TY - JOUR

T1 - Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

AU - Karetnikov, Dmitry I

AU - Vasiliev, Gennady V

AU - Toshchakov, Stepan V

AU - Shmakov, Nikolay A

AU - Genaev, Mikhail A

AU - Nesterov, Mikhail A

AU - Ibragimova, Salmaz M

AU - Rybakov, Daniil A

AU - Gavrilenko, Tatjana A

AU - Salina, Elena A

AU - Patrushev, Maxim V

AU - Kochetov, Alex V

AU - Afonnikov, Dmitry A

N1 - Funding: This work was funded by the Kurchatov Genome Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, in agreement with the Ministry of Education and Science of the Russian Federation, no. 075-15-2019-1662. Acknowledgments The data analysis was performed using computational resources of the Novosibirsk State University High-Performance Computing Center and the “Bioinformatics” Joint Computational Center supported by the budget project № FWNR-2022-0020. Multiplication of the plant material was conducted in the Laboratory of Artificial Plant Growth of ICG SB RAS within the budgetary project FWNR-2022-0017.

PY - 2023/3/16

Y1 - 2023/3/16

N2 - 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.

AB - 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.

KW - POTATO

KW - SOLANUM TUBEROSUM L.

KW - BREEDING CULTIVARS

KW - GENOME STRUCTURAL VARIATION

KW - COPY NUMBER VARIATION

KW - POTATO DIVERSIFICATION

KW - GENOME ANNOTATION

KW - NBS-LRR GENES

KW - PHOTOPERIOD CONTROL

KW - PHYTOCHROME A

KW - POLY(ADP-RIBOSE) GLYCOHYDROLASE

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85151109799&origin=inward&txGid=05bead1bb270bcb0a38260bf6c590475

UR - https://elibrary.ru/item.asp?id=50478000

UR - https://www.mendeley.com/catalogue/903a98de-65f5-3396-87fa-26895f5f8d3e/

U2 - 10.3390/ijms24065713

DO - 10.3390/ijms24065713

M3 - Article

C2 - 36982787

VL - 24

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 6

M1 - 5713

ER -