Abstract：In order to determine a set of SSR core primers fitting for maize hybrids’ purity identification, 420 maize hybrids were analyzed by 10 SSR primers: bnlg439, bnlg125, umc2105, phi072, umc1705, bnlg161, bnlg1792, bnlg162, phi065 and bnlg1450. Primer polymorphism and heterogosite rate were evaluated, which varied much among different primers with PIC value ranged from 0.838 (bnlg1450) to 0.482 (phi072) and heterogosite rate ranged from 0.888 (bnlg161) to 0.431 (bnlg162). There have no obvious relevance between the two parameters. Based the evaluating result, two primers bnlg161 and bnlg1450 were determined as preferred core primers for maize hybrid purity identification; five primers bnlg439、bnlg125、umc2105、umc1705、bnlg1792 were determined as candidate core primers for maize hybrid purity identification; three primers phi072, bnlg162 and phi065 were deleted because of their low polymorphism or low heterozygosis rate. 412 hybrids (accounting for 98％) have heterozygosis band type in at least one primer if the two preferred core primers bnlg161 and bnlg1450 were used,, and if another primer bnlg439 added, 419 hybrids except one hybrid ShennongT11 have heterozygosis band type. It indicated that 2-3 carefully selected core primers could solve most hybrids’ purity identification if only need detect selfed individuals.
Specific primers for purity identification were also studied, which could reduce the cost and time of purity identification. There are two sorts of specific primer: (1) within specific range of varieties, the genotype of a primer appeared only in one variety, then the primer could be used as specific primer of the variety; (2) the genotype of a primer had a genotype frequency lower than a specific value, then the primer could be used as specific primer of the varieties with such genotype. 29 varieties have specific primers within the 420 varieties, Both umc1705 and bnlg1450 were used as specific primers of 8 varieties, while phi072 and phi065 were not used as specific primers of any variety. Specific primer have no direct relevance to primer polymorphism and heterozygosis rate, but have some relevance to gene frequency of different alleles in a primer.
Primers with complementary band types were further screened, and DNA fingerprint maps for maize purity identification were constructed.
Based the above results, we bring forward that the core primers fitting for maize hybrids’ purity identification should have both high polymorphism and high heterogosite rate, and specific primers for a specific maize hybrid should have complementary band type and low genotype frequency.
