Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid Biosynthesis Genes

Abstract

Raspberry is a valuable berry crop containing a large amount of antioxidants that correlates with the color of the berries. We evaluated the genetic diversity of differently colored raspberry cultivars by the microsatellite markers developed using the flavonoid biosynthesis structural and regulatory genes. Among nine tested markers, seven were polymorphic. In total, 26 alleles were found at seven loci in 19 red (Rubus idaeus L.) and two black (R. occidentalis L.) raspberry cultivars. The most polymorphic marker was RiMY01 located in the MYB10 transcription factor intron region. Its polymorphic information content (PIC) equalled 0.82. The RiG001 marker that previously failed to amplify in blackberry also failed in black raspberry. The raspberry cultivar clustering in the UPGMA dendrogram was unrelated to geographical and genetic origin, but significantly correlated with the color of berries. The black raspberry cultivars had a higher homozygosity and clustered separately from other cultivars, while at the same time they differed from each other. In addition, some of the raspberry cultivars with a yellow-orange color of berries formed a separate cluster. This suggests that there may be not a single genetic mechanism for the formation of yellow-orange berries. The data obtained can be used prospectively in future breeding programs to improve the nutritional qualities of raspberry fruits.

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

“…Castillo et al [28] found that this marker was not amplified in blackberry and hybrids. We demonstrated it also in black raspberry earlier [23] and in cloudberry, arctic bramble, and hybrid Arctic bramble in this study. This marker appears to be a good identifier for red raspberry among cultivated Rubus species.…”

“…Gonzalez et al [24] found three allele variants in the EST-SSRs designed for the PsMYB10 TF gene. In our study of 21 varieties of red and black raspberries presented here, we showed that the RiMY01 marker representing the R. idaeus MYB10 gene had a significantly greater polymorphism compared to six markers representing structural genes of flavonoid biosynthesis-9 vs. 2-4 alleles per locus and PIC of 0.82 vs. 0.05-0.35 [23]. This is consistent with high PCR amplification efficiency and high polymorphism found for SSR markers representing TF genes in a number of crops [72].…”

“…Among SSR markers, those that are located in introns and untranslated regions (UTRs) are more polymorphic and potentially can combine advantages of both ncSSR and EST-SSR markers, while those that are located in exons are less polymorphic, but more likely to be under direct selection or represent selectively different alleles, and therefore are more useful for MAS because they might better represent functional traits important for breeding. We studied diploid Rubus species and confirmed that SSR markers located in introns were more variable in comparison to EST-SSR located in exons [23]. However, development of such markers complete nucleotide sequences of important adaptive and breeding trait related genes.…”

“…The SSR markers in the TF gene in plants were first developed by Kujur et al [73], which showed the influence of the SSR polymorphism on secondary structure of proteins and on such traits as seed weight and number of pods and seeds. Since then, there have been few similar studies in Rosaceae where similar markers have been developed for Japanese plum [24], but no such markers have been reported for Rubus and Fragaria before our first study, where we developed a SSR marker representing the RiMYB10 TF gene, an activator of transcription of flavonoid biosynthesis [23]. The association between the MYB10 gene and fruit color has been demonstrated for apple [45] and peach [74].…”

“…For comparison, we also used a pair of primers designed for the RiG001 locus from the R. idaeus aromatic polyketide synthase (RiPKS3) gene [28]. Unlike the RiPKS1, the typical naringenin chalcone synthase (CHS), the RiPKS3 produced predominantly p-coumaryltriacetic acid lactone [44], but the sequences of both genes amplified by their PCR primer pairs are almost identical [23]. Among the MYB TFs genes we used the MYB10 orthologs involved in the anthocyanin biosynthesis during ripening in more than 20 commercially important Rosaceae species [45].…”