Segregation distortion in doubled haploid lines caused by spontaneous haploid genome doubling

Temperate maize (Zea mays L.) breeding programs often rely on limited genetic diversity, which can be expanded by incorporating exotic germplasm. A major barrier to take advantage of exotic germplasm is the lengthy process of developing inbred lines. The production of doubled haploids (DH) can shorten the timeframe of inbred line development considerably. The main question addressed in this study was whether spontaneous haploid genome doubling (SHGD) can further facilitate this process. The aims of this study were to perform genotypic characterization of inbred lines derived from the tropical BS39 population using different breeding methods, to identify genomic regions showing segregation distortion in inbred lines derived by the DH process using SHGD, i.e., regions potentially underlying SHGD, and use case-control association mapping to identify loci controlling SHGD. Four different inbred line derivation processes were used: BS39_DH and BS39_SSD were derived from the BS39 population by doubled haploid (DH) and single-seed descent (SSD) methods, and BS39×A427_DH and BS39×A427_SSD from the cross between BS39 and A427, used as a SHGD donor. A total of 663 inbred lines were genotyped using Genotype-by-Sequencing (GBS) and Diversity Array Technology Sequencing (DArtSeq). The analyses of gene diversity (HS) and genetic differentiation (FST) for the DH sets provided evidence of the presence of a SHGD inducing locus near the centromere of chromosome 5. The case-control GWAS for the DH set pinpointed this locus more precisely. Our results further indicate that the DH process captures genetic variability from the source population comparable to the SSD process. Haplotype sharing analysis showed almost 100% exclusive contribution of the A427 genome in the region near the centromere on chromosome 5 of BS39×A427_DH, presumably due to an allele in this region affecting SHGD. This locus enables DH line production in exotic populations without colchicine or other artificial haploid genome doubling.