Identification of AFLP fragments linked to seedlessness in Ponkan mandarin (Citrus reticulata Blanco) and conversion to SCAR markers

Seedlessness is a desirable trait in citrus and has been an important breeding objective. In this study, we employed the amplified fragment length polymorphism (AFLP) technique to find molecular markers linked to the seedless trait in the Ponkan mandarin (Citrus reticulata Blanco). After screening with 72 primer pairs, 5 AFLP markers were identified that putatively correlated with the target trait. Their association was also tested by analyzing the AFLP profile from pooled individual accessions. The five fragments were cloned and sequenced, and BLAST searches showed that four of the markers had high homology to functional genes, providing some promising information that may aid in understanding the molecular mechanism of seedlessness in citrus. Based on the sequence information, eight specific primers were designed and eventually fragments AFLP-2 and AFLP-5 were successfully converted into sequence characterized amplified region (SCAR) markers. Thus, the markers detected could be useful for accelerating citrus breeding programmes by enabling early screening for seedlessness mutations using marker-assisted selection.