Identification of QTNs, QTN-by-environment interactions for plant height and ear height in maize multi-environment GWAS

Abstract

Plant height (PH) and ear height (EH) are important traits associated with biomass, lodging resistance, and grain yield in maize. There were strong effects of genotype x environment interaction (GEI) on plant height and ear height of maize. In this study, 203 maize inbred lines were grown at five locations across China’s Spring and Summer corn belts, and plant height (PH) and ear height (EH) phenotype data were collected and grouped using GGE biplot. Five locations fell into two distinct groups (or mega environments) that coincide with two corn ecological zones called Summer Corn Belt and Spring Corn Belt. In total, 73,174 SNPs collected using GBS sequencing platform were used as genotype data and a recently released multi-environment GWAS software package IIIVmrMLM was employed to identify QTNs and QTN x environment (corn belt) interaction (QEIs); 12 and 11 statistically significant QEIs for PH and EH were detected respectively and their phenotypic effects were further partitioned into Add*E and Dom*E components. There were 28 and 25 corn-belt-specific QTNs for PH and EH identified, respectively. The result shows that there are a large number of genetic loci underlying the PH and EH GEIs and IIIVmrMLM is a powerful tool in discovering QTNs that have significant QTN-by-Environment interaction. PH and EH candidate genes were annotated based on transcriptomic analysis and haplotype analysis. EH related-QEI S10_135 (Zm00001d025947, saur76, small auxin up RNA76) and PH related-QEI S4_4 (Zm00001d049692, mads32, encoding MADS-transcription factor 32), and corn-belt specific QTNs including S10_4 (Zm00001d023333, sdg127, set domain gene127) and S7_1 (Zm00001d018614, GLR3.4, and glutamate receptor 3.4 or Zm00001d018616, DDRGK domain-containing protein) were reported, and the relationship among GEIs, QEIs and phenotypic plasticity and their biological and breeding implications were discussed.