NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species

Abstract

The long history of potato breeding includes the numerous introgressions of resistance genes from many wild species of South and Central America as well as from cultivated species into the breeding genepool. Most R genes belong to the NLR family with nucleotide-binding site–leucine-rich repeat. The aim of this research concerns an evaluation of NLR genes expression in transcriptomes of three potato cultivars (Evraziya, Siverskij, Sudarynya), which combine genetic material from wild and cultivated potato species, and each bears intragenic markers of RB/Rpi-blb1/Rpi-sto1 genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the Phytophthora infestans inoculation. The induction of RB/Rpi-blb1/Rpi-sto1 transcript after 24 h of inoculation was detected in the resistant cultivars Siverskij and Sudarynya but not in susceptible cv. Evraziya. This demonstrates the importance of transcriptomic assay for understanding the results of marker-assisted selection and phenotyping. Interestingly, assembling the transcriptomes de novo and analysis with NLR-parser tool revealed significant fractions of novel NLR genes with no homology to the reference genome from 103 (cv. Siverskij) to 160 (S. stoloniferum, 30514/15). Comparison of novel NLRs demonstrated a relatively small intersection between the genotypes that coincided with their complex pedigrees with several interspecific hybridization events. These novel NLRs may facilitate the discovery of new efficient R genes.

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

“…Clearly, they represent variable parts of the NBS-LRR proteins in Russian potato cultivars and their fraction is quite large (~60%). This may indicate that potato accessions contain a diverse pool of R -genes, a significant proportion of which are unique to specific genomes, which is consistent with our results obtained earlier [ 34 ].…”

“…First of all, these are plant immune response genes containing NB-ARC, LRR, and TIR domains (clusters 1,5,10). This is not surprising since immune response receptors in potatoes show a high level of diversity [ 19 , 34 , 35 , 45 ], which is also consistent with the results of the NBS-LRR sequence analysis ( Table 4 ). A specific set of combinations of genes of resistance to particular pathogens could have been formed during the selection of these cultivars.…”

“…The diversity of immune response genes in potatoes is the basis for the development of new improved cultivars resistant to biotic stresses [ 31 , 32 , 33 ]. Reconstruction of potato genomes and transcriptomes reveals sequences encoding R -genes for further study [ 34 , 35 ]. The average number of complete NBS-LRR proteins in Russian potato cultivar genomes is ~230.…”

“…The average number of complete NBS-LRR proteins in Russian potato cultivar genomes is ~230. Note that in the DM1-3 genome, 257 NBS-LRR genes were identified [ 34 , 36 ]. Estimates of the number of NBS domains alone for several dozen potato cultivars based on nucleotide marker alignment are about twice that number, 575–590 [ 35 ].…”

Influence of environmental conditions on the duration of ontogenesis phases in wheat-rye 5R(5A) substituted lines

“…The work was funded by the Kurchatov Genome Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, agreement with the Ministry of Education and Science of the Russian Federation, no. 075-15-2019-1662.The main publications of authors on the subject of the abstract:Vasiliev, G.V. ;Toshchakov, S.V.…”