Universal chloroplast primer pairs for Simple Sequence Repeat analysis in diverse genera of fruit crops

To provide an alternative method to investigate chloroplast genome (cpDNA) diversity in sub-tropical and tropical fruit crops, where cpDNA sequences are unknown, a universal set of chloroplast simple sequence repeat (cpSSR) primers were developed. Thirty-three cpSSR primers from rice (Oryza sativa), pine (Pinus thunbergii), tobacco (Nicotiana tabacum) and Arabidopsis thaliana were applied to 45 fruit species (or varieties) belonging to 27 genera in 20 families. After being screened, the utility of these primers was verified. Experiments revealed that nine out of 14 primer pairs from N. tabacum, and seven out of 11 from A. thaliana, specifically amplified bands in cpDNA from most species tested, and polymorphisms were observed. While four out of the five primers from O. sativa generated intensive bands in agarose gels, but only a smear in polyacrylamide gels, all cpSSR primers from P thunbergii failed to generate any specific amplified products in polyacrylamide gels. The results illustrate the feasibility of exploring diversity among unknown cpDNA sequences in exotic minor fruit crops by PCR methods.