Identification of SNP Markers Associated to Protein and Oil Content in Doubled Haploid Maize Lines Derived from Subtropical Breeding Populations

Genes related to oil and protein accumulation have been identified in maize, however, many loci underlying the variation in these traits are still unidentified. In this study, 49 doubled haploids (DH) lines derived from subtropical maize recombinant populations were genotyped through DArTSeq technology, resulting in 29,398 single nucleotide polymorphisms (SNPs), of which 20,202 markers with minor allele frequency > 0.05 were kept. Oil content in DH lines ranged from 4 to 8.3%, whereas protein content ranged from 8.44 to 15.63%. A genome-wide association study (GWAS) was conducted to detect significant SNPs associated with oil and protein content. The physical position of SNPs was mapped and a 100-kb window surrounding the significant SNPs was scanned to identify genes associated with the phenotype. Three significant SNPs were close to genes related to oil accumulation, and one was close to a gene related to protein accumulation. The favorable alleles for the SNPs 5589069 (A/G), 100156460 (C/T), and 2412207 (G/T) were present in 70.9%, 35.4%, and 22.5% of the DH lines with high oil (> 6%) content (HOC), respectively. The favorable allele (A/G) for SNP 5586538 was present in 14.63% of the DH lines with high protein (> 10%) content (HPC). Once the favorable alleles were detected, a genotyping validation by High-Resolution Melting (HRM) technique was performed, showing similarity rates with DArTSeq between 56% and 78.9% for the assayed SNPs. These novel SNPs could be useful for further marker-assisted breeding of HOC or HPC in subtropical maize.