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

V V Zheltova,N S Klimenko,O Yu Antonova,D A Rybakov,L Yu Novikova,T A Gavrilenko,N A Fomina

doi:10.30901/2658-6266-2020-4-o2

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.

Highlights

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
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
Что для SSR-генотипирования отечественных сортов были использованы разные технологии разделения SSR-фрагментов – электрофорез в проточном полиакриламидном геле на секвенаторе Li-Cor (Shvachko, 2012; Antonova et al, 2016; Klimenko et аl., 2020; Fomina et al, 2020 (a); Rybakov et al, в этом выпуске; Fomina et al (b), в этом выпуске) и капиллярный электрофорез (Kolobova et al, 2017; Shanina, Klyukina, 2018; Potato cultivars, 2018)

Summary

Introduction

5. Аллельный полиморфизм российских сортов картофеля по ядерному SSR-локусу StI046 1) ‘Нальчикский’; 2) ‘Любава’; 3) ‘Сиреневый туман’; 4) ‘Златка’; 5) ‘Лина’; 6) ‘Сафо’; 7) ‘Юна’; 8) ‘Солнечный’; 9) ‘Арлекин’; 10) ‘Крепыш’; 11) ‘Любава’; 12) ‘Накра’; 13) ‘Вымпел’; 14) ‘Ильинский’; 15) ‘Колобок’; 16) ‘Василек’; 17) ‘Гулливер’; 18) ‘Люкс’; 19) ‘Старт’; 20) ‘Браво’; 21) ‘Ирбитский’; 22) ‘Самба’; 23) ‘Матушка’; 24) ‘Русский сувенир’; 25) ‘Арлекин’; 26) ‘Бабушка’; 27) ‘Танго’; 28) ‘Фрителла’; М – маркер молекулярного веса.

Results

Conclusion