Genotypic Variation and Association Mapping for Plant Stature and Anthesis‐Silking Interval in Set of Temperate‐Adapted Maize Lines Developed by DH and SSD Methods

ABSTRACT BS39 is a broad‐based population of tropical maize adapted to temperate environments that can provide useful and unique alleles to US Corn Belt breeding programmes. Doubled‐haploid (DH) has been used as an efficient alternative method to speed up the development of maize lines. Our objectives were to compare genetic parameters for plant height (PH), ear height (EH) and anthesis‐silking interval (ASI) among the BS39‐derived lines using single‐seed descent (SSD) and DH methods; identify SNP markers associated with these traits; and investigate the relationship among BS39‐derived lines and their testcross performance for PH and EH. We developed four sets of 96 lines derived from BS39 and from a cross between BS39 and A427, a spontaneous haploid genome doubling (SHGD) donor, by DH and SSD methods, named BS39_DH, BS39_SSD, BS39xA427_DH and BS39xA427_SSD. DH lines were genotyped using genotype‐by‐sequencing, whereas SSD lines were genotyped using diversity array technology sequencing. We observed extensive genotypic variation for PH, EH and ASI in all sets of lines. Lines developed by the SSD method had larger genotypic variation and higher predicted genetic gains for all traits at all selection intensities than those developed using the DH method. However, the production of DH lines associated with SHGD appears to be a feasible strategy to reduce the costs and time required to complete the breeding cycle and enhance genetic gains in maize breeding programmes. PH and EH presented moderate‐to‐strong positive correlations between BS39‐derived lines and their testcross performance. We found nine significant SNPs for PH and EH in DH lines, and most of them are involved in the development process in plants.