NLR genes related transcript sets in potato cultivars bearing genetic material of wild Mexican solanum species

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In: Agronomy, Vol. 11, No. 12, 2426, 12.2021.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{b559a15f357a469896068c4537d33f1e,

title = "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.",

keywords = "Introgression, NLR genes, Novel genes, P. infestans, Potato cultivars",

author = "Kochetov, {Alex V.} and Afonnikov, {Dmitry A.} and Nikolay Shmakov and Vasiliev, {Gennady V.} and Antonova, {Olga Y.} and Shatskaya, {Natalja V.} and Glagoleva, {Anastasiya Y.} and Ibragimova, {Salmaz M.} and Aleksander Khiutti and Afanasenko, {Olga S.} and Gavrilenko, {Tatjana A.}",

note = "The research was supported by Kurchatov Genomics Center of IC&G (Agreement with Ministry of Science and Higher Education RF 075-15-2019-1662) in the frame of potato pangenome and pantranscriptome sequencing and bioinformatics analysis. NGS sequencing was conducted in the ICG Joint Center for Genome Studies (supported in the frame of ICG budget project 0259-2021-0012). The computational data analysis was conducted using the resources of the ICG Bioinformatics Joint Computational Center. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2021",

month = dec,

doi = "10.3390/agronomy11122426",

language = "English",

volume = "11",

journal = "Agronomy",

issn = "2073-4395",

publisher = "MDPI AG",

number = "12",

}

RIS

TY - JOUR

T1 - NLR genes related transcript sets in potato cultivars bearing genetic material of wild Mexican solanum species

AU - Kochetov, Alex V.

AU - Afonnikov, Dmitry A.

AU - Shmakov, Nikolay

AU - Vasiliev, Gennady V.

AU - Antonova, Olga Y.

AU - Shatskaya, Natalja V.

AU - Glagoleva, Anastasiya Y.

AU - Ibragimova, Salmaz M.

AU - Khiutti, Aleksander

AU - Afanasenko, Olga S.

AU - Gavrilenko, Tatjana A.

N1 - The research was supported by Kurchatov Genomics Center of IC&G (Agreement with Ministry of Science and Higher Education RF 075-15-2019-1662) in the frame of potato pangenome and pantranscriptome sequencing and bioinformatics analysis. NGS sequencing was conducted in the ICG Joint Center for Genome Studies (supported in the frame of ICG budget project 0259-2021-0012). The computational data analysis was conducted using the resources of the ICG Bioinformatics Joint Computational Center. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2021/12

Y1 - 2021/12

N2 - 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.

AB - 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.

KW - Introgression

KW - NLR genes

KW - Novel genes

KW - P. infestans

KW - Potato cultivars

UR - http://www.scopus.com/inward/record.url?scp=85121736578&partnerID=8YFLogxK

U2 - 10.3390/agronomy11122426

DO - 10.3390/agronomy11122426

M3 - Article

AN - SCOPUS:85121736578

VL - 11

JO - Agronomy

JF - Agronomy

SN - 2073-4395

IS - 12

M1 - 2426

ER -

ID: 35203770