SSR analysis of modern Russian potato varieties using DNA samples of nomenclatural standards

Abstract

The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) is developing new approaches to documentation of national cultivars, taking into account recommendations of the International Code of Nomenclature for Cultivated Plants in parallel with methods of genetic certification. The nomenclatural standard of a particular cultivar represented by a herbarium specimen can be used as a reference for verifying authenticity and uniformity of cultivar specimens obtained from various sources. The verification requires fast and reliable methods for cultivar genotyping. This paper presents protocols for modified methods of DNA extraction, PCR-analysis and SSR-genotyping, which allow potato cultivars identification without the use of expensive reagent kits. A set of ten chromosome-specific microsatellite markers was used to study polymorphisms in 66 modern Russian potato cultivars, as well as in 11 pre-cultivars and breeding clones, represented by nomenclatural standards and voucher specimens, respectively. This subset of 77 specimens has demonstrated a high level of polymorphism in ten studied microsatellite loci. The SSR analysis identified 73 alleles; 7.3 alleles per locus were observed on average, the number of which varied from 3 (STG0025 locus) to 11 (locus StI046). The PIC values varied from 0.544 (STG0025 locus) to 0.836 (StI046 locus). The alleles, unique for this subset, were found at six studied loci. The high level of polymorphism at the SSR loci made it possible to unambiguously identify almost every cultivar, with the exception of the expected coincidence of microsatellite profiles of two cultivars, which are somaclonal variants. Using an optimized set of eight microsatellite markers, the genetic relationships of modern Russian potato cultivars were studied.

Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile

“…Salimi et al (2016) used SSRs to determine allelic diversity within and among potatoes from different geographical regions and reported numerous alleles per locus, ranging from two (STM1049) to nine (STM1104), respectively, which is consistent with the present data, where STM1049 showed three alleles and STM1104 showed eight alleles. Antonova et al (2020) investigated the genetic diversity of potatoes using the set of alleles in the 14 examined SSR loci but indicated that with an increased number of the genotyped accessions, the resolving power of only these 14 SSR markers was not sufficient because of the low values of bootstrap coefficients. Duan et al (2019) used 16 parental cultivars widely used in breeding to screen 138 SSR markers, where 20 were polymorphic that were used to analyze the genetic diversity of 217 potato cultivars grown in China.…”

“…UPGMA dendrogram indicated that American genotypes exhibit higher expected heterozygosity than European genotypes, concluding that SSRs are appropriate markers for evaluating genetic diversity within and among potatoes from different geographical regions. Antonova et al (2020) found that a variety of potatoes from different countries were combined into mixed groups, probably indicating the intensive exchange of breeding material, using the set of alleles in the 14 examined SSR loci. Due to the increased number of the genotyped accessions, the resolving power of only these 14 SSR markers was not sufficient because of the low values of bootstrap coefficients.…”

A system of molecular markers to identify alleles of the Rht-B1 and Rht-D1 genes controlling reduced height in bread wheat

“…DNA extraction. DNA was extracted from 10-day-old seedlings using a modified CTAB extraction technique (Antonova et al, 2020).…”

Nomenclatural standards and genetic passports of potato cultivars bred by the Omsk Agrarian Research Center

“…В ВИР данное направление включает дополнительные молекулярно-генетические и биотехнологические подходы, с целью создания генетических паспортов образцов сортов, переданных их авторами в Гербарий ВИР, и сохранения генотипированных клонов в живом виде в контролируемых условиях in vitro и крио коллекций . Развитие данной комплексной стратегии уже привело к созданию более 60 Биотехнология и селекция растений 2022;5(4) номенклатурных стандартов и молекулярно-генетических паспортов российских сортов картофеля Antonova et al, 2020;Klimenko et al, 2020;Fomina et al, 2020a,b;Rybakov et al, 2020). (Fomina et al, 2020a;Rybakov et al, 2020), то же относится к условиям ПЦР и контрольным образцам для проведения молекулярного скрининга и SSR-анализа (Antonova et al, 2020;Klimenko et al, 2020;Rybakov et al, 2020) (см.…”

“…Развитие данной комплексной стратегии уже привело к созданию более 60 Биотехнология и селекция растений 2022;5(4) номенклатурных стандартов и молекулярно-генетических паспортов российских сортов картофеля Antonova et al, 2020;Klimenko et al, 2020;Fomina et al, 2020a,b;Rybakov et al, 2020). (Fomina et al, 2020a;Rybakov et al, 2020), то же относится к условиям ПЦР и контрольным образцам для проведения молекулярного скрининга и SSR-анализа (Antonova et al, 2020;Klimenko et al, 2020;Rybakov et al, 2020) (см. Приложение 1/ Supplement 1).…”