Genetic variability in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers

Abstract

Rubus ellipticus Smith. commonly known as ‘Yellow Himalayan raspberry’ is an important member of Rosaceae family with high medicinal importance having antioxidant and antibacterial properties. This study was done with the objective of characterizing 21 R. ellipticus collections from different regions of India, based on morphological descriptors and expressed sequence tags-simple sequence repeat (EST-SSR) markers. Broad phenotypic variability among the R. ellipticus collections was detected by using morphological descriptors. The Euclidian distance matrix discriminated two groups, based on morphological characters. A set of 68 EST-SSR markers were developed based on 7777 unigenes generated by us from ‘Kumarhatti-1’ collection of R. ellipticus using assembled pair—end sequences from Illumina NextSeq 500. The ESTs containing simple sequence repeat motifs were extracted using Microsatellite identification tool and primers were designed. Out of 68 EST-SSRs polymorphism was detected using 61 (89.7%) primer pairs, indicating high genetic variability in the R. ellipticus collections. Effective multiplex ratio, marker index and polymorphism information content were 0.43, 0.24 and 0.50, respectively. The unweighted pair group method with arithmetic mean coincided with the bootstrap analysis and two groups were formed, separating the collections Uttrakhand from the other. Morphological descriptors along with EST-SSR markers proved efficient in detecting the levels of genetic variability among the collections maintained in the field. These results can be used as an additional source of exploitation in R. ellipticus breeding programs.

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Abbreviations

EST-SSR:

Expressed sequence tags-simple sequence repeat

UPGMA:

Unweighted pair group method with arithmetic mean

TSS:

Total soluble solid

CTAB:

Cetyl tri-methyl ammonium bromide

EDTA:

Ethylene diamine tetra acetic acid

PVP:

Poly vinyl pyrrolidone

DNA:

Deoxyribonucleic acid

RNA:

Ribonucleic acid

SAHN:

Sequential agglomerative hierarchical nesting

PIC:

Polymorphism information content

E:

Effective multiplex ratio

MI:

Marker index

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Sharma, S., Kaur, R., Kumar, K. et al. Genetic variability in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers. J. Plant Biochem. Biotechnol. 30, 37–55 (2021). https://doi.org/10.1007/s13562-020-00567-8

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Keywords

  • Rubus ellipticus
  • Molecular markers
  • EST-SSRs
  • Morphological traits
  • Genetic diversity