Genetic characterization and association mapping in near-isogenic lines of waxy maize using seed characteristics and SSR markers.

Background: Association mapping has been advocated as the method of choice for identifying loci involved in the inheritance of complex traits in crop species. This method involves identifying markers with significant differences in allele frequency between individuals with a phenotype of interest and a set of unrelated control individuals.

Objective: The purpose of our study is not only to investigate the genetic diversity and relationships of the basic molecular markers of near-isogenic lines (NILs) of waxy maize, but it is also to identify molecular markers related to interesting seed characteristics including 4 seed quantity traits and 4 seed phenotypic traits using association analysis with population structure.

Methods: We performed association mapping of 200 SSR markers and 8 seed characteristics among 10 NILs of waxy maize and two parental lines (HW3, HW9) (recurrent parent) of "Mibaek 2" variety.

Results: In population structure and cluster analysis, the 10 NILs and two parental lines were divided into two groups. Seven inbred lines, including HW3, were assigned to Group I. Group II contained 5 inbred lines, including HW9. In addition, we found that 32 SSR markers associate with 8 seed characteristics in 10 NILs. In particular, five SSR markers (umc1986, umc1747, umc2275, phi078, umc1366) were together associated with more than one seed characteristics such as EL, 100 KW, SCC, R, L*, and V.

Conclusion: This study demonstrated the utility of SSR analysis for studying GD, population structure, and association mapping in 10 NILs and two parental lines (HW3, HW9) of "Mibaek 2" variety.