Development and characterization of a core set of SSR markers for fingerprinting analysis of Chinese maize varieties


A core set of 60 SSRs was selected and modified using 231 Chinese and USA maize (Zea mays L.) inbred lines
from more than 2000 SSRs for DNA fingerprinting analysis. All 60 SSR markers met the following criteria: (1) amplification
of a single locus; (2) distinct amplification products; (3) adequate intervals between adjacent alleles; (4)
suitable PCR fragment size; (5) reasonable discrimination power (DP); and (6) even distribution across the maize
genome. Furthermore, the 60 SSR primers were re-designed to adjust the PCR product size. Together with the
application of four different fluorescent dyes, a high-throughput 10-plex capillary electrophoresis platform was
explored. The 60 core SSR markers were further divided into three groups (20 SSRs per group) according to
peak morphology and DP value. Groups I, II and III were used in DNA fingerprinting analysis as a basic core, an
expanded core and a candidate core set respectively. The allele number per locus varied from three to 22 with an
average of 8.95; the average number of alleles per group I, II and III was a respective 7.35, 7.8 and 11.4. The DP
values ranged from 0.366 to 0.913, with an average of 0.718 among all loci; the average group DP values were
0.697, 0.718 and 0.737 for groups I, II and III respectively; and the cumulative values of discrimination power (CDP)
approached 1 for all groups. Cluster analysis results using 60 selected loci divided the Chinese inbred lines into six
groups, including Luda Red Cob, P, Improved Reid, Tang-si-ping-tou, Waxy and Lancaster. The USA inbred lines
were segregated into four groups, including SSS, Lancaster, Iodent and Oh43/Oh07Mid mixed.

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Maydica - A journal devoted to maize and allied species

ISSN: 2279-8013