NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species
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...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Agronomy |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4395/11/12/2426 |
| _version_ | 1797506981998624768 |
|---|---|
| author | Alex V. Kochetov Dmitry A. Afonnikov Nikolay Shmakov Gennady V. Vasiliev Olga Y. Antonova Natalja V. Shatskaya Anastasiya Y. Glagoleva Salmaz M. Ibragimova Aleksander Khiutti Olga S. Afanasenko Tatjana A. Gavrilenko |
| author_facet | Alex V. Kochetov Dmitry A. Afonnikov Nikolay Shmakov Gennady V. Vasiliev Olga Y. Antonova Natalja V. Shatskaya Anastasiya Y. Glagoleva Salmaz M. Ibragimova Aleksander Khiutti Olga S. Afanasenko Tatjana A. Gavrilenko |
| author_sort | Alex V. Kochetov |
| collection | DOAJ |
| description | 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 <i>RB/Rpi-blb1/Rpi-sto1</i> genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the <i>Phytophthora infestans</i> 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 (<i>S. stoloniferum,</i> 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. |
| first_indexed | 2024-03-10T04:40:12Z |
| format | Article |
| id | doaj.art-14e3b9c233bd437aa439e812247ec92e |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T04:40:12Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-14e3b9c233bd437aa439e812247ec92e2023-11-23T03:21:41ZengMDPI AGAgronomy2073-43952021-11-011112242610.3390/agronomy11122426NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum SpeciesAlex V. Kochetov0Dmitry A. Afonnikov1Nikolay Shmakov2Gennady V. Vasiliev3Olga Y. Antonova4Natalja V. Shatskaya5Anastasiya Y. Glagoleva6Salmaz M. Ibragimova7Aleksander Khiutti8Olga S. Afanasenko9Tatjana A. Gavrilenko10Institute of Cytology & Genetics, 630090 Novosibirsk, RussiaInstitute of Cytology & Genetics, 630090 Novosibirsk, RussiaInstitute of Cytology & Genetics, 630090 Novosibirsk, RussiaInstitute of Cytology & Genetics, 630090 Novosibirsk, RussiaN.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, RussiaInstitute of Cytology & Genetics, 630090 Novosibirsk, RussiaInstitute of Cytology & Genetics, 630090 Novosibirsk, RussiaInstitute of Cytology & Genetics, 630090 Novosibirsk, RussiaAll Russian Institute of Plant Protection, 196608 Saint Petersburg, RussiaAll Russian Institute of Plant Protection, 196608 Saint Petersburg, RussiaN.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, RussiaThe 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 <i>RB/Rpi-blb1/Rpi-sto1</i> genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the <i>Phytophthora infestans</i> 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 (<i>S. stoloniferum,</i> 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.https://www.mdpi.com/2073-4395/11/12/2426potato cultivarsNLR genes<i>P. infestans</i>novel genesintrogression |
| spellingShingle | Alex V. Kochetov Dmitry A. Afonnikov Nikolay Shmakov Gennady V. Vasiliev Olga Y. Antonova Natalja V. Shatskaya Anastasiya Y. Glagoleva Salmaz M. Ibragimova Aleksander Khiutti Olga S. Afanasenko Tatjana A. Gavrilenko NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species Agronomy potato cultivars NLR genes <i>P. infestans</i> novel genes introgression |
| title | NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species |
| title_full | NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species |
| title_fullStr | NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species |
| title_full_unstemmed | NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species |
| title_short | NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species |
| title_sort | nlr genes related transcript sets in potato cultivars bearing genetic material of wild mexican solanum species |
| topic | potato cultivars NLR genes <i>P. infestans</i> novel genes introgression |
| url | https://www.mdpi.com/2073-4395/11/12/2426 |
| work_keys_str_mv | AT alexvkochetov nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT dmitryaafonnikov nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT nikolayshmakov nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT gennadyvvasiliev nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT olgayantonova nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT nataljavshatskaya nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT anastasiyayglagoleva nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT salmazmibragimova nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT aleksanderkhiutti nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT olgasafanasenko nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies AT tatjanaagavrilenko nlrgenesrelatedtranscriptsetsinpotatocultivarsbearinggeneticmaterialofwildmexicansolanumspecies |