DNA Fingerprinting and Genetic Diversity Analysis with Simple Sequence Repeat Markers of 217 Potato Cultivars (Solanum tuberosum L.) in China

Abstract

Since 1950, more than 620 potato cultivars have been released from Chinese breeding programs, some of which have similar genetic background and phenotype. In this study, 16 parental cultivars widely used in breeding were used to screen 138 simple sequence repeat (SSR) markers. Out of 138 SSR markers, 20 were polymorphic that were used to analyze the genetic diversity of 217 potato cultivars grown in China. In total, 249 alleles were detected with these 20 markers and 244 of them (97.99%) showed polymorphism. The number of alleles ranged from 7 to 22 with an average of 12.45 alleles per primer and polymorphic information content (PIC) ranged from 0.64-0.93 with an average of 0.83. Fragment sizes varied from 80 to 380 bp. Based on PIC values and the clarity of PCR amplification bands, 11 SSR markers were selected and able to differentiate all of the 217 cultivars. The estimated similarity using these polymorphic SSR markers between the cultivars ranged from 0.63 to 0.99, indicating a narrow genetic base. Fingerprinting and genetic diversity analysis in this study provides useful information for the protection of intellectual property, as well as the exploration and utilization of these potato cultivars. Resumen Desde 1950, se han liberado más de 620 variedades de papa de los programas chinos de mejoramiento, algunos de los cuales tienen antecedentes genéticos y fenotipo similares. En este estudio, se usaron 16 variedades parentales utilizadas ampliamente en mejoramiento, para hacer un estudio de 138 marcadores de repeticiones simples de secuencia (SSR). De los 138 marcadores SSR, 20 fueron polimórficos que fueron usados para analizar la diversidad genética de 217 variedades de papa cultivadas en China. En total, se detectaron 249 alelos con estos 20 marcadores y 244 de ellos (97.99%) mostraron polimorfismo. El número de alelos tuvo un rango de 7-22 con un promedio de 12.45 alelos por iniciador, y el contenido de la información polimórfica (PIC) varió de 0.64-0.93 con un promedio de 0.83. Los tamaños de los fragmentos variaron de 80-380 pb. Con base en los valores PIC y la claridad de las bandas de amplificación, se seleccionaron 11 marcadores SSR y fue posible diferenciar a la totalidad de las 217 variedades. La similitud estimada usando estos marcadores polimórficos SSR entre las variedades varió de 0.63 a 0.99, indicando una base genética angosta. Los análisis de huellas y diversidad genética en este estudio proporcionan información útil para la protección de propiedad intelectual, así como para la exploración y utilización de estas variedades de papa.

Collection and Evaluation of Genetic Diversity and Population Structure of Potato Landraces and Varieties in China

“…Previous efforts to explore the genetic diversity in Chinese potato germplasm as done by Duan et al (2018), focused on local and foreign cultivars. The genetic diversity of Chinese potato landraces has not been reported previously.…”

“…Molecular markers have been used to explore the population structure and genetic diversity of various crops. Peculiarly in potato, the marker-assisted selection (Ghislain et al, 1999), high-resolution mapping (Meksem et al, 1995), fingerprinting for intellectual property rights claims (McGregor et al, 2000; Duan et al, 2018) genetic diversity (Hoque et al, 2013; Siddappa et al, 2014; Onamu et al, 2016) and phylogenetic studies (Spooner et al, 2005a) were based on AFLP, RFLP, RAPD, and SSR markers. Among molecular marker types, in present research, SSRs were often selected for their high polymorphism level and reproducibility.…”

“…In China, the predominant potato cultivars were developed by manipulation of European tetraploid genotypes from 1950 to 1960 (Jian et al, 2017). Among the 288 cultivars released in China during 1950–2007, 34.7% (100), 32.3% (93), 18.4% (53) cultivars were derived from American, German and Polish genotypes, respectively, the remainder arose from CIP and Dutch cultivars (Duan et al, 2018). The use of a limited number of parental genotypes may have resulted in the narrow genetic base of present Chinese potato cultivars.…”

“…Therefore, the evaluation of genetic relationship among foreign elite lines, local landraces and improved cultivars is essential for successful exploitation, genetic stability and enhanced heterotic effect in the available germplasm. In a recent study, Duan et al (2018) studied the genetic diversity among the alien and domestically improved cultivars but present study is the first to report the genetic variability and the contribution of locally adapted potato landraces in Chinese cultivars.…”

“…Among DNA markers, simple sequence repeats (SSR) have been used successfully in polyploid species such as Brassica napus (Hasan et al, 2008; Xiao et al, 2012), Arachis (Huang et al, 2012), sweet potato (Yang et al, 2015) and potato species (Ghislain et al, 2009; Duan et al, 2018). SSR markers have been preferred due to their random genome distribution, high level of polymorphism, simplicity of use, high clarity and reproducibility, low operational cost, hyper-variability, amenability to automation, ease of multiplexing and use with low quality DNA (Ghislain et al, 2009; Yang et al, 2015; Jian et al, 2017; Duan et al, 2018). SSR markers have been widely used in determination of genetic diversity, germplasm fingerprinting, heterosis analysis, tracing germplasm migrations, gene flow, genetic linkage mapping and phylogenetic studies.…”