Molecular marker analyses of pistachio rootstocks by Simple Sequence Repeats and Sequence-Related Amplified Polymorphisms

Summary

Simple Sequence Repeat (SSR) and Sequence-Related Amplified Polymorphism (SRAP) molecular marker systems were used to analyse four commercially important pistachio rootstocks: two species of Pistacia atlantica (cv. ‘Standard Atlantica’), P. integerrima (cv. ‘Pioneer Gold’) and two interspecific hybrids of the same, ‘Pioneer Gold II’ (‘PGII’) and ‘University of California at Berkeley 1’ (‘UCB-1’). A total of 35 putative alleles were detected by 12 SSR primer pairs with an average of 2.9 alleles per locus. The number of putative alleles ranged from 2 to 5 in the pistachio rootstocks tested. The number of bands produced by the SRAP protocol was highly variable, ranging from 11 to 38, with an average of 25.2 per primer combination. Eight primer combinations resulted in 104 (51%) polymorphic markers in these samples. SSR and SRAP markers successfully identified all pistachio rootstocks tested from their unique fingerprints. Both SSR and SRAP molecular markers confirmed that the observed variation in ‘UCB-1’ rootstock is genetic.Thus, there will always be variation among ‘UCB-1’ hybrid seedling progeny due to the segregation of alleles when propagated by seed.We also found evidence of contaminating pollen other than from P. integerrima in some hybrid ‘UCB-1’ rootstock progeny produced by closed pollination. Only alleles from the cultivar ‘Standard Atlantica’ were observed in abnormal ‘UCB-1’ rootstock in the nursery. We found that the poor performance of the scion cv. ‘Kerman’ on ‘UCB-1’ rootstock was not due to ‘UCB-1' rootstocks displaying abnormal behaviour in the nursery. We have successfully developed two efficient marker systems for genome analyses in pistachio, which can be used for identification and management in pistachio rootstock production.