Genetic diversity, GWAS, and candidate genes identification for plant architecture traits in maize (Zea mays L.)

We provide a foundation for elucidating the molecular regulatory mechanisms of candidate genes involved in plant architecture and yield related traits. Plant height (PH), leaf angle (LA), ear shank length (ESL), and tassel branch number (TBN) are key plant architecture traits that play crucial roles in improving grain yield in maize. In this study, a genome-wide association study (GWAS) combined with genomic prediction was conducted on these four-plant architecture-related traits in a structured population of 206 inbred lines. Phenotypic data collected over 3 years demonstrated high heritability for all traits. After quality control, a total of 1,191,363 high-quality single-nucleotide polymorphisms (SNP) markers were identified across the 206 inbred lines. The population was divided into four sub-populations, and 830 SNPs exhibited significant associations with the four phenotypic traits. The associated genes were predominantly transcription factors, and functional proteins primarily involved in growth and development, hormone signaling, tissue differentiation, and stress response. Candidate genes associated with TBN and ESL were cloned and identified as Zm00001eb219130 (ZmARM5) and Zm00001eb310680 (ZmNRT1), respectively. RT-qPCR analysis of these genes, along with phenotypic evaluation of transgenic lines, confirmed that ZmARM5 positively regulates TBN, whereas ZmNRT1 negatively regulates ESL. This study provides a foundation for further understanding the genetic control of plant architecture traits in maize and provides valuable molecular insights and genetic resources for efficient transgenic breeding of maize.