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Open AccessArticle

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

Pushchino State Institute of Natural Sciences, Prospekt Nauki 3, 142290 Pushchino, Moscow Region, Russia
Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Moscow Region, Russia
All-Russian Research Institute of Agricultural Biotechnology, Timiriazevskaya Str. 42, 127550 Moscow, Russia
Department of Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences and Forest Ecology, Georg-August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, Albrecht-Thaer-Weg 3, D-37075 Göttingen, Germany
Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Str. 3, 119333 Moscow, Russia
Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 660036 Krasnoyarsk, Russia
Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA
Author to whom correspondence should be addressed.
Agronomy 2019, 9(9), 518;
Received: 4 August 2019 / Revised: 4 September 2019 / Accepted: 4 September 2019 / Published: 6 September 2019
(This article belongs to the Special Issue Molecular Marker Technology for Crop Improvement)
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. View Full-Text
Keywords: flavonoid biosynthesis; fruit coloration; marker-assisted selection; microsatellites; Rubus flavonoid biosynthesis; fruit coloration; marker-assisted selection; microsatellites; Rubus
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Lebedev, V.G.; Subbotina, N.M.; Maluchenko, O.P.; Krutovsky, K.V.; Shestibratov, K.A. Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid Biosynthesis Genes. Agronomy 2019, 9, 518.

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