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Tomato shelf-life is important for its fresh market usage especially for exporting and transporting tomato in tropical climate. To increase the shelf-life, delaying maturity is one of the powerful methods. A ripening gene related to the fruit maturity delaying was previously known through tomato mutation. RIPENING-INHIBITOR (Rin) from the recessive mutation effectively blocks the ripening process, and when the hybrid (Rin/rin) was formed it shows slow-ripening and long shelf-life. Since breeders need the long shelf-life character in the tomato breeding program, we had set out a series of experiments to develop a Rin related DNA marker. We searched for the proper primer sequences in the deletion region between Rin and rin mRNA sequences, and also in the intron region of rin. Primers that simultaneously amplified two bands with a co-dominant pattern were selected and converted to the Sequence Characterized Amplified Region (SCAR) marker. As a preliminary data, the SCAR marker clearly distinguished genotypes between heterozygote (Rin/rin) and homozygote (Rin/Rin, rin/rin), and this would help select the tomato lines that have a characteristic of long shelf-life. [ABSTRACT FROM AUTHOR]

Molecular genetic markers have been widely used as powerful tools for analyzing the genome. In particular, SSR markers have practical applications in breeding systems because they can be used in high-throughput analyses for genetic mapping, heritable diversity testing, purity analysis, and marker-assisted selection. Currently, due to technical advances in DNA sequencing, large sequence databases are available for large-scale SSR mining and marker development. Here, we describe an automated method, the SSR Finder program, for SSR discovery in the onion sequence database, and primer design for amplifying the detected SSRs. A total of 1,049 SSR primers were obtained for genetic purity testing, and 100 SSR sets were analyzed in 14 bulb onion breeding lines using clustering analysis. A total of 20 selected markers from screening of all 1,049 SSR primers, were finally applied for genetic purity testing in three breeding lines, NW1, NW9, and NW10. The initial tests showed that 15%, 71%, and 97% of individuals within NW1, NW9, and NW10, respectively, were genetically homogeneous. These markers produced using the SSR Finder will be useful for investigating the genetic purity of onion breeding lines. [ABSTRACT FROM AUTHOR]