Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs

Abstract

The Solanum tuberosum L. Phureja Group consists of potato landraces widely grown in the Andes from western Venezuela to central Bolivia, and forms an important breeding stock due to their excellent culinary properties and other traits for developing modern varieties. They have been distinguished by short-day adaptation, diploid ploidy (2n = 2x = 24), and lack of tuber dormancy. This nuclear simple sequence repeat (nSSR or microsatellite) study complements a prior random ampliWed polymorphic DNA (RAPD) study to explore the use of these markers to form a core collection of cultivar groups of potatoes. Like this prior RAPD study, we analyzed 128 accessions of the Phureja Group using nuclear microsatellites (nSSR). Twenty-six of the 128 accessions were invariant for 22 nSSR markers assayed. The nSSR data uncovered 25 unexpected triploid and tetraploid accessions. Chromosome counts of the 102 accessions conWrmed these nSSR results and highlighted seven more triploids or tetraploids. Thus, these nSSR markers (except 1) are good indicators of ploidy for diploid potatoes in 92% of the cases. The nSSR and RAPD results: (1) were highly discordant for the remaining 70 accessions that were diploid and variable in nSSR, (2) show the utility of nSSRs to eVectively uncover many ploidy variants in cultivated potato, (3) support the use of a cultivargroup (rather than a species) classiWcation of cultivated potato, (4) fail to support a relationship between genetic distance and geographic distance, (5) question the use of any single type of molecular marker to construct core collections.

Molecular characterization of potato (Solanum tuberosum L.) genotypes using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers

“…Previous studies of genetic diversity using PCR based molecular markers reported similar results. Rocha et al (2010) and Ghislain et al (2006), observed low correlation between RAPD and SSR. Similarly, Milbourne et al (1997), obtained low correlation between RAPD, AFLP and SSR.…”

“…Similarly, Milbourne et al (1997), obtained low correlation between RAPD, AFLP and SSR. The reason for these findings could be due to the kind of information obtained by different molecular markers since different molecular markers amplify different repetitive and non-repetitive regions of the genome (Ghislain et al, 2006). Further analysis between RAPD and RAPD + ISSR showed low correlation (0.47) and ISSR and RAPD + ISSR showed a high correlation (0.74).…”

Using SSR to Evaluate the Genetic Diversity of Potato Cultivars from Yunnan Province (SW China)

“…Ghislain et al (2006) from CIP showed the superior polymorphism detection power of nSSR as compared to RAPD markers. SSR and SNP techniques are presently considered the best methods to use in constructing a core collection and fingerprinting cultivars.…”

Genome sequence of a divergent Colombian isolate of potato virus V (PVV) infecting Solanum phureja

“…phureja cv. Criolla is a diploid potato species that produces tubers with yellow skin and fl esh widely grown in the Andes from western Venezuela to the center of Bolivia (Ghislain et al, 2006). Th is crop has received increasing attention in Colombia as a potential exotic export product due to its excellent organoleptic properties; high levels of vitamins A, B, C; short production cycle and reduced tuber dormancy (Rodríguez et al, 2009).…”