Genome-wide association study for plant height and ear height in maize under well-watered and water-stressed...

Both plant height (PH) and ear height (EH) are critical traits in maize and are closely associated with grain yield and mechanized harvesting. Increasing the number of molecular markers and mining functional genes by combining approaches such as genotype and phenotype analysis will contribute to elucidating the molecular mechanism underlying PH and EH in maize.

We analyzed these traits in an association panel of 200 inbred lines across 4 locations (Yulin, Yinchuan, Zhangye and Taiyuan) under both well-watered (WW) and water-stressed (WS) conditions during 2019-2020. A genome-wide association study (GWAS) was conducted employing 42,504 high-quality SNP loci, which identified 70 PH-related SNPs including 49 loci under WS conditions, and 28 EH-related SNPs including 17 loci under WS conditions. We further detected 13 stable SNPs that were consistently detected across multiple environments, including two loci associated with PH and EH. The phenotypic variance explained (PVE) of these stable SNPs ranged from 0.02 to 9.22%. Among them, two SNP loci, Affx-291391226 and Affx-291401269, were found to influence both PH and EH. Overall, 71 genes within the confidence intervals of these 13 stable SNPs were annotated. Six and nine candidate genes were linked to two major PH-related SNPs, Affx-291428750 and Affx-291442780, respectively. Among them, Zm00001d010175 and Zm00001d047994 encode an ethylene response transcription factor and inositol-tetrakisphosphate 1-kinase (ITPK1), respectively. Zm00001d017550, corresponding to Affx-291436626, encodes an S-acyltransferase.

These SNP markers and candidate genes provide valuable insights into the genetic mechanisms governing plant height and ear height in maize under drought conditions, and these findings may offer potential applications in breeding programs aimed at improving plant architecture and drought resistance.