Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Abstract

Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.

Assembly and Analysis of Plastomes for 15 Potato Cultivars Grown in Russia

“…We used libraries of raw reads of 15 potato cultivars grown in Russia from previous work [22]: Golubizna, Krepysh, Nevsky, Meteor, Zhukovsky, Severnoe siyanie, Krasa Meshchery, Fritella, Udacha, Krasavchik, Grand, Sudarinya, Gusar, Nikulinsky and Symphonia. The dataset includes 14 cultivars developed by different Russian breeding programs and one Dutch cultivar (Symphonia).…”

“…The dataset includes 14 cultivars developed by different Russian breeding programs and one Dutch cultivar (Symphonia). These varieties demonstrate very broad ecological plasticity [22]. Some cultivars (Nevsky, Zhukovsky, Udacha) have been approved for 12, 10 and 9 regions of the Russian Federation, respectively (relating to the contrasting light zones).…”

“…Some cultivars (Krasavchik, Severnoe Siyanie and the Dutch variety Symphonia) are approved for only one region of the Russian Federation. Since the number of narrow adaptive varieties in the study was small, we included Symphonia in the analysis as well [22].…”

“…To evaluate genetic diversity between plastomes of the Russian potato cultivars [22] and potato cultivars of the Ural selection [23], as well as South American accessions [7] and European/North American cultivars [24], we performed phylogenetic tree reconstruction using the IQ-TREE with automatic model selection [36] based on cpDNA multiple sequence alignment. The inverted repeat region (IRb) was removed in the multiple alignment to avoid duplication.…”

“…In the present work, we reconstructed the full plastome sequences of 15 potato cultivars grown in Russia using short-paired reads we obtained earlier [22]. We annotated the chloroplast genomes, identified single-nucleotide polymorphisms and InDels, and assessed the variability of the cpDNA.…”