Structural genome analysis in cultivated potato taxa

Maria Kyriakidou, Sai Reddy Achakkagari, José Héctor Gálvez López, Xinyi Zhu, Chen Yu Tang, Helen H. Tai, Noelle L. Anglin, David Ellis & Martina V. Strömvik

Theoretical and Applied Genetics March 2020, volume 133: 951–966

Key message

Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes.

Abstract

The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

See https://link.springer.com/article/10.1007/s00122-019-03519-6

Figure 2: Summary of the total number of small variants (SNPs, indels) identified in 13 potato genomes in intergenic, exonic and intronic regions compared to the a DM1-3 and b M6 reference genomes. Overall, more SNPs are present in the intergenic regions of the landrace genomes compared with the both reference genomes (DM1-3 on the left and M6 on the right of the figure). Not surprisingly, there are fewest SNPs in exonic regions, and most SNPs are found in the intergenic regions.