potato (Solanum tuberosum L.) is a genetically complex, polysomic tetraploid (2n = 4x = 48), highly heterozygous crop, which makes genetic research and utilization of potato wild relatives in breeding difficult. Notwithstanding, the potato reference genome, transcriptome, resequencing, and single nucleotide polymorphism (SNP) genotyping analysis provide new means for increasing the understanding of potato genetics and cytogenetics. An alternative approach based on the use of haploids (2n = 2x = 24) produced from tetraploid S. tuberosum along with available genomic tools have also provided means to get insights into natural mechanisms that take place within the genetic load and chromosomal architecture of tetraploid potatoes. This chapter gives an overview of potato genetic and cytogenetic research relevant to germplasm enhancement and breeding. The reader will encounter findings that open new doors to explore inbred line breeding in potato and strategic roads to access the diversity across the polyploid series of this crop’s genetic resources. The text includes classical concepts and explains the foundations of potato genetics and mechanisms underlying natural cytogenetics phenomena as well as their breeding applications. Hopefully, this chapter will encourage further research that will lead to successfully develop broad-based potato breeding populations and derive highly heterozygous cultivars that meet the demands of having a resilient crop addressing the threats brought by climate change