Development and testing of microsatellite markers for genetic mapping in papaya

Abstract

Microsatellites, or simple sequence repeats (SSRs), are tandem1y repeated mono-to hexanucleotide DNA motifs. Due to their co-dominant nature, ability to detect high levels of allelic diversity and ubiquitous genome distribution, they are widely used as genetic markers for diversity analysis and mapping projects. SSRs are also thought to serve a functional purpose in coding (genic) regions, where they have recently received considerable attention due to their role in several human diseases. Genomic research on papaya (Carica papaya L.) has yielded significant quantities of sequence data, which can be used to efficiently and economically develop microsatellites. The present project mined 2S.1 Mb of BES, 5.S Mb cDNA and 1.6 Mb random genomic sequences for SSRs. A total of939 SSR markers were identified with sufficient flanking sequences to design primers for PCR amplification. Of these, 831 produced acceptable amplicons (88.5%) with 444 displaying polymorphism (53.4%). Among seven parental varieties of five mapping populations tested, Kaek Dhom x 2H94 had the highest level of polymorphism with 210 markers followed by UH928 x SunUp with 194. AU9x SunUp with 189, UH91S x SunUp with 177 and Kapoho x SunUp, with 97, had the fewest. Dinucleotides were the most predominant motif class, accounting for 695 of the 939 mined SSRs (74.0%). The repeat motif AT/TA alone accounted for 481 SSRs (51.2%). Differences were observed between the genomic and genic fractions in levels of polymorphism, motif class predominance and motif length, indicating different selection pressures acting on SSRs between these two regions. The availability of the SSRs developed in this study will greatly assist in the genetic and physical mapping of the papaya genome as well as enhance the capacity for papaya improvement.