Open-access Molecular-genetic and phenotypic evaluation of potato varieties and hybrids resistance from the germplasm of Kazakhstan to the golden potato cyst nematode

Avaliação molecular-genética e fenotípica da resistência ao nematoide de cisto dourado da batata em variedades e híbridos provenientes do germoplasma do Cazaquistão

Abstract

The golden potato cyst nematode, (GN), Globodera rostochiensis, is a major quarantine pest of potato. This study investigated the resistance of domestic and foreign potato varieties and breeding lines widely cultivated in Kazakhstan to GN. This was the first time that domestic varieties were evaluated using molecular and phenotypic methods. The Miras variety and the breeding lines KС-26, KС-24 and KС-37 were found to be the most valuable in terms of resistance, as was the Chinese variety Xisen 6 zoned in Kazakhstan. Foreign varieties Juwel, Secura, Colomba, Queen Anne, Lisana, Sanjava and Paroli also showed resistance to the pest. These genotypes represent a valuable source material for the breeding of potato varieties, resistant to G. rostochiensis.

The 57R molecular marker provided 91% diagnostic accuracy, with no false-positives and only 9% false-negative. The calculation of the Fechner sign correlation coefficient showed a strong positive correlation between phenotypic resistance and the 57R marker detection, confirming its high diagnostic value and suitability for marker-assisted selection.

Keywords:
Globodera rostochiensis; cultivar; breeding line; molecular marker; H1 gene

Resumo

O nematoide de cisto dourado da batata, Globodera rostochiensis, é uma importante praga quarentenária da batata. O estudo investigou a resistência de variedades nacionais e estrangeiras de batata, bem como linhagens amplamente cultivadas no Cazaquistão. As variedades nacionais foram avaliadas pela primeira vez por meio de métodos moleculares e fenotípicos. A variedade Miras e os híbridos KC-26, KC-24, KC-37 revelaram-se as mais promissoras em termos de resistência, junto com a variedade chinesa Xisen 6, zoneada para o Cazaquistão. As variedades estrangeiras Juwel, Secura, Colomba, Queen Anne, Lisana, Sanjava e Paroli também demonstraram resistência ao patógeno. Esses genótipos representam fonte valiosa de material genético para o melhoramento de variedades de batata resistentes aG. rostochiensis.

O marcador molecular 57R apresentou 91% de precisão diagnóstica, com 9% de resultados falso-negativos e nenhum resultado falso-positivo. O cálculo do coeficiente de correlação de sinais de Fechner evidenciou uma forte correlação positiva entre a resistência fenotípica e a detecção do marcador 57R, confirmando seu alto valor diagnóstico e adequação para a seleção assistida por marcadores.

Palavras-chave:
Globodera rostochiensis; cultivar; linhagem de melhoramento; marcador molecular; gene H1

1. Introduction

Potato (Solanum tuberosum L.) is one of the key agricultural crops, characterized by high yield, adaptability and versatility. It is widely cultivated by farmers in open fields, demonstrating high profitability. However, the crop is susceptible to many diseases of viral, fungal and bacterial origin, as well as damage by phytopathogenic nematodes. One of the most dangerous pests is the golden potato cyst nematode, Globodera rostochiensis, (Woll.) Behrens (Akhatov et al., 2013).

The yellow potato cyst nematode (golden nematode, GN) G. rostochiensis infects many plant species in the Solanaceae family. The main crops affected are potatoes and tomatoes (European and Mediterranean Plant Protection Organization (EPPO), n.d.). The GN originated in the Andean highlands in South America and was brought to Europe with potatoes. Currently, the pest has spread widely in many countries around the world. The main routes of spread of the nematode include infected seed potatoes, table potatoes and other plant parts, as well as the movement of contaminated soil on non-host plants such as seedlings and bulbs (EPPO, 2026).

The GN undergoes the following developmental stages: eggs, larvae (four larval stages) and adults. Females have a cyst stage (dead females with eggs and larvae). Cysts, depending on nutritional and developmental conditions, can contain 50 to 600 eggs with larvae. GN persists in the soil in the cyst stage which is filled with eggs and larvae (Dankvert et al., 2009). Damage to potatoes caused by GN begins to appear when the soil is infested with 1000 larvae per 100 cm3. When the density of GN larvae in the soil reaches 15 thousand per 100 cm3, potato crop losses reach 85-90% (Volovik et al., 1989). There are five pathotypes of GN (Ro1-Ro5), differing in their ability to reproduce on various species of affected plants. Currently, the level of distribution of the various GN pathotypes in Kazakhstan remains unknown.

