Mining and Validation of Polymorphic EST-SSR Markers for Analysing Genetic Diversity among Interspecific Hybrids of Tea

R. C. Muoki; J. A. Maangi; R. K. Korir; J. L. Bargul; S. M. Kamunya

doi:10.20425/ijts1515

R. C. Muoki Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization - Tea Research Institute, P.O. Box 820-20200, Kericho, Kenya
J. A. Maangi Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
R. K. Korir Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization - Tea Research Institute, P.O. Box 820-20200, Kericho, Kenya
J. L. Bargul International Centre for Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
S. M. Kamunya Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization - Tea Research Institute, P.O. Box 820-20200, Kericho, Kenya

DOI: https://doi.org/10.20425/ijts1515

Keywords: Interspecific hybrids, microsatellite marker, polymorphism information content, Camellia spp., Discriminating power

Abstract

Molecular markers are useful tools for studying gene flow and genetic diversity within a population. With the establishment of online databases, sequence can be now be downloaded for identification of Expressed Sequence Tags- Simple Sequence Repeat (SSR) markers designed to amplify the microsatellite loci present in the genes. Of the 170 microsatellites detected from the downloaded 789 ESTs belonging to the nine Camellia spp, only fourteen showed functional EST-SSR markers. Among them, five polymorphic markers specific to tri-nucleotide SSRs were randomly selected and screened alongside five established primers on four tea genotypes (TRFK 570/2, TRFK 688/1, TRFK 83/1, and TRFK 6/8,) The polymorphism information content (PIC) of the SSR markers had mean of 0.33 that ranged between 0.16 and 0.53, whereas discriminating power (D) had mean value of 0.23 ranging between 0.00 and 0.75 with. A total of 64 alleles were detected with an average of 6.4 alleles per SSR locus. Based on a PIC greater than or equal to 0.40, D value greater than or equal to 0.20 and number of polymorphic bands greater than or equal to 1, five functional SSR markers comprising two novel EST-SSRs (Camjap A1, Camjap A4) and three adapted microsatellite markers (TM 134, A37, and A47) were recommended for use in discriminating interspecific hybrids of tea.