Determination of SSR Core Primers for Maize Hybrid Purity Identification

In order to determine a set of SSR core primers fitting for maize hybrids'purity identification, 420 maize(Zea mays)hybrids were analyzed by 10 SSR primers, bnlg439, bnlg125, umc2105, phi072, umc1705, bnlg161, bnlg1792, bnlg162, phi065 and bnlg1450, respectively, and two primers bnlg161 and bnlg1450 were determined according to their polymorpism and heterogosite rate as preferred core primers for maize hybrid purity identification. Four hundred and twelve hybrids (accounting for 98%) have heterozygosis band type in at least one primer if the two preferred core primers bnlg161 and bnlg1450 were used; five primers bnlg439,bnlg125,umc2105,umc1705 and bnlg1792 were determined as candidate core primers for maize hybrid purity identification. Specific primers for purity identification were also studied, there were two sorts of specific primer: (1) within specific range of varieties, the genotype of a primer appeared only in one variety, then the primer was used as specific primer of the variety. Twenty-nine varieties had 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. (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, if genotype frequency lower than 2.40 E-03 (1/420) were treated as specific genotype, eight primers except phi072 and bnlg161 might become the second sort of specific primers of varieties with such genotype. Primers with complementary band types were further screened with the seven recommended core primes, and DNA fingerprint maps for maize purity identification were constructed.