Assessing genetic diversity, population structure, and linkage disequilibrium is important in identifying potential parental lines for breeding programs. In this study, we assessed the genetic and phenotypic variation of 174 normal maize (Zea mays) inbred lines and made association analyses with respect to nine agronomical traits, using 150 simple sequence repeats (SSR). From population structure analysis, the lines were divided into three groups. Association analysis was done with a mixed linear model and a general linear model. Twenty one marker-trait associations involving 19 SSR markers were observed using the mixed model, with a significance level of P<0.01. All of these associations, as well as 120 additional marker-trait associations involving 77 SSR markers, were observed with the general model. Two significant marker-trait associations (SMTAs) were detected at P ≤ 0.0001. In the mixed linear model, one locus was associated with water content, two loci were associated with 100-kernel weight, setted ear length, ear thickness and stem thickness; three loci were associated with ear height, four loci were associated with total kernel weight and five loci were associated with plant height. These results should prove useful to breeders in the selection of parental lines and markers.

Our study is performed to confirm the level of genetic diversity and population structure with 80 maize inbred lines (40 waxy inbred lines and 40 flint inbred lines) and to explain the genetic basis of agronomic traits using an association mapping. The 200 SSR loci are confirmed a total of 1,610 alleles in total 80 maize inbred lines. The average number of alleles per locus was 8.05. The average GD was 0.72. The average PIC value was 0.68. The average MAF was 0.40. Population structure was revealed for K=2. Total 80 maize inbred lines were divided by groups I, II and admixed group. The 14 waxy inbred lines were assigned to group I. The 45 inbred lines include 5 waxy inbred lines and 40 flint inbred lines were contained to group II. The 21 waxy inbred lines were contained in the admixed group with lower than membership threshold 0.8. Association mapping between 200 SSR markers and 10 phenotypic traits of waxy/flint maize inbred lines were performed by Q GLM and Q+K MLM. In significant level at 0.01, 72 SSR markers were associated with 10 phenotypic traits using Q GLM. The 4 marker-trait association were detected in Q+K MLM. The results derived from this study will be used for designing efficient new maize breeding programs.