GN is included on the list of quarantine pests in many countries. In Europe, it is included in the EPPO A2 list in countries such as: Russia, Ukraine, Switzerland, Serbia, Turkey, Georgia, Norway, Belarus and Azerbaijan. In Asia, the nematode is listed as A1 in Bahrain, Jordan and Uzbekistan, while China, Iran and Israel consider it as a quarantine pest or included in list A2 (EPPO, 2025). In Kazakhstan, GN is included in the A2 quarantine pest list that are limited in distribution within the republic (The Parliament of the Republic of Kazakhstan, 1999).

GN has been detected in a number of regions of Kazakhstan. In particular, its presence was recorded in the Almaty region (Raiymbek district), as well as in East Kazakhstan region, including the cities of Semey and Zyryanovsk, including the Bobrovka area (Kurmangozhin, 2018).

In 2016, cases of importation of infected products, infected with GN into the territory of Kazakhstan from the Kyrgyz Republic were recorded. In 2017, in the city of Uralsk (West Kazakhstan region), a consignment of 20 tons of potatoes was identified, which came from the Nizhny Novgorod region of the Russian Federation (Rakhmetova, 2017). According to phytosanitary control data, a total of 79 cases of importation of potatoes infected with GN were established (Informburo, 2024).

In accordance with the legislation of the Republic of Kazakhstan, quarantine-regulated products that have not passed phytosanitary control or are recognized as infected are not subject to movement and sale in the country (Akimat of Baiterek District, 2024). These factors indicate the presence of a potential phytosanitary risk when importing potatoes.

The current phytosanitary state in the Republic of Kazakhstan necessitates a comprehensive study of the resistance of potato germplasm cultivated in the country to GN.

Currently, one of the most effective methods of GN control is considered to be the cultivation of resistant varieties. The resistance of potato plants to GN (Ro1 pathotype) is determined by the presence of dominant alleles of the H1, GroVI and Gro1-4 genes in the genotype. The source of the H1 gene is the semi-cultural species Solanum tuberosum subsp. andigenum. The GroVI gene was obtained from the wild species Solanum vernei and the Gro1-4 gene was introduced from the wild species Solanum spegazzinii (Gebhardt et al., 2006). A number of molecular markers have been developed for the molecular identification of resistance genes. SCAR markers TG689, 57R (Biryukova et al., 2008; Schultz et al., 2012), as well as markers N146 and N195 are used to detect the H1 gene (Mori et al., 2011). To detect the Gro1-4 gene, the STS marker Gro1-4-1 is used (Asano et al., 2012), which makes it possible to effectively carry out marker-assisted selection of potato genotypes resistant to GN.

Therefore, we hypothesized that potato varieties and breeding lines cultivated in Kazakhstan differ in their level of resistance to G. rostochiensis pathotype Ro1, and that phenotypic resistance is associated with the presence of molecular markers linked to the H1 resistance gene. The specific objectives of this study were: i) to evaluate the phenotypic resistance of domestic (Kazakhstan germplasm) and introduced potato genotypes to G. rostochiensis (pathotype Ro1) under controlled infection conditions; ii) to screen these genotypes for the 57R and N195 molecular markers associated with the H1 gene; iii) to compare molecular-marker results with phenotypic resistance data; and iv) to identify resistant potato varieties and breeding lines that could be used as source material for breeding programs in Kazakhstan.

2. Materials and Methods

The molecular analyses were carried out in the Laboratory of Molecular Diagnostics of Phytopathogens and the Laboratory of Plant Biotechnology of the Institute of Agriculture and Forestry, NCJSC “S. Seifullin Kazakh Agrotechnical Research University” (S. Seifullin KATRU), Astana, Kazakhstan. Phenotypic assessment of resistance to Globodera rostochiensis pathotype Ro1 was performed at the A.G. Lorch Federal Potato Research Center.

The study included 12 potato varieties and 12 breeding lines, representing the potato germplasm of the Republic of Kazakhstan (Table 1). The potato samples were grown in the field collection of S. Seifullin Kazakh Agrotechnical Research University. In addition, 2 varieties developed in China were studied, as well as 7 European varieties commonly cultivated by potato growers in Kazakhstan.

Table 1
List of potato samples studied, origin and growing region (Agromart, 2026).

Phenotypic resistance of potato genotypes to the golden potato cyst nematode, G. rostochiensis, was evaluated in accordance with official protocols for testing new potato varieties (Mugniéry et al., 1989). The experiments were carried out in a specialized quarantine laboratory using an infested substrate containing a standard population of G. rostochiensis pathotype Ro1. Tubers of the tested genotypes were planted in plastic pots with a volume of 250–300 cm3. The susceptible potato cultivar Lorch was used as the reference control. Plants were grown at a soil temperature of 25 °C and soil moisture of 70–80%

The results were recorded 92 days after seedling emergence. The relative susceptibility of the tested potato variety compared to the susceptibility of the reference susceptible control variety was determined by the formula: Relative susceptibility (%) = (Pf of the tested genotype / Pf of the susceptible reference control) × 100.

The assay was considered valid only when the susceptible reference cultivar Lorch supported nematode reproduction with a multiplication factor of Pf/Pi ≥ 20, where Pi is the initial nematode abundance in the soil before planting and Pf is the final nematode abundance after completion of the experiment. This criterion confirmed normal development of the parasite and ensured the reliability of the resistance assessment. The resistance of potato samples to GN was evaluated on the appropriate scale (Mugniéry et al., 1989) (Table 2).

Table 2
Assessment scales of potato plants resistance to G. rostochiensis.

DNA was extracted from leaf tissue of potato plants using the FitoSorb kit (Synthol, Russia) in accordance with the manufacturer’s instructions. PCR was performed using MasterCycler Gradient amplifiers (Eppendorf, USA) and T100 thermal cyclers (Bio-Rad, USA). A 25 μL reaction mixture was prepared using OneTaq® Quick-Load® 2X Master Mix reagent (New England Biolabs, #M0486L), N195 and 57R marker-specific oligonucleotide primers at a final concentration of 0.5 pM/μL, and 100 ng of DNA template. The oligonucleotide primer sequences and PCR conditions used for amplification of the N195 and 57R markers are shown in Table 3. The amplification temperature profiles followed the published protocols of Gebhardt et al. (2006), Shanina et al. (2011), and Simko et al. (2007). The Lorch variety was used as a positive control for phenotypic assessment and as a negative control for PCR. The Courtney variety (Tatar Research Institute of Agriculture, Kazan, Russia) served as the positive control for PCR analysis of both molecular markers (Table 3). PCR analysis of each genotype-marker combination was performed in duplicate. Electrophoretic separation of the amplification products was performed on a 1.6% agarose gel containing ethidium bromide at 0.5 μg/mL in a Max HU10 horizontal electrophoresis chamber (Scie-Plas Ltd, UK) using a Consort EV 243 power supply. A 1× TAE buffer was used as the electrode buffer.

Table 3
Oligonucleotides and PCR regimens for the detection of molecular markers of the H1 gene.

The correlation between the results of molecular marker detection and the phenotypic resistance of potato samples to GN was determined by calculating the Fechner sign correlation coefficient using the following Formula 1:

C F = n a − n b / n a + n b (1)

where na – the number of coinciding sign pairs; nb – the number of opposite pairs (Ferster and Renz, 1983).

3. Results

Table 4 summarizes the results of phenotypic resistance assessment of potato genotypes to Globodera rostochiensis pathotype Ro1, together with the detection of the H1-linked molecular markers N195 and 57R.

Table 4
H1 gene molecular marker results and susceptibility level of potato samples to Globodera rostochiensis.

Phenotypic assessment revealed a very high level of resistance to G. rostochiensis pathotype Ro1 in 13 potato genotypes, corresponding to a resistance score of 9 and 0% relative susceptibility. These included five samples from the potato germplasm of Kazakhstan: the variety Miras and the breeding lines KC-26, KC-24, KC-37, and 17-204-2. A very high level of resistance was also detected in the Chinese variety Xisen 6 and confirmed in the European varieties Juwel, Secura, Colomba, Queen Anne, Paroli, Lisana, and Sanjava, all of which are cultivated by potato growers in Kazakhstan.

Overall, 13 of the 33 tested potato genotypes showed very high resistance, corresponding to 39% of the analyzed material. These genotypes are of interest as source material for breeding potato varieties resistant to the golden potato cyst nematode. Nineteen potato genotypes, corresponding to 57% of the tested material, were susceptible to G. rostochiensis pathotype Ro1. The breeding line KC-38 showed low relative susceptibility, 4%, and was assigned a resistance score of 7.

Representative examples of cyst formation on potato roots are shown in Figure 1. The susceptible reference cultivar Lorch showed abundant cyst formation and was used as the reference value corresponding to 100% relative susceptibility. In this cultivar, the multiplication factor of G. rostochiensis pathotype Ro1 exceeded the required threshold of Pf/Pi ≥ 20, confirming the validity of the phenotypic resistance assay. In comparison with Lorch, the relative susceptibility values were 88% for Adil and 41% for Babaev, corresponding to resistance scores of 2 and 3, respectively. In contrast, the Kazakhstan variety Miras showed no cyst formation under the test conditions and was assigned a resistance score of 9.

Figure 1
Representative examples of cyst formation during phenotypic assessment of potato resistance to Globodera rostochiensis pathotype Ro1. A – Adil; B – Babaev; C – Miras; D – Control variety Lorch.

Molecular marker analysis showed that, among the 33 tested potato genotypes, six carried both N195 and 57R markers and exhibited a very high level of phenotypic resistance, with a resistance score of 9 and 0% relative susceptibility. These genotypes were Colomba, Lisana, Sanjava, Xisen 6, KC-26, and KC-24. Thus, within the tested genotype set, the simultaneous presence of both markers was associated with very high phenotypic resistance to G. rostochiensis pathotype Ro1.

The positive PCR control cultivar Lorch was included in Table 4 as a control for H1-linked marker amplification but was not counted among the 33 tested potato genotypes and was excluded from the phenotypic resistance assessment and marker–phenotype correlation analysis. No H1-linked molecular markers were detected in Adil, Babaev, Vid-2, 15 seedling 7P41 × Dobro, Kostanayskie Novosti, Kiru, Mechta Krasavina, Xisen 3 and in the breeding line 17-212-19.

The molecular marker 57R was detected in 10 of the 13 genotypes with very high resistance to G. rostochiensis pathotype Ro1, corresponding to 77% of the resistant group. However, this marker was not detected in three highly resistant genotypes, corresponding to 23% of the resistant group. Based on the comparison between molecular and phenotypic data, the 57R marker showed 91% correct results, 9% false-negative results, and no false-positive results. The 57R marker was detected in the resistant Kazakhstan variety Miras, the breeding line 17-204-2, and the European varieties Juwel and Paroli, whereas the N195 marker was not detected in these genotypes.

The molecular marker N195 was detected in 9 of the 13 genotypes with very high resistance to G. rostochiensis pathotype Ro1, corresponding to 69% of the resistant group. Based on the comparison between molecular and phenotypic data, this marker showed 55% correct results, 12% false-negative, and 33% false-positive.

The correspondence between molecular marker detection and phenotypic resistance was assessed using the Fechner sign correlation coefficient (Table 5). The 57R marker showed a strong positive association with phenotypic resistance, with CF = +0.82, whereas the N195 marker showed weak agreement with phenotypic resistance, with CF = −0.09. Therefore, the 57R marker was the most effective molecular marker for diagnosing H1-linked resistance to G. rostochiensis pathotype Ro1 in the tested potato germplasm. However, the N195 marker also had diagnostic value, as it was detected in three highly resistant genotypes, Secura, Queen Anne, and KC-37, in which the 57R marker was absent.

Table 5
Correspondence between the results of molecular testing and the phenotypic resistance of potato samples to Globodera rostochiensis.

4. Discussion

GN poses a serious economic threat to potato production. Therefore, the study of host resistance is highly relevant for breeding, varietal selection, and especially seed potato production.

Resistance to GN is most often monogenic and is due to the presence of H1 or Gro1-4 genes, which are localized on chromosomes V and VII, respectively. Nematode-resistant varieties developed by breeders in different countries mainly carry the H1 gene (Schultz et al., 2012). Earlier studies by Totsky et al. (2021) showed a high frequency of genotypes with the SCAR marker 57R associated with the H1 gene, which determines resistance to the Ro1 pathotype of G. rostochiensis. The data obtained in our study fully support these observations.

DNA marker methods have been successfully used in breeding centers to assess the genetic protection of the potato gene pool against GN. Our data confirm the high diagnostic value of the 57R marker in the identification of genotypes resistant to GN. However, the absence of the 57R marker in three highly resistant genotypes Secura, (Queen Anne), and KC-37 may indicate possible limitations of marker-based diagnostics and supports the importance of integrated phenotypic and molecular evaluation. The presence of both molecular markers (57R and N195) in highly resistant genotypes suggests a more reliable genetic background for resistance and may be considered a valuable criterion for marker-assisted selection. The Colomba variety, studied in Portugal, showed resistance to GN, which is consistent with the results of our studies (Camacho et al., 2020). In the present study, the European varieties Juwel, Paroli, Secura and Queen Anne also demonstrated a very high level of resistance to G. rostochiensis pathotype Ro1, with 0% relative susceptibility and a resistance score of 9. In addition, the variety catalogs contain information on the presence of resistance to GN in the varieties Lisana and Sanjava (DIRECT.FARM, 2025; PotatoPRO, 2025).

Of particular importance is the analysis of the consistency between the results of molecular analysis and the phenotypic assessment of resistance to GN. In previous studies by Biryukova et al. (2017), cases of false positive and false negative results were noted. The authors found that the degree of agreement between molecular and phenotypic data for H1 gene markers was: 96% for 57R , 91% for N146 , 90% for N195 , and 64% for TG689 markers. These data support the high diagnostic value of the 57R marker and the need for a comprehensive assessment of resistance, taking into account both molecular and phenotypic indicators. Our results are entirely consistent with these observations.

Varieties and breeding lines of the potato gene pool of Kazakhstan were first evaluated for resistance to GN. In the Kazakhstan variety Miras, the Chinese variety Xisen 6, as well as in the breeding lines KC-26, KC-24 and 17-204-2, a very high level of resistance to GN was accompanied by the presence of the molecular marker 57R in the genotype of these samples. The same pattern was observed in the European potato varieties: Juwel, Secura, Colomba, Lisana, Sanjava, and Paroli. However, in the European variety Queen Anne and the KC-37 breeding line, a very high level of resistance to GN was accompanied only by the presence of the molecular marker N195. Thus, the findings highlight the importance of using an integrated approach in potato selection that combines molecular and phenotypic methods for assessing resistance to GN.

5. Conclusion

In this study, potato germplasm from Kazakhstan was evaluated for resistance to GN at both the molecular and phenotypic levels. Of the 12 Kazakhstani varieties studied, only Miras showed a high level of resistance to GN, accounting for 8% of the varieties examined. Of the 12 breeding lines, four lines (33.3%) - KC-24, KC-26, KC-37, and 17-204-2 - showed high resistance. A very high level of resistance was identified for the Chinese variety Xisen 6 for the first time, and was also confirmed for the European varieties: Juwel, Secura, Colomba, Queen Anne, Lisana, Sanjava, and Paroli. Resistance in these genotypes was associated with the H1 gene, as confirmed by the detection of the 57R and N195 molecular markers. Genotypes carrying both molecular markers demonstrated the highest resistance level (score 9), indicating a more reliable genetic basis for resistance. These genotypes represent valuable source material for breeding programs aimed at developing potato varieties resistant to GN. Cultivation of genetically resistant varieties is currently considered the most effective and sustainable strategy for controlling this quarantine pest.

Acknowledgements

This research was funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan under project AP22685460 “Justification of correlated inheritance of resistance genes in promising potato varieties and hybrids to the main viruses and quarantine pests”.

Data Availability Statement

Data available upon request from corresponding author.

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Editor:

Takako Matsumura Tundisi

Publication Dates

  • Publication in this collection
    18 Sept 2026
  • Date of issue
    2026

History

  • Received
    10 Apr 2026
  • Accepted
    17 July 2026
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This is an Open Access article distributed under the terms of the Creative Commons Attribution license (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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