Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

BACKGROUND: Increasing grain yield is a primary objective of maize breeding. Dissecting the genetic architecture of grain yield furthers genetic improvements to increase yield. Presented here is an association panel composed of 126 maize inbreds (AM126), which were genotyped by the genotyping-by-sequencing (tGBS) method. We performed genetic characterization and association analysis related to grain yield in the association panel. RESULTS: In total, 46,046 SNPs with a minor allele frequency (MAF) ≥0.01 were used to assess genetic diversity and kinship in AM126. The results showed that the average MAF and polymorphism information content (PIC) were 0.164 and 0.198, respectively. The Shaan B group, with 11,284 unique SNPs, exhibited greater genetic diversity than did the Shaan A group, with 2644 SNPs. The 61.82% kinship coefficient in AM126 was equal to 0, and only 0.15% of that percentage was greater than 0.7. A total of 31,983 SNPs with MAF ≥0.05 were used to characterize population structure, LD decay and association mapping. Population structure analysis suggested that AM126 can be divided into 6 subgroups, which is consistent with breeding experience and pedigree information. The LD decay distance in AM126 was 150 kb. A total of 51 significant SNPs associated with grain yield were identified at P < 1 × 10(− 3) across two environments (Yangling and Yulin). Among those SNPs, two loci displayed overlapping regions in the two environments. Finally, 30 candidate genes were found to be associated with grain yield. CONCLUSIONS: These results contribute to the genetic characterization of this breeding population, which serves as a reference for hybrid breeding and population improvement, and demonstrate the genetic architecture of maize grain yield, potentially facilitating genetic improvement. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-018-0669-9) contains supplementary material, which is available to authorized users.