Genotypic variation and identification of genomic regions associated with plant architecture traits in set of temperate-adapted maize lines

BS39 is a broad-based population of tropical maize adapted to temperate environments. A set of DH and SSD lines were derived from this population and introduced into tropical environment by Maize Breeding Program of Universidade Federal de Viçosa. Our objectives were to do a phenotypic and molecular characterization of a large set of BS39 lines under tropical environments and identify candidate genes associated with plant architecture traits. Thus, we evaluated a set of 192 BS39 lines across two locals, Viçosa and Coimbra, MG, under tropical environments during 2023/2024 and 2024/2025 seasons. The lines were genotyped using a 25k Single Nucleotide Polymorphism (SNP) chip. There is genetic variability among the BS39 lines (P<0.01) for all tested traits. We found a mean LD decay distance of 650k base pair for all chromosomes. No population structure was detected based on the principal component analyses (PCA). We found six significant SNPs associated with EH and BENN, and three out of them were linked to genes responsible for plant growth. Therefore, these lines show genetic variability and potential to be used as a source of plant architecture favorable alleles.