Genomic regions of Solanum tuberosum L. associated with the tuber eye depth
Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding pro...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2020-08-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/2708 |
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| author | I. V. Totsky I. V. Rozanova A. D. Safonova A. S. Batov Yu. A. Gureeva A. V. Kochetov E. K. Khlestkina |
| author_facet | I. V. Totsky I. V. Rozanova A. D. Safonova A. S. Batov Yu. A. Gureeva A. V. Kochetov E. K. Khlestkina |
| author_sort | I. V. Totsky |
| collection | DOAJ |
| description | Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth. |
| format | Article |
| id | doaj-art-cf6ba40f109946cdab68d7a1a9d01370 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2020-08-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-cf6ba40f109946cdab68d7a1a9d013702025-02-01T09:58:09ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592020-08-0124546547310.18699/VJ20.6381072Genomic regions of Solanum tuberosum L. associated with the tuber eye depthI. V. Totsky0I. V. Rozanova1A. D. Safonova2A. S. Batov3Yu. A. Gureeva4A. V. Kochetov5E. K. Khlestkina6Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Siberian Research Institute of Plant Production and Breeding – Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)Siberian Research Institute of Plant Production and Breeding – Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesSiberian Research Institute of Plant Production and Breeding – Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesSiberian Research Institute of Plant Production and Breeding – Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.https://vavilov.elpub.ru/jour/article/view/2708gwassnppotatoeye depth |
| spellingShingle | I. V. Totsky I. V. Rozanova A. D. Safonova A. S. Batov Yu. A. Gureeva A. V. Kochetov E. K. Khlestkina Genomic regions of Solanum tuberosum L. associated with the tuber eye depth Вавиловский журнал генетики и селекции gwas snp potato eye depth |
| title | Genomic regions of Solanum tuberosum L. associated with the tuber eye depth |
| title_full | Genomic regions of Solanum tuberosum L. associated with the tuber eye depth |
| title_fullStr | Genomic regions of Solanum tuberosum L. associated with the tuber eye depth |
| title_full_unstemmed | Genomic regions of Solanum tuberosum L. associated with the tuber eye depth |
| title_short | Genomic regions of Solanum tuberosum L. associated with the tuber eye depth |
| title_sort | genomic regions of solanum tuberosum l associated with the tuber eye depth |
| topic | gwas snp potato eye depth |
| url | https://vavilov.elpub.ru/jour/article/view/2708 |
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