Graduate Thesis Or Dissertation
 

Simple sequence repeat marker development and fingerprinting in Cuphea lanceolata Ait. and C. viscosissima Jacq

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  • Microsatellites or simple sequence repeats (SSRs) are highthroughput sequence based DNA markers that have been exploited as tools for measuring genetic distance and diversity in evolutionary studies, protection of intellectual property, genetic resource conservation management, cultivar identification and molecular breeding of crop plants. We isolated and sequenced 1095 clones from genomic libraries enriched for CA, GA and GAA repeats. Unique SSRs were identified in 425 clones and primers were designed for 271 SSR sequences. Of the latter, 184 primer pairs produced clean SSR markers. Twenty nine functional SSR markers were used for genetic diversity study on 94 accessions of Cuphea. The Cuphea genotypes in the study panel included 20 accessions of C. lanceolata and 74 accessions of C.viscosissima. The mean number of alleles for C. lanceolata and C. viscosissima were 10.97 and 4.76 respectively. Similarly, markers amplifying C. lanceolata had a higher mean polymorphic information content (PlC) score (0.74) as compared to C. viscosissima (0.42). In C. lanceolata, a positive correlation was observed between maximum repeat count (MRC) and number of alleles (r=0.40) as well as MRC and standard deviation of molecular weight (SDMw) (r=0.72). C. viscosissima demonstrated a similar trend, albeit with a greater magnitude of correlation, between MRC and number of alleles (r=0.70) and MRC and SDMw (r=0.78). The SSR markers described herein are powerful tools for efficiently and accurately discriminating between Cuphea genotypes.
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