Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize

Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers.

High-density genetic mapping must precede to find molecular markers associated with a particular trait. The objectives of this study were to (1) construct a high-density linkage map using SNP markers and (2) detect the QTLs for grain yield and quality related traits of the Mo17/KW7 RIL population.

In this study, two parental lines, Mo17 (normal maize inbred line) and KW7 (waxy inbred line) and 80 F_7:8 lines in the Mo17/KW7 RIL population were genotyped using the MaizeSNP50 BeadChip, an Illumina BeadChip array of 56,110 maize SNPs. Marker integration and detection of QTLs was performed using the inclusive composite interval mapping (ICIM) method within the QTL IciMapping software.

This study was genotyped using the Illumina MaizeSNP50 BeadChip for maize Mo17/KW7 recombinant inbred line (RIL) population. The 2904 SNP markers were distributed along all 10 maize chromosomes. The total length of the linkage map was 3553.7 cm, with an average interval of 1.22 cm between SNPs. A total of 18 QTLs controlling eight traits were detected in the Mo17/KW7 RIL population. Three QTLs for plant height (PH) were detected on chromosomes 4 and 8 and showed from 16.01% (qPH8) to 19.85% (qPH4a) of phenotypic variance. Five QTLs related to ear height (EH) were identified on chromosomes 3, 4, and 6 and accounted for 3.79% (qEH6) to 27.57% (qEH4b) of phenotypic variance. Five QTLs related to water content (WC) on chromosomes 1, 4, 8, and 9 accounted for 9.55% (qWC8b) to 23.30% (qWC4) of phenotypic variance. One QTL (qAC9) relating to amylose content (AC) on chromosome 9 showed 82.10% of phenotypic variance.

The high-density linkage map and putative QTLs of the maize RIL population detected in this study can be effectively utilized in waxy and normal maize breeding programs to facilitate the selection process through marker-assisted selection (MAS) breeding programs